From a.janke at gmail.com  Tue Mar  1 00:35:50 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 1 Mar 2011 15:35:50 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
Message-ID: <AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>

Hi again Lisa,

> I am trying to create average infant head templates similar to what Fonov et
> al 2011 have created with the pediatric population.
> (He informed me that the infant templates available online were created
> using similar methods as stated in his 2011 paper involving pediatric data)

> Thanks for guiding me on how to modify the configurations.
> As a start, I will play around with nlpfit and fit config (I'll use what
> Fonov et al used for their settings as a guidance).

OK, now I am with you. Vladimir (Fonov) wrote a ruby? script that
behaves much as 'volgenmodel'
(http://packages.bic.mni.mcgill.ca/scripts/volgenmodel)  does. The
difference as he mentions in his paper is that he doesn't start
fitting from scratch at each step. volgenmodel does but there are
other reasons for this.

You are welcome to use it as a start if only because last I looked at
Vladimir's scripts they use a lot of his own mashups of others code
(mincANTS, ITK etc). In time you should be able to get his version
working but I suspect volgenmodel will make a good starting step.

It has a few dependencies on other scripts that I have also uploaded
to the scripts directory, note that a run of this script will take a
LONG time if you dont run it on a batch (SGE/gridengine) setup.  For
example a run on 200 elderly brains takes approximately 1 week on a
50core linux cluster.

Usage is like this:

   $ volgenmodel -check -clean -symmetric -normalise -extend 5 \
      -output_model <model.mnc> -workdir genmodel-work \
      <infiles>

The -check option generated JPG files in the workdir, -clean removes a
bunch of working files as it goes along, -symmetric makes a symmetric
model, -normalise takes care of global intensity differences between
images, -extend 5 adds a 5 voxel boundary around all the images in
case the cropping/framing is off.

Note that for 100 subjects this will need about 700GB of spare space
in the -workdir directory if the -clean option isn't used.

Good luck.


-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883

From lrisa87 at uw.edu  Tue Mar  1 14:16:48 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 1 Mar 2011 11:16:48 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
Message-ID: <AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>

Hi Andrew,

Thank you once again - I am always surprised (in a good way, of course) and
thankful for how supportive people, like you, are on this MINC mailing list!

Thanks for suggesting me "volgenmodel".
Yes, by reading his paper, I realized that Vladimir used other codes like
ITK in his model creation process.
Seems like volgemodel will be a great start off for this project. I will
definitely try out volgenmodel.

The difference as he mentions in his paper is that he doesn't start
> fitting from scratch at each step. volgenmodel does but there are
> other reasons for this.


What are some of the reasons for this?

Thank you.


Best,
Lisa

On Mon, Feb 28, 2011 at 9:35 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi again Lisa,
>
> > I am trying to create average infant head templates similar to what Fonov
> et
> > al 2011 have created with the pediatric population.
> > (He informed me that the infant templates available online were created
> > using similar methods as stated in his 2011 paper involving pediatric
> data)
>
> > Thanks for guiding me on how to modify the configurations.
> > As a start, I will play around with nlpfit and fit config (I'll use what
> > Fonov et al used for their settings as a guidance).
>
> OK, now I am with you. Vladimir (Fonov) wrote a ruby? script that
> behaves much as 'volgenmodel'
> (http://packages.bic.mni.mcgill.ca/scripts/volgenmodel)  does. The
> difference as he mentions in his paper is that he doesn't start
> fitting from scratch at each step. volgenmodel does but there are
> other reasons for this.
>
> You are welcome to use it as a start if only because last I looked at
> Vladimir's scripts they use a lot of his own mashups of others code
> (mincANTS, ITK etc). In time you should be able to get his version
> working but I suspect volgenmodel will make a good starting step.
>
> It has a few dependencies on other scripts that I have also uploaded
> to the scripts directory, note that a run of this script will take a
> LONG time if you dont run it on a batch (SGE/gridengine) setup.  For
> example a run on 200 elderly brains takes approximately 1 week on a
> 50core linux cluster.
>
> Usage is like this:
>
>   $ volgenmodel -check -clean -symmetric -normalise -extend 5 \
>      -output_model <model.mnc> -workdir genmodel-work \
>      <infiles>
>
> The -check option generated JPG files in the workdir, -clean removes a
> bunch of working files as it goes along, -symmetric makes a symmetric
> model, -normalise takes care of global intensity differences between
> images, -extend 5 adds a 5 voxel boundary around all the images in
> case the cropping/framing is off.
>
> Note that for 100 subjects this will need about 700GB of spare space
> in the -workdir directory if the -clean option isn't used.
>
> Good luck.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Brisbane->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From lrisa87 at uw.edu  Tue Mar  1 16:58:17 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 1 Mar 2011 13:58:17 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
Message-ID: <AANLkTi=eyCFZVMU+nTmuU-AGEz+vKuqjdG+urDcUD8vr@mail.gmail.com>

Hi Andrew,

I'm trying to use volgenmodel, but have been running into the following
error:

> Can't exec "volpad": No such file or directory at
> /usr/local/bic/bin/volgenmodel line 656.
> Died at /usr/local/bic/bin/volgenmodel line 656.


I tried finding volpad from http://mavis.anu.edu.au/scripts/ as mentioned on
http://www.bic.mni.mcgill.ca/ServicesHelpDocs/MinctraccError,
but couldn't access it.
Is volpad available elsewhere?

Thanks.


Best,
Lisa

On Tue, Mar 1, 2011 at 11:16 AM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Hi Andrew,
>
> Thank you once again - I am always surprised (in a good way, of course) and
> thankful for how supportive people, like you, are on this MINC mailing list!
>
> Thanks for suggesting me "volgenmodel".
> Yes, by reading his paper, I realized that Vladimir used other codes like
> ITK in his model creation process.
> Seems like volgemodel will be a great start off for this project. I will
> definitely try out volgenmodel.
>
> The difference as he mentions in his paper is that he doesn't start
>> fitting from scratch at each step. volgenmodel does but there are
>> other reasons for this.
>
>
> What are some of the reasons for this?
>
> Thank you.
>
>
> Best,
> Lisa
>
> On Mon, Feb 28, 2011 at 9:35 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Hi again Lisa,
>>
>> > I am trying to create average infant head templates similar to what
>> Fonov et
>> > al 2011 have created with the pediatric population.
>> > (He informed me that the infant templates available online were created
>> > using similar methods as stated in his 2011 paper involving pediatric
>> data)
>>
>> > Thanks for guiding me on how to modify the configurations.
>> > As a start, I will play around with nlpfit and fit config (I'll use what
>> > Fonov et al used for their settings as a guidance).
>>
>> OK, now I am with you. Vladimir (Fonov) wrote a ruby? script that
>> behaves much as 'volgenmodel'
>> (http://packages.bic.mni.mcgill.ca/scripts/volgenmodel)  does. The
>> difference as he mentions in his paper is that he doesn't start
>> fitting from scratch at each step. volgenmodel does but there are
>> other reasons for this.
>>
>> You are welcome to use it as a start if only because last I looked at
>> Vladimir's scripts they use a lot of his own mashups of others code
>> (mincANTS, ITK etc). In time you should be able to get his version
>> working but I suspect volgenmodel will make a good starting step.
>>
>> It has a few dependencies on other scripts that I have also uploaded
>> to the scripts directory, note that a run of this script will take a
>> LONG time if you dont run it on a batch (SGE/gridengine) setup.  For
>> example a run on 200 elderly brains takes approximately 1 week on a
>> 50core linux cluster.
>>
>> Usage is like this:
>>
>>   $ volgenmodel -check -clean -symmetric -normalise -extend 5 \
>>      -output_model <model.mnc> -workdir genmodel-work \
>>      <infiles>
>>
>> The -check option generated JPG files in the workdir, -clean removes a
>> bunch of working files as it goes along, -symmetric makes a symmetric
>> model, -normalise takes care of global intensity differences between
>> images, -extend 5 adds a 5 voxel boundary around all the images in
>> case the cropping/framing is off.
>>
>> Note that for 100 subjects this will need about 700GB of spare space
>> in the -workdir directory if the -clean option isn't used.
>>
>> Good luck.
>>
>>
>> --
>> Andrew Janke
>> (a.janke at gmail.com || http://a.janke.googlepages.com/)
>> Brisbane->Australia    +61 (402) 700 883
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From lconcha at gmail.com  Tue Mar  1 17:49:26 2011
From: lconcha at gmail.com (Luis Concha)
Date: Tue, 1 Mar 2011 16:49:26 -0600
Subject: [MINC-users] volpad
Message-ID: <AANLkTi=vBkvcs64DfUui8-+Np2dOXSz-BpzbxOPspevn@mail.gmail.com>

Hello all. While trying to use volgenmodel, I found that I do not have
a script named volpad. I looked all over the net for it, and found a
link that seems to be dead:
http://mavis.anu.edu.au/scripts/

Other scripts that were also needed where available at
http://packages.bic.mni.mcgill.ca/scripts/

Where can I get a copy of volpad? I hope this would be the last unmet
dependency.

Thanks.

Luis


>
> ? $ volgenmodel -check -clean -symmetric -normalise -extend 5 \
> ? ? ?-output_model <model.mnc> -workdir genmodel-work \
> ? ? ?<infiles>
>
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Brisbane->Australia ? ?+61 (402) 700 883

From a.janke at gmail.com  Tue Mar  1 18:16:15 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 09:16:15 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTi=eyCFZVMU+nTmuU-AGEz+vKuqjdG+urDcUD8vr@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTi=eyCFZVMU+nTmuU-AGEz+vKuqjdG+urDcUD8vr@mail.gmail.com>
Message-ID: <AANLkTinOxCin+o_=eCtDiuaC6jVKOwJe3NMEDEEE8yV6@mail.gmail.com>

Hi Lisa,

> I'm trying to use volgenmodel, but have been running into the following
> error:
>
>> Can't exec "volpad": No such file or directory at
>> /usr/local/bic/bin/volgenmodel line 656.
>> Died at /usr/local/bic/bin/volgenmodel line 656.

Whoops, try here now:

   http://packages.bic.mni.mcgill.ca/scripts/

Sorry about that.



-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883

From lrisa87 at uw.edu  Tue Mar  1 18:34:39 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 1 Mar 2011 15:34:39 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTinOxCin+o_=eCtDiuaC6jVKOwJe3NMEDEEE8yV6@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTi=eyCFZVMU+nTmuU-AGEz+vKuqjdG+urDcUD8vr@mail.gmail.com>
	<AANLkTinOxCin+o_=eCtDiuaC6jVKOwJe3NMEDEEE8yV6@mail.gmail.com>
Message-ID: <AANLkTimLStO7r4O7t5ULjYgfWiL5Mqsyo0RGBY-DiGYh@mail.gmail.com>

Hi Andrew,

Thanks for uploading volpad!

However, now I am running into the following error:

+++ pre-processing input data
>    | genmodel-work/00-pre/0000-15331.nrm.mnc - normalising
> Usage: mincnorm [options] <in.mnc> <out.mnc>
>        mincnorm -help to list options
> unknown option: -threshold
> Died at /usr/local/bic/bin/volgenmodel line 656.


Is the version of my mincnorm not compatible with volgenmodel?
I currently have mincnorm 1.0.0 and volgenmodel 1.4.1.

Thanks.


Best,
Lisa




On Tue, Mar 1, 2011 at 3:16 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Lisa,
>
> > I'm trying to use volgenmodel, but have been running into the following
> > error:
> >
> >> Can't exec "volpad": No such file or directory at
> >> /usr/local/bic/bin/volgenmodel line 656.
> >> Died at /usr/local/bic/bin/volgenmodel line 656.
>
> Whoops, try here now:
>
>   http://packages.bic.mni.mcgill.ca/scripts/
>
> Sorry about that.
>
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Brisbane->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue Mar  1 18:38:47 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 09:38:47 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTimLStO7r4O7t5ULjYgfWiL5Mqsyo0RGBY-DiGYh@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTi=eyCFZVMU+nTmuU-AGEz+vKuqjdG+urDcUD8vr@mail.gmail.com>
	<AANLkTinOxCin+o_=eCtDiuaC6jVKOwJe3NMEDEEE8yV6@mail.gmail.com>
	<AANLkTimLStO7r4O7t5ULjYgfWiL5Mqsyo0RGBY-DiGYh@mail.gmail.com>
Message-ID: <AANLkTi==L+DOJcf_WvRumEzta4EBjQ7xjKe=xSSM2rDw@mail.gmail.com>

> +++ pre-processing input data
>> ? ?| genmodel-work/00-pre/0000-15331.nrm.mnc - normalising
>> Usage: mincnorm [options] <in.mnc> <out.mnc>
>> ? ? ? ?mincnorm -help to list options
>> unknown option: -threshold
>> Died at /usr/local/bic/bin/volgenmodel line 656.
>
>
> Is the version of my mincnorm not compatible with volgenmodel?
> I currently have mincnorm 1.0.0 and volgenmodel 1.4.1.

Yes you will have to use mincnorm v1.2 which is in the scripts directory.


a

From a.janke at gmail.com  Tue Mar  1 18:41:52 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 09:41:52 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
Message-ID: <AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>

> The difference as he mentions in his paper is that he doesn't start
>> fitting from scratch at each step. volgenmodel does but there are
>> other reasons for this.
>
> What are some of the reasons for this?

Mainly philosophical. :)

A bit of a history lesson...

Many moons ago (2000?), Alexandre Guimond started to do recursive
fitting of the ICBM database to itself, the problem at the time
(beyond computation time) was that the model was unstable. It would
continue to grow. I then visited the MNI (2002?) and decided to have
another crack at this a few years on not even realising it had been
done before. Louis Collins pointed me to what Alexandre had been doing
and between the two of us we surmised that the problem was possibly a
registration bias/overshoot. So I added an extra step of averaging
transformations and removing this from the average at each iteration.
At the time we were also fitting both the original data and a mirrored
version in order to make a symmetric model.

This seemed to make the whole process more stable and as such we
managed to make the first iteration of what became known as the
nonlinear ICBM model. This was included in a release of FSL at some
stage.  Around this time a rather clever Austrian who had worked with
me in Oz also visited the MNI (Gunther Grabner) and we decided to try
the same technique on some elderly data. In short he polished off a
lot of rough edges and published a conference abstract on this.

   Grabner G, Janke AL, Budge MM, Smith D, Pruessner J, Collins DL.
Symetric Atlasing and Model Based Segmentation: An Application to the
Hippocampus in Older Adults. Medical Image Computing and Computer
Assisted Intervention (MICCAI) 2006.

Then things exploded.

Alex + Claude then optimised the whole process for the ICBM dataset:

   http://packages.bic.mni.mcgill.ca/tgz/mni-models_icbm152-nl-2009-1.0.tar.gz

As part of this they (or was it Vlad? I forget) produced an "optimal"
fitting scheme for heads

# ICBM nlin conf

@conf = (
   {'step' => 32, 'blur_fwhm' => 16, 'iterations' => 20},
   {'step' => 16, 'blur_fwhm' => 8,  'iterations' => 20},
   {'step' => 12, 'blur_fwhm' => 6,  'iterations' => 20},
   {'step' => 8,  'blur_fwhm' => 4,  'iterations' => 20},
   {'step' => 6,  'blur_fwhm' => 3,  'iterations' => 20},
   {'step' => 4,  'blur_fwhm' => 2,  'iterations' => 10},
   {'step' => 2,  'blur_fwhm' => 1,  'iterations' => 10},
   );

Vladimir Fonov made a bunch of changes, made the pediatric models and
published a paper on another bunch of models using the same technique
for some MS? data with Zografos (Aki) Caramanos.

At the time, I was using a loosely cobbled together directory of shell
and perl scripts to make the whole process happen, the main reason for
this was that my original ICBM models took 3 months to complete across
a rough and ready linux cluster. Vlad made a lot of progress turning
this all into a nice script to do everthing in one but it was in Ruby
(for dependency tracking) and he used all sorts of (clever) special
sauce of his own via resampling with ITK and registration with ANTS?
in short it would have been slightly difficult to distribute. Vlad
also changed the fitting procedure and as such all the rest of us
copied in that we all started fitting the model to the individual. The
reason for this was that it made the xfm averaging much more straight
forward.

I then wrote volgenmodel for my own purposes with dependencies on
distributed MINC things only. So, there will be differences the main
one being the fitting strategy whereby volgenmodel starts from the
initial linear xfm at each fitting stage and Vlads starts from the
previous nonlinear xfm. Certainly this will mean that Vlad's approach
will be faster. The reasoning for starting from the linear xfm was to
avoid continually fitting to a local minima. This was a problem I
originally experienced with minctracc. It possibly is no longer a
problem but I haven't checked so prefer to leave things as they were.
Remember also that Vlad wasn't using minctracc for his nonlinear
fitting so perhaps this is more a difference in ANTS vs minctracc.

So, yes they are different. The idea is still the same but the devil
is often in the details. What is also clear is that the fitting scheme
can vary quite a bit dependant on what you are fitting.

a


PS: For all those involved sorry if I got the timeline wrong somewhere
things really did explode and I never really kept track of everything.

From a.janke at gmail.com  Tue Mar  1 18:44:12 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 09:44:12 +1000
Subject: [MINC-users] volpad
In-Reply-To: <AANLkTi=vBkvcs64DfUui8-+Np2dOXSz-BpzbxOPspevn@mail.gmail.com>
References: <AANLkTi=vBkvcs64DfUui8-+Np2dOXSz-BpzbxOPspevn@mail.gmail.com>
Message-ID: <AANLkTimL89xT1WyK7zEC6sjrGF-YJY=-LcH4F_MTSnD8@mail.gmail.com>

Hi Luis,

> Hello all. While trying to use volgenmodel, I found that I do not have
> a script named volpad. I looked all over the net for it, and found a
> link that seems to be dead:
> http://mavis.anu.edu.au/scripts/

Yes, sorry, since my move from ANU back to UQ this has sort of died..

> Other scripts that were also needed where available at
> http://packages.bic.mni.mcgill.ca/scripts/
>
> Where can I get a copy of volpad? I hope this would be the last unmet
> dependency.

I have uploaded it to the scripts directory.


a

From lrisa87 at uw.edu  Tue Mar  1 18:55:41 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 1 Mar 2011 15:55:41 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTi==L+DOJcf_WvRumEzta4EBjQ7xjKe=xSSM2rDw@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTi=eyCFZVMU+nTmuU-AGEz+vKuqjdG+urDcUD8vr@mail.gmail.com>
	<AANLkTinOxCin+o_=eCtDiuaC6jVKOwJe3NMEDEEE8yV6@mail.gmail.com>
	<AANLkTimLStO7r4O7t5ULjYgfWiL5Mqsyo0RGBY-DiGYh@mail.gmail.com>
	<AANLkTi==L+DOJcf_WvRumEzta4EBjQ7xjKe=xSSM2rDw@mail.gmail.com>
Message-ID: <AANLkTinxHue4a8h_9wqUuD4ODojN42bnkqon8vBSEG8o@mail.gmail.com>

Hi Andrew,

I think the mincnorm you just uploaded on to the scripts directory is
version 1.0.0.

Thanks.


Best,
Lisa



On Tue, Mar 1, 2011 at 3:38 PM, Andrew Janke <a.janke at gmail.com> wrote:

> > +++ pre-processing input data
> >>    | genmodel-work/00-pre/0000-15331.nrm.mnc - normalising
> >> Usage: mincnorm [options] <in.mnc> <out.mnc>
> >>        mincnorm -help to list options
> >> unknown option: -threshold
> >> Died at /usr/local/bic/bin/volgenmodel line 656.
> >
> >
> > Is the version of my mincnorm not compatible with volgenmodel?
> > I currently have mincnorm 1.0.0 and volgenmodel 1.4.1.
>
> Yes you will have to use mincnorm v1.2 which is in the scripts directory.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue Mar  1 19:02:41 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 10:02:41 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTinxHue4a8h_9wqUuD4ODojN42bnkqon8vBSEG8o@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTi=eyCFZVMU+nTmuU-AGEz+vKuqjdG+urDcUD8vr@mail.gmail.com>
	<AANLkTinOxCin+o_=eCtDiuaC6jVKOwJe3NMEDEEE8yV6@mail.gmail.com>
	<AANLkTimLStO7r4O7t5ULjYgfWiL5Mqsyo0RGBY-DiGYh@mail.gmail.com>
	<AANLkTi==L+DOJcf_WvRumEzta4EBjQ7xjKe=xSSM2rDw@mail.gmail.com>
	<AANLkTinxHue4a8h_9wqUuD4ODojN42bnkqon8vBSEG8o@mail.gmail.com>
Message-ID: <AANLkTik16fnFWPTwLzqrxo9e+20HAZUrW39gOJTCJwx=@mail.gmail.com>

Be sure to reload/clear your cache, I just updated it.

   $ wget http://packages.bic.mni.mcgill.ca/scripts/mincnorm

May prove more fruitful.


a

> I think the mincnorm you just uploaded on to the scripts directory is
> version 1.0.0.
>
> Thanks.
>
>
> Best,
> Lisa

From vladimir.fonov at gmail.com  Tue Mar  1 19:10:00 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 01 Mar 2011 19:10:00 -0500
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
Message-ID: <4D6D8AD8.5000707@gmail.com>

Hello,

Andrew Janke wrote:
> Then things exploded.
> 
> Alex + Claude then optimised the whole process for the ICBM dataset:
> 
>    http://packages.bic.mni.mcgill.ca/tgz/mni-models_icbm152-nl-2009-1.0.tar.gz

That was me, Claude have only created a package.


> As part of this they (or was it Vlad? I forget) produced an "optimal"
> fitting scheme for heads
This was Claude.

> Vladimir Fonov made a bunch of changes, made the pediatric models and
> published a paper on another bunch of models using the same technique
> for some MS? data with Zografos (Aki) Caramanos.
Published only for NIHPD and ICBM.


> problem but I haven't checked so prefer to leave things as they were.
> Remember also that Vlad wasn't using minctracc for his nonlinear
> fitting so perhaps this is more a difference in ANTS vs minctracc.
No, I am still using minctracc in the model creation script. ANTS have 
it's own version, by the way.


-- 
Best regards,
  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info

From lrisa87 at uw.edu  Tue Mar  1 19:27:10 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 1 Mar 2011 16:27:10 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <4D6D8AD8.5000707@gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
Message-ID: <AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>

Hello,

> "History" Lesson
Thank you, Andrew (and Vladimir for the corrections) for the detailed
background information.
It is great to have all of this information summed up simply for outsiders
like myself.

> mincnorm 1.2.0
Oops, my bad. Sorry! I got the new version now.

>New error - gennlxfm

> Can't exec "gennlxfm": No such file or directory at
> /usr/local/bic/bin/volgenmodel line 656.
> Died at /usr/local/bic/bin/volgenmodel line 656.


Is this another one of your scripts that I am missing?

Thank you.


Best,
Lisa



On Tue, Mar 1, 2011 at 4:10 PM, Vladimir S. FONOV
<vladimir.fonov at gmail.com>wrote:

> Hello,
>
>
> Andrew Janke wrote:
>
>> Then things exploded.
>>
>> Alex + Claude then optimised the whole process for the ICBM dataset:
>>
>>
>> http://packages.bic.mni.mcgill.ca/tgz/mni-models_icbm152-nl-2009-1.0.tar.gz
>>
>
> That was me, Claude have only created a package.
>
>
>
>  As part of this they (or was it Vlad? I forget) produced an "optimal"
>> fitting scheme for heads
>>
> This was Claude.
>
>
>  Vladimir Fonov made a bunch of changes, made the pediatric models and
>> published a paper on another bunch of models using the same technique
>> for some MS? data with Zografos (Aki) Caramanos.
>>
> Published only for NIHPD and ICBM.
>
>
>
>  problem but I haven't checked so prefer to leave things as they were.
>> Remember also that Vlad wasn't using minctracc for his nonlinear
>> fitting so perhaps this is more a difference in ANTS vs minctracc.
>>
> No, I am still using minctracc in the model creation script. ANTS have it's
> own version, by the way.
>
>
> --
> Best regards,
>  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue Mar  1 19:15:55 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 10:15:55 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <4D6D8AD8.5000707@gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
Message-ID: <AANLkTi=sya27otmd3rL_Un4UxGTX6GpPAYdX9qdeXfNA@mail.gmail.com>

> That was me, Claude have only created a package.
>
> This was Claude.
>
> Published only for NIHPD and ICBM.
>
> No, I am still using minctracc in the model creation script. ANTS have it's
> own version, by the way.

Thanks for the corrections Vladimir!   :)

I am sure there is even more to the story than this (from other perspectives).


a

From a.janke at gmail.com  Tue Mar  1 19:32:09 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 10:32:09 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
Message-ID: <AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>

>>New error - gennlxfm
>
>> Can't exec "gennlxfm": No such file or directory at
>> /usr/local/bic/bin/volgenmodel line 656.
>> Died at /usr/local/bic/bin/volgenmodel line 656.
> Is this another one of your scripts that I am missing?

Aaaargh! I expect the Benny Hill music to start soon.

   http://packages.bic.mni.mcgill.ca/scripts/gennlxfm

Which needs:

   http://packages.bic.mni.mcgill.ca/scripts/volextents

Are now both there.


a

From lrisa87 at uw.edu  Tue Mar  1 20:07:48 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 1 Mar 2011 17:07:48 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
Message-ID: <AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>

THANKS for gennlxfm and volextents.

Yiiikes. One more script (hopefully this will be the last; I really need to
stop bugging you) that I need... : bestlinreg.

Thanks, Andrew.


Best,
Lisa




On Tue, Mar 1, 2011 at 4:32 PM, Andrew Janke <a.janke at gmail.com> wrote:

> >>New error - gennlxfm
> >
> >> Can't exec "gennlxfm": No such file or directory at
> >> /usr/local/bic/bin/volgenmodel line 656.
> >> Died at /usr/local/bic/bin/volgenmodel line 656.
> > Is this another one of your scripts that I am missing?
>
> Aaaargh! I expect the Benny Hill music to start soon.
>
>   http://packages.bic.mni.mcgill.ca/scripts/gennlxfm
>
> Which needs:
>
>   http://packages.bic.mni.mcgill.ca/scripts/volextents
>
> Are now both there.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue Mar  1 20:22:40 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 2 Mar 2011 11:22:40 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
Message-ID: <AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>

> Yiiikes. One more script (hopefully this will be the last; I really need to
> stop bugging you) that I need... : bestlinreg.

Ah, well this one is Claudes. It's a condensed version of mritotal
using the same code layout as nlpfit.

I have uploaded the version I have of it to the scripts directory but
note that it may not be the latest or best version. Claude will no
doubt correct me.

Another way around this is if you know that your brains are all fairly
close to each other is to do this:

   $ volgenmodel -linmethod 'minctracc -lsq9' ....

I should also mention that once you have it all working, if you have a
gridengine install add -batch argument and watch the fun begin as it
brings your network/cluster to a crawl.


a

From lrisa87 at uw.edu  Wed Mar  2 14:50:56 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Wed, 2 Mar 2011 11:50:56 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
	<AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
Message-ID: <AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>

Hi Andrew,

Thanks for uploading your copy of bestlinreg and suggesting an alternative
way (using -linmethod 'minctracc -lsq9').

I got rid of the previous errors I was getting, but now I get the following:

Initial objective function val = 0.16510932
> Final objective function value = 0.14109196
> mv -f /tmp/bestlinreg-SMx3R3ux/Sfit-model-iso_4.xfm
> genmodel-work/00/0003-SEA0094_6mo_May2009_t1mpr.xfm
> Died at /usr/local/bic/bin/xfmavg line 310.
> Died at /usr/local/bic/bin/volgenmodel line 656.


I get the above when using your copy of bestlinreg, a copy of bestlinreg
that Claude had provided me, and even when running with the -linmethod
'minctracc -lsq9' option.
The output file that I specified the name of is no where to be found in the
workdir or the dir where I have stored my input files.

Any tips?

Many thanks.


Best,
Lisa



On Tue, Mar 1, 2011 at 5:22 PM, Andrew Janke <a.janke at gmail.com> wrote:

> > Yiiikes. One more script (hopefully this will be the last; I really need
> to
> > stop bugging you) that I need... : bestlinreg.
>
> Ah, well this one is Claudes. It's a condensed version of mritotal
> using the same code layout as nlpfit.
>
> I have uploaded the version I have of it to the scripts directory but
> note that it may not be the latest or best version. Claude will no
> doubt correct me.
>
> Another way around this is if you know that your brains are all fairly
> close to each other is to do this:
>
>   $ volgenmodel -linmethod 'minctracc -lsq9' ....
>
> I should also mention that once you have it all working, if you have a
> gridengine install add -batch argument and watch the fun begin as it
> brings your network/cluster to a crawl.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From MKeaser at umaryland.edu  Wed Mar  2 19:00:18 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Wed, 2 Mar 2011 19:00:18 -0500
Subject: [MINC-users] mincbundle installation probllems with Ubuntu 10.04
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055E427087@UMBEXMBX2.campus.umaryland.edu>
References: <00EF2C3B391AF84C8ED343F4469D4D56055E427087@UMBEXMBX2.campus.umaryland.edu>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055E427088@UMBEXMBX2.campus.umaryland.edu>

Hello,

I'm having trouble installing the mincbundle package on Ubuntu 10.04.

I added this line:

deb http://packages.bic.mni.mcgill.ca/ubuntu-lucid ./

to my /etc/apt/source.list file. I typed "sudo apt-get update", and

However, when  i typed "sudo apt-get install mincbundle", I received the following message:

pkg: dependency problems prevent configuration of mincbundle:
 mincbundle depends on display; however:
  Package display is not installed.
dpkg: error processing mincbundle (--configure):
 dependency problems - leaving unconfigured
No apport report written because the error message indicates its a followup error from a previous failure.
                          Errors were encountered while processing:
 display
 mincbundle
E: Sub-process /usr/bin/dpkg returned an error code (1)

I then tried to install the display package with the update manager of Ubuntu, and then I received this message:

"You have 1 broken package on your system"

I then install the display package, and place the /usr/local/bic/bin directory in the path file to call different commands. However, when i type a command like "volperf", I receive this message:

volperf: error while loading shared libraries: libvolume_io2.so.1: cannot open shared object file: No such file or directory

So, I'm not exactly sure what is going on here. Any ideas?

Thanks,

Michael

From a.janke at gmail.com  Thu Mar  3 08:15:19 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 3 Mar 2011 23:15:19 +1000
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
	<AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
	<AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>
Message-ID: <AANLkTimu3XFmgfofKZE9xZDMgHmOR1SVyKatgwSOvZcS@mail.gmail.com>

Hi Lisa,

>> Died at /usr/local/bic/bin/xfmavg line 310.
>> Died at /usr/local/bic/bin/volgenmodel line 656.
>
> The output file that I specified the name of is no where to be found in the
> workdir or the dir where I have stored my input files.

I think the output is a big misleading in that I think the problem is
in the transform averaging not in the fitting. Do you have octave
installed?  xfmavg uses this.

perhaps if you add a -verbose argument things might become a bit more
clear?  volgenmodel is designed such that you can just re-run whatever
you did last and it will pick up from where it left off.

There is even a copy of the original command you used in the
genmodel-work directory.


a

From lrisa87 at uw.edu  Thu Mar  3 14:08:30 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Thu, 3 Mar 2011 11:08:30 -0800
Subject: [MINC-users] best_nonlin_reg.pl ?
In-Reply-To: <AANLkTimu3XFmgfofKZE9xZDMgHmOR1SVyKatgwSOvZcS@mail.gmail.com>
References: <AANLkTinqOrw0G9dC-o4obCD62=eyzyJL=4oj+9zvnpsc@mail.gmail.com>
	<201102250344.p1P3i5tq002657@cassio.bic.mni.mcgill.ca>
	<AANLkTinRWRtwxpXCm3N=BiuCTF2cpifgX2Ta_shkGAvX@mail.gmail.com>
	<AANLkTinxoxfGz9T2eYk2RnMHgeHWbhqreJkxSzWAKdpX@mail.gmail.com>
	<AANLkTimYRbWUbZ10-jCrg-SOr8x9tJ17kvviv++Dc6rj@mail.gmail.com>
	<AANLkTim9krZyo5W=9oDhgGmLhrt5xhYGfbg27RALLQ5K@mail.gmail.com>
	<AANLkTin8V9TVxxd5kx2VPEeE5CoCe-y8kgzTNC780tbK@mail.gmail.com>
	<4D6D8AD8.5000707@gmail.com>
	<AANLkTi=qP=89E-KJo=Qy=bNDg5keOMNZdgNjcskqRdtF@mail.gmail.com>
	<AANLkTika+hX+3On4ro+ExMZ=f7hpzyTCXNdB3z+aMBQ1@mail.gmail.com>
	<AANLkTim1OH+Exj7fXMrtn7VR-sKWPZ0kWN49c-qUzPii@mail.gmail.com>
	<AANLkTi=zuYHxSUMwmUcTaLhU7mtR7mLMs-TwwbjMtHtL@mail.gmail.com>
	<AANLkTi=PKHN51grinEVpF=HeRgjHJC+EbA+27WxLE-9N@mail.gmail.com>
	<AANLkTimu3XFmgfofKZE9xZDMgHmOR1SVyKatgwSOvZcS@mail.gmail.com>
Message-ID: <AANLkTimw3cqJs_+zjngwj-JqCxpTVRdHFz+ejbeTktZ0@mail.gmail.com>

Hi Andrew,

I did not have Octave installed.
Right now I am re-running volgenmodel after I installed Octave
and so far it seems like it is chugging along without any errors at all.

Thanks for all the tips and suggestions!


Best,
Lisa




On Thu, Mar 3, 2011 at 5:15 AM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Lisa,
>
> >> Died at /usr/local/bic/bin/xfmavg line 310.
> >> Died at /usr/local/bic/bin/volgenmodel line 656.
> >
> > The output file that I specified the name of is no where to be found in
> the
> > workdir or the dir where I have stored my input files.
>
> I think the output is a big misleading in that I think the problem is
> in the transform averaging not in the fitting. Do you have octave
> installed?  xfmavg uses this.
>
> perhaps if you add a -verbose argument things might become a bit more
> clear?  volgenmodel is designed such that you can just re-run whatever
> you did last and it will pick up from where it left off.
>
> There is even a copy of the original command you used in the
> genmodel-work directory.
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gstoynev at biospective.com  Thu Mar  3 14:16:12 2011
From: gstoynev at biospective.com (George Stoynev)
Date: Thu, 3 Mar 2011 14:16:12 -0500
Subject: [MINC-users] mincbundle installation probllems with Ubuntu 10.04
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055E427088@UMBEXMBX2.campus.umaryland.edu>
References: <00EF2C3B391AF84C8ED343F4469D4D56055E427087@UMBEXMBX2.campus.umaryland.edu>
	<00EF2C3B391AF84C8ED343F4469D4D56055E427088@UMBEXMBX2.campus.umaryland.edu>
Message-ID: <AANLkTi=-WMtZ+=SfRdADrs45RzQ2J9Yp791+v0jujRP0@mail.gmail.com>

Hi,

run "sudo apt-get install display", then repeat "sudo apt-get install
mincbundle". Once this is installed, create symlink "cd /usr/local/bic/lib
&& ln -s libvolume_io2.so.1.1.2 libvolume_io2.so.1", if not made by the
installer.

Cheers,
---
George Stoynev


On Wed, Mar 2, 2011 at 7:00 PM, Keaser, Michael L <MKeaser at umaryland.edu>wrote:

> Hello,
>
> I'm having trouble installing the mincbundle package on Ubuntu 10.04.
>
> I added this line:
>
> deb http://packages.bic.mni.mcgill.ca/ubuntu-lucid ./
>
> to my /etc/apt/source.list file. I typed "sudo apt-get update", and
>
> However, when  i typed "sudo apt-get install mincbundle", I received the
> following message:
>
> pkg: dependency problems prevent configuration of mincbundle:
>  mincbundle depends on display; however:
>  Package display is not installed.
> dpkg: error processing mincbundle (--configure):
>  dependency problems - leaving unconfigured
> No apport report written because the error message indicates its a followup
> error from a previous failure.
>                          Errors were encountered while processing:
>  display
>  mincbundle
> E: Sub-process /usr/bin/dpkg returned an error code (1)
>
> I then tried to install the display package with the update manager of
> Ubuntu, and then I received this message:
>
> "You have 1 broken package on your system"
>
> I then install the display package, and place the /usr/local/bic/bin
> directory in the path file to call different commands. However, when i type
> a command like "volperf", I receive this message:
>
> volperf: error while loading shared libraries: libvolume_io2.so.1: cannot
> open shared object file: No such file or directory
>
> So, I'm not exactly sure what is going on here. Any ideas?
>
> Thanks,
>
> Michael
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Thu Mar  3 14:54:31 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 03 Mar 2011 14:54:31 -0500
Subject: [MINC-users] mincbundle installation probllems with Ubuntu 10.04
In-Reply-To: <AANLkTi=-WMtZ+=SfRdADrs45RzQ2J9Yp791+v0jujRP0@mail.gmail.com>
References: <00EF2C3B391AF84C8ED343F4469D4D56055E427087@UMBEXMBX2.campus.umaryland.edu>	<00EF2C3B391AF84C8ED343F4469D4D56055E427088@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTi=-WMtZ+=SfRdADrs45RzQ2J9Yp791+v0jujRP0@mail.gmail.com>
Message-ID: <4D6FF1F7.8010401@gmail.com>

Hello,

you just need to set LD_LIBRARY_PATH to include /usr/local/bic/lib, no 
need to create symbolic links. i.e

export LD_LIBRARY_PATH=/usr/local/bic/lib:$LD_LIBRARY_PATH


Also, Display package is broken - it is empty.

i.e

$ dpkg -L display
/.
/usr
/usr/local
/usr/local/bic
/usr/local/bic/bin




George Stoynev wrote:
> Hi,
> 
> run "sudo apt-get install display", then repeat "sudo apt-get install
> mincbundle". Once this is installed, create symlink "cd /usr/local/bic/lib
> && ln -s libvolume_io2.so.1.1.2 libvolume_io2.so.1", if not made by the
> installer.
> 
> Cheers,
> ---
> George Stoynev
> 
> 
> On Wed, Mar 2, 2011 at 7:00 PM, Keaser, Michael L <MKeaser at umaryland.edu>wrote:
> 
>> Hello,
>>
>> I'm having trouble installing the mincbundle package on Ubuntu 10.04.
>>
>> I added this line:
>>
>> deb http://packages.bic.mni.mcgill.ca/ubuntu-lucid ./
>>
>> to my /etc/apt/source.list file. I typed "sudo apt-get update", and
>>
>> However, when  i typed "sudo apt-get install mincbundle", I received the
>> following message:
>>
>> pkg: dependency problems prevent configuration of mincbundle:
>>  mincbundle depends on display; however:
>>  Package display is not installed.
>> dpkg: error processing mincbundle (--configure):
>>  dependency problems - leaving unconfigured
>> No apport report written because the error message indicates its a followup
>> error from a previous failure.
>>                          Errors were encountered while processing:
>>  display
>>  mincbundle
>> E: Sub-process /usr/bin/dpkg returned an error code (1)
>>
>> I then tried to install the display package with the update manager of
>> Ubuntu, and then I received this message:
>>
>> "You have 1 broken package on your system"
>>
>> I then install the display package, and place the /usr/local/bic/bin
>> directory in the path file to call different commands. However, when i type
>> a command like "volperf", I receive this message:
>>
>> volperf: error while loading shared libraries: libvolume_io2.so.1: cannot
>> open shared object file: No such file or directory
>>
>> So, I'm not exactly sure what is going on here. Any ideas?
>>
>> Thanks,
>>
>> Michael
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


-- 
Best regards,
  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info

From MKeaser at umaryland.edu  Fri Mar  4 13:17:01 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Fri, 4 Mar 2011 13:17:01 -0500
Subject: [MINC-users] mincbundle installation probllems with Ubuntu 10.04
In-Reply-To: <4D6FF1F7.8010401@gmail.com>
References: <00EF2C3B391AF84C8ED343F4469D4D56055E427087@UMBEXMBX2.campus.umaryland.edu>
	<00EF2C3B391AF84C8ED343F4469D4D56055E427088@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTi=-WMtZ+=SfRdADrs45RzQ2J9Yp791+v0jujRP0@mail.gmail.com>,
	<4D6FF1F7.8010401@gmail.com>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055E427090@UMBEXMBX2.campus.umaryland.edu>

Hello,

Thank you Vladimir and George for your reponses. I tried out Valdimir's suggestion and it worked.

I have one additional question. Although i installed mincbundle, i noticed that packages such as "mincsample" are included in mincbundle, but packages such as "mni-autoreg" are not. Is this true? And if so, would i simply install the other additional packages like I did for mincbundle and setup the library path again for them as well.

Michael
________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
Sent: Thursday, March 03, 2011 2:54 PM
To: MINC users mailing list
Subject: Re: [MINC-users] mincbundle installation probllems with Ubuntu 10.04

Hello,

you just need to set LD_LIBRARY_PATH to include /usr/local/bic/lib, no
need to create symbolic links. i.e

export LD_LIBRARY_PATH=/usr/local/bic/lib:$LD_LIBRARY_PATH


Also, Display package is broken - it is empty.

i.e

$ dpkg -L display
/.
/usr
/usr/local
/usr/local/bic
/usr/local/bic/bin




George Stoynev wrote:
> Hi,
>
> run "sudo apt-get install display", then repeat "sudo apt-get install
> mincbundle". Once this is installed, create symlink "cd /usr/local/bic/lib
> && ln -s libvolume_io2.so.1.1.2 libvolume_io2.so.1", if not made by the
> installer.
>
> Cheers,
> ---
> George Stoynev
>
>
> On Wed, Mar 2, 2011 at 7:00 PM, Keaser, Michael L <MKeaser at umaryland.edu>wrote:
>
>> Hello,
>>
>> I'm having trouble installing the mincbundle package on Ubuntu 10.04.
>>
>> I added this line:
>>
>> deb http://packages.bic.mni.mcgill.ca/ubuntu-lucid ./
>>
>> to my /etc/apt/source.list file. I typed "sudo apt-get update", and
>>
>> However, when  i typed "sudo apt-get install mincbundle", I received the
>> following message:
>>
>> pkg: dependency problems prevent configuration of mincbundle:
>>  mincbundle depends on display; however:
>>  Package display is not installed.
>> dpkg: error processing mincbundle (--configure):
>>  dependency problems - leaving unconfigured
>> No apport report written because the error message indicates its a followup
>> error from a previous failure.
>>                          Errors were encountered while processing:
>>  display
>>  mincbundle
>> E: Sub-process /usr/bin/dpkg returned an error code (1)
>>
>> I then tried to install the display package with the update manager of
>> Ubuntu, and then I received this message:
>>
>> "You have 1 broken package on your system"
>>
>> I then install the display package, and place the /usr/local/bic/bin
>> directory in the path file to call different commands. However, when i type
>> a command like "volperf", I receive this message:
>>
>> volperf: error while loading shared libraries: libvolume_io2.so.1: cannot
>> open shared object file: No such file or directory
>>
>> So, I'm not exactly sure what is going on here. Any ideas?
>>
>> Thanks,
>>
>> Michael
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


--
Best regards,
  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From lrisa87 at uw.edu  Fri Mar  4 14:00:35 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 4 Mar 2011 11:00:35 -0800
Subject: [MINC-users] mincaverage error
Message-ID: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>

Hello,

I am trying to run mincaverage on 43 minc files, all which have been N3
intensity nonuniformity normalized, neck portion cropped off, and
mincnorm-ed.
The following is the error that I receive:

Processing:........................miicv_attach: MINC package entry point
> *ncvarid: ncid -1: NetCDF: Not a valid ID*


When I run mincaverage on individual files and on subsets of the 43 files,
mincaverage runs fine.
What is the issue?

Thank you in advance.


Best,
Lisa

From jared.rowley at gmail.com  Fri Mar  4 14:05:29 2011
From: jared.rowley at gmail.com (Jared Rowley)
Date: Fri, 4 Mar 2011 14:05:29 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
Message-ID: <AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>

Hi Lisa,

I think you need to to do mincaverage -clobber.

My guess is that the output.mnc already exists and you need to do -clobber
to overwrite it.

Jared


On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Hello,
>
> I am trying to run mincaverage on 43 minc files, all which have been N3
> intensity nonuniformity normalized, neck portion cropped off, and
> mincnorm-ed.
> The following is the error that I receive:
>
> Processing:........................miicv_attach: MINC package entry point
> > *ncvarid: ncid -1: NetCDF: Not a valid ID*
>
>
> When I run mincaverage on individual files and on subsets of the 43 files,
> mincaverage runs fine.
> What is the issue?
>
> Thank you in advance.
>
>
> Best,
> Lisa
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Jared Rowley
Translational Neuroimaging Laboratory
McGill Centre for Studies in Aging
Douglas Hospital Research Center
McGill University
6825 LaSalle Blvd.
Montreal, QC Canada
H4H 1R3

From lrisa87 at uw.edu  Fri Mar  4 14:23:32 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 4 Mar 2011 11:23:32 -0800
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
	<AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
Message-ID: <AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>

Hi Jared,

I tried re-running mincaverage with the -clobber extention.
I also ran it using a totally new output filename too, but it still gives me
the same error message.

Thanks.


Best,
Lisa



On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <jared.rowley at gmail.com>wrote:

> Hi Lisa,
>
> I think you need to to do mincaverage -clobber.
>
> My guess is that the output.mnc already exists and you need to do -clobber
> to overwrite it.
>
> Jared
>
>
> On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>
> > Hello,
> >
> > I am trying to run mincaverage on 43 minc files, all which have been N3
> > intensity nonuniformity normalized, neck portion cropped off, and
> > mincnorm-ed.
> > The following is the error that I receive:
> >
> > Processing:........................miicv_attach: MINC package entry point
> > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
> >
> >
> > When I run mincaverage on individual files and on subsets of the 43
> files,
> > mincaverage runs fine.
> > What is the issue?
> >
> > Thank you in advance.
> >
> >
> > Best,
> > Lisa
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
>
> --
> Jared Rowley
> Translational Neuroimaging Laboratory
> McGill Centre for Studies in Aging
> Douglas Hospital Research Center
> McGill University
> 6825 LaSalle Blvd.
> Montreal, QC Canada
> H4H 1R3
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From andrew at biospective.com  Fri Mar  4 14:52:30 2011
From: andrew at biospective.com (Andrew Wood)
Date: Fri, 4 Mar 2011 14:52:30 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
	<AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
	<AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>
Message-ID: <AANLkTimE5MPzaJwfv05xcqfQQrADKBNPSofsZSCMhTwr@mail.gmail.com>

Hi Lisa,

Is there any chance that the problem is with your input minc files? I just
gave minc average a few good minc volumes plus a filename that didn't exist
and I got back your error message.

Andrew


On Fri, Mar 4, 2011 at 2:23 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Hi Jared,
>
> I tried re-running mincaverage with the -clobber extention.
> I also ran it using a totally new output filename too, but it still gives
> me
> the same error message.
>
> Thanks.
>
>
> Best,
> Lisa
>
>
>
> On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <jared.rowley at gmail.com
> >wrote:
>
> > Hi Lisa,
> >
> > I think you need to to do mincaverage -clobber.
> >
> > My guess is that the output.mnc already exists and you need to do
> -clobber
> > to overwrite it.
> >
> > Jared
> >
> >
> > On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> >
> > > Hello,
> > >
> > > I am trying to run mincaverage on 43 minc files, all which have been N3
> > > intensity nonuniformity normalized, neck portion cropped off, and
> > > mincnorm-ed.
> > > The following is the error that I receive:
> > >
> > > Processing:........................miicv_attach: MINC package entry
> point
> > > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
> > >
> > >
> > > When I run mincaverage on individual files and on subsets of the 43
> > files,
> > > mincaverage runs fine.
> > > What is the issue?
> > >
> > > Thank you in advance.
> > >
> > >
> > > Best,
> > > Lisa
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> >
> >
> > --
> > Jared Rowley
> > Translational Neuroimaging Laboratory
> > McGill Centre for Studies in Aging
> > Douglas Hospital Research Center
> > McGill University
> > 6825 LaSalle Blvd.
> > Montreal, QC Canada
> > H4H 1R3
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From lrisa87 at uw.edu  Fri Mar  4 15:17:30 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 4 Mar 2011 12:17:30 -0800
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTimE5MPzaJwfv05xcqfQQrADKBNPSofsZSCMhTwr@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
	<AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
	<AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>
	<AANLkTimE5MPzaJwfv05xcqfQQrADKBNPSofsZSCMhTwr@mail.gmail.com>
Message-ID: <AANLkTim8QJOUv7PoQ0UbwT8h+cahaGXZGYqKau-50NzJ@mail.gmail.com>

Hi Andrew,

I double checked each minc file (displayed them in register) and they all
seemed to be fine...

Don't know if this helps at all..., but here are some more information:

1. A correction to what I wrote earlier:

> I am trying to run mincaverage on 43 minc files, all which have been N3
> intensity nonuniformity normalized, neck portion cropped off, mincnorm-ed,
> *and linearly (9parameter) registered to a standard template*.


2. I am using the -filelist option. I have a .txt file with each file name
listed on separate lines. Is this the correct format for the filelist?

3. The version I am using:

> > mincaverage -version
> program: 2.1.00
> libminc: 2.1.00
> netcdf : 4.1.1 of May 15 2010 04:10:51 $
> HDF5   : 1.8.4



Thanks.


Best,
Lisa

On Fri, Mar 4, 2011 at 11:52 AM, Andrew Wood <andrew at biospective.com> wrote:

> Hi Lisa,
>
> Is there any chance that the problem is with your input minc files? I just
> gave minc average a few good minc volumes plus a filename that didn't exist
> and I got back your error message.
>
> Andrew
>
>
> On Fri, Mar 4, 2011 at 2:23 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>
> > Hi Jared,
> >
> > I tried re-running mincaverage with the -clobber extention.
> > I also ran it using a totally new output filename too, but it still gives
> > me
> > the same error message.
> >
> > Thanks.
> >
> >
> > Best,
> > Lisa
> >
> >
> >
> > On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <jared.rowley at gmail.com
> > >wrote:
> >
> > > Hi Lisa,
> > >
> > > I think you need to to do mincaverage -clobber.
> > >
> > > My guess is that the output.mnc already exists and you need to do
> > -clobber
> > > to overwrite it.
> > >
> > > Jared
> > >
> > >
> > > On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
> wrote:
> > >
> > > > Hello,
> > > >
> > > > I am trying to run mincaverage on 43 minc files, all which have been
> N3
> > > > intensity nonuniformity normalized, neck portion cropped off, and
> > > > mincnorm-ed.
> > > > The following is the error that I receive:
> > > >
> > > > Processing:........................miicv_attach: MINC package entry
> > point
> > > > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
> > > >
> > > >
> > > > When I run mincaverage on individual files and on subsets of the 43
> > > files,
> > > > mincaverage runs fine.
> > > > What is the issue?
> > > >
> > > > Thank you in advance.
> > > >
> > > >
> > > > Best,
> > > > Lisa
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > >
> > >
> > >
> > > --
> > > Jared Rowley
> > > Translational Neuroimaging Laboratory
> > > McGill Centre for Studies in Aging
> > > Douglas Hospital Research Center
> > > McGill University
> > > 6825 LaSalle Blvd.
> > > Montreal, QC Canada
> > > H4H 1R3
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Fri Mar  4 15:42:59 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 4 Mar 2011 15:42:59 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTim8QJOUv7PoQ0UbwT8h+cahaGXZGYqKau-50NzJ@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
	<AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
	<AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>
	<AANLkTimE5MPzaJwfv05xcqfQQrADKBNPSofsZSCMhTwr@mail.gmail.com>
	<AANLkTim8QJOUv7PoQ0UbwT8h+cahaGXZGYqKau-50NzJ@mail.gmail.com>
Message-ID: <AANLkTik_oP-mYAs8V51mMzwf8Wr1kTfT33dY79VKXFZC@mail.gmail.com>

Hello,

On Fri, Mar 4, 2011 at 3:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> 2. I am using the -filelist option. I have a .txt file with each file name
> listed on separate lines. Is this the correct format for the filelist?

did you try to specify all the file names in the command line?


-- 
Best regards,

?Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From zijdenbos at gmail.com  Fri Mar  4 15:44:58 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 4 Mar 2011 15:44:58 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTim8QJOUv7PoQ0UbwT8h+cahaGXZGYqKau-50NzJ@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
	<AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
	<AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>
	<AANLkTimE5MPzaJwfv05xcqfQQrADKBNPSofsZSCMhTwr@mail.gmail.com>
	<AANLkTim8QJOUv7PoQ0UbwT8h+cahaGXZGYqKau-50NzJ@mail.gmail.com>
Message-ID: <AANLkTi=Es_Wa9VfJ9G7Empmf2O-Tg0Zb2UvG_szpFAOM@mail.gmail.com>

Hi Lisa,

On the off-chance that this is the problem - are you sure you have
write access and free disk space in the location where you are trying
to write the output file?

-- Alex

On Fri, Mar 4, 2011 at 3:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>
> Hi Andrew,
>
> I double checked each minc file (displayed them in register) and they all
> seemed to be fine...
>
> Don't know if this helps at all..., but here are some more information:
>
> 1. A correction to what I wrote earlier:
>
> > I am trying to run mincaverage on 43 minc files, all which have been N3
> > intensity nonuniformity normalized, neck portion cropped off, mincnorm-ed,
> > *and linearly (9parameter) registered to a standard template*.
>
>
> 2. I am using the -filelist option. I have a .txt file with each file name
> listed on separate lines. Is this the correct format for the filelist?
>
> 3. The version I am using:
>
> > > mincaverage -version
> > program: 2.1.00
> > libminc: 2.1.00
> > netcdf : 4.1.1 of May 15 2010 04:10:51 $
> > HDF5 ? : 1.8.4
>
>
>
> Thanks.
>
>
> Best,
> Lisa
>
> On Fri, Mar 4, 2011 at 11:52 AM, Andrew Wood <andrew at biospective.com> wrote:
>
> > Hi Lisa,
> >
> > Is there any chance that the problem is with your input minc files? I just
> > gave minc average a few good minc volumes plus a filename that didn't exist
> > and I got back your error message.
> >
> > Andrew
> >
> >
> > On Fri, Mar 4, 2011 at 2:23 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> >
> > > Hi Jared,
> > >
> > > I tried re-running mincaverage with the -clobber extention.
> > > I also ran it using a totally new output filename too, but it still gives
> > > me
> > > the same error message.
> > >
> > > Thanks.
> > >
> > >
> > > Best,
> > > Lisa
> > >
> > >
> > >
> > > On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <jared.rowley at gmail.com
> > > >wrote:
> > >
> > > > Hi Lisa,
> > > >
> > > > I think you need to to do mincaverage -clobber.
> > > >
> > > > My guess is that the output.mnc already exists and you need to do
> > > -clobber
> > > > to overwrite it.
> > > >
> > > > Jared
> > > >
> > > >
> > > > On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
> > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I am trying to run mincaverage on 43 minc files, all which have been
> > N3
> > > > > intensity nonuniformity normalized, neck portion cropped off, and
> > > > > mincnorm-ed.
> > > > > The following is the error that I receive:
> > > > >
> > > > > Processing:........................miicv_attach: MINC package entry
> > > point
> > > > > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
> > > > >
> > > > >
> > > > > When I run mincaverage on individual files and on subsets of the 43
> > > > files,
> > > > > mincaverage runs fine.
> > > > > What is the issue?
> > > > >
> > > > > Thank you in advance.
> > > > >
> > > > >
> > > > > Best,
> > > > > Lisa
> > > > > _______________________________________________
> > > > > MINC-users at bic.mni.mcgill.ca
> > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jared Rowley
> > > > Translational Neuroimaging Laboratory
> > > > McGill Centre for Studies in Aging
> > > > Douglas Hospital Research Center
> > > > McGill University
> > > > 6825 LaSalle Blvd.
> > > > Montreal, QC Canada
> > > > H4H 1R3
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From vladimir.fonov at gmail.com  Fri Mar  4 16:43:57 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Fri, 04 Mar 2011 16:43:57 -0500
Subject: [MINC-users] build almost everything minc Makefile and git
	repository for EZminc
Message-ID: <4D715D1D.1090404@gmail.com>

Hello Everybody,

in an effort to simplify minc installation I have made publicly 
available a "build almost everything minc" makefile:

https://github.com/vfonov/EZminc/raw/master/build_quarantine/Makefile

The main purpose of it is to build most of the publicly available minc 
tools inside a quarantine with minimum dependencies on the system 
libraries. So, everything is compiled statically.

Following packages are built by default:

netcdf-4.0.1 hdf5-1.8.6 minc-2.1.00 bicpl-1.4.6 ebtks-1.6.4 
oobicpl-0.4.4 N3-1.12.0 classify-1.1.0 conglomerate-1.6.6 
mni_autoreg-0.99.6 mni_perllib-0.08 mincblob-1.2.1 mincmorph-1.4 
ray_trace-1.0.3 glim_image-1.2 InsightToolkit-3.20.0 fftw-3.2.2 
cmake-2.8.4 gsl-1.14 Getopt-Tabular-0.3 ezminc-r83 netpbm-10.35.74


following packages may also be built if needed:

Register-1.4.0 Display-1.5.0
fltk-1.3.x-r7725 vtk-5.6.1

To use:

make PREFIX=<location of your quarantine> TEMP=<location where packages 
will be built> PARALLEL_BUILD=-j<number of CPUs available> all

Also, as you can notice I have created a clone of EZminc repository on 
the github:  https://github.com/vfonov/EZminc , hopefully it will be 
easier to use it this way.


-- 
Best regards,
  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info

From lrisa87 at uw.edu  Fri Mar  4 17:14:48 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 4 Mar 2011 14:14:48 -0800
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTi=Es_Wa9VfJ9G7Empmf2O-Tg0Zb2UvG_szpFAOM@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
	<AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
	<AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>
	<AANLkTimE5MPzaJwfv05xcqfQQrADKBNPSofsZSCMhTwr@mail.gmail.com>
	<AANLkTim8QJOUv7PoQ0UbwT8h+cahaGXZGYqKau-50NzJ@mail.gmail.com>
	<AANLkTi=Es_Wa9VfJ9G7Empmf2O-Tg0Zb2UvG_szpFAOM@mail.gmail.com>
Message-ID: <AANLkTik9mNFFqQR4unCBnUoiqq2W1inHXOmT9886jLZy@mail.gmail.com>

Hi Vladimir,
Yes, I specified all the file names.
I also re-ran it including the full path in the filelist, but it still gave
me the same error.
I re-ran it without a filelist (just listed all filenames in the command),
but it failed.

Hi Alex,
Yes, I have writing permission and that there is ample free space (over
120GB) in my current location.
I copied all of my input file to a different location, made sure I had the
correct permission and ample space, and re-ran mincaverage, but failed
again.

Another tidbit:
The output file is created (3.2MB), but when I open it in register, it is
just a black image.


Thanks.


Best,
Lisa


On Fri, Mar 4, 2011 at 12:44 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi Lisa,
>
> On the off-chance that this is the problem - are you sure you have
> write access and free disk space in the location where you are trying
> to write the output file?
>
> -- Alex
>
> On Fri, Mar 4, 2011 at 3:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> >
> > Hi Andrew,
> >
> > I double checked each minc file (displayed them in register) and they all
> > seemed to be fine...
> >
> > Don't know if this helps at all..., but here are some more information:
> >
> > 1. A correction to what I wrote earlier:
> >
> > > I am trying to run mincaverage on 43 minc files, all which have been N3
> > > intensity nonuniformity normalized, neck portion cropped off,
> mincnorm-ed,
> > > *and linearly (9parameter) registered to a standard template*.
> >
> >
> > 2. I am using the -filelist option. I have a .txt file with each file
> name
> > listed on separate lines. Is this the correct format for the filelist?
> >
> > 3. The version I am using:
> >
> > > > mincaverage -version
> > > program: 2.1.00
> > > libminc: 2.1.00
> > > netcdf : 4.1.1 of May 15 2010 04:10:51 $
> > > HDF5   : 1.8.4
> >
> >
> >
> > Thanks.
> >
> >
> > Best,
> > Lisa
> >
> > On Fri, Mar 4, 2011 at 11:52 AM, Andrew Wood <andrew at biospective.com>
> wrote:
> >
> > > Hi Lisa,
> > >
> > > Is there any chance that the problem is with your input minc files? I
> just
> > > gave minc average a few good minc volumes plus a filename that didn't
> exist
> > > and I got back your error message.
> > >
> > > Andrew
> > >
> > >
> > > On Fri, Mar 4, 2011 at 2:23 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
> wrote:
> > >
> > > > Hi Jared,
> > > >
> > > > I tried re-running mincaverage with the -clobber extention.
> > > > I also ran it using a totally new output filename too, but it still
> gives
> > > > me
> > > > the same error message.
> > > >
> > > > Thanks.
> > > >
> > > >
> > > > Best,
> > > > Lisa
> > > >
> > > >
> > > >
> > > > On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <
> jared.rowley at gmail.com
> > > > >wrote:
> > > >
> > > > > Hi Lisa,
> > > > >
> > > > > I think you need to to do mincaverage -clobber.
> > > > >
> > > > > My guess is that the output.mnc already exists and you need to do
> > > > -clobber
> > > > > to overwrite it.
> > > > >
> > > > > Jared
> > > > >
> > > > >
> > > > > On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
> > > wrote:
> > > > >
> > > > > > Hello,
> > > > > >
> > > > > > I am trying to run mincaverage on 43 minc files, all which have
> been
> > > N3
> > > > > > intensity nonuniformity normalized, neck portion cropped off, and
> > > > > > mincnorm-ed.
> > > > > > The following is the error that I receive:
> > > > > >
> > > > > > Processing:........................miicv_attach: MINC package
> entry
> > > > point
> > > > > > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
> > > > > >
> > > > > >
> > > > > > When I run mincaverage on individual files and on subsets of the
> 43
> > > > > files,
> > > > > > mincaverage runs fine.
> > > > > > What is the issue?
> > > > > >
> > > > > > Thank you in advance.
> > > > > >
> > > > > >
> > > > > > Best,
> > > > > > Lisa
> > > > > > _______________________________________________
> > > > > > MINC-users at bic.mni.mcgill.ca
> > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Jared Rowley
> > > > > Translational Neuroimaging Laboratory
> > > > > McGill Centre for Studies in Aging
> > > > > Douglas Hospital Research Center
> > > > > McGill University
> > > > > 6825 LaSalle Blvd.
> > > > > Montreal, QC Canada
> > > > > H4H 1R3
> > > > > _______________________________________________
> > > > > MINC-users at bic.mni.mcgill.ca
> > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > >
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Sat Mar  5 08:47:41 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 5 Mar 2011 23:47:41 +1000
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTik9mNFFqQR4unCBnUoiqq2W1inHXOmT9886jLZy@mail.gmail.com>
References: <AANLkTimK42p6DaZ1TYH9_SfYzqAniUUk0h+VBf9AiGER@mail.gmail.com>
	<AANLkTinyud0Gs_bYi65wNW5i+TYCriQU0unRrJpCqLq5@mail.gmail.com>
	<AANLkTintfUDYztJEpLXV9p8-Nc5P7yFRJ_Myv3yeab8i@mail.gmail.com>
	<AANLkTimE5MPzaJwfv05xcqfQQrADKBNPSofsZSCMhTwr@mail.gmail.com>
	<AANLkTim8QJOUv7PoQ0UbwT8h+cahaGXZGYqKau-50NzJ@mail.gmail.com>
	<AANLkTi=Es_Wa9VfJ9G7Empmf2O-Tg0Zb2UvG_szpFAOM@mail.gmail.com>
	<AANLkTik9mNFFqQR4unCBnUoiqq2W1inHXOmT9886jLZy@mail.gmail.com>
Message-ID: <AANLkTinq_cWMO+LcP8nw1rK+6Z9Z3gp7dFJi5d3JPgMj@mail.gmail.com>

Hi Lisa,

I think this bug might be related to one I have seen as of late (only
on Ubuntu Maverick and the latest Debian release). In combination with
various phases of the moon you get this self same error. Even
something as simple as changing the input files order can make it go
away. I have noticed it more with register than anything else but
still haven't seen anything all that consistent yet to track it down.
:(

If changing the input file order fixes things then it most likely is
the same as I have seen.  Another thing that seems to exacerbate the
problem is a mix of MINC 1 and MINC 2 files. What does "file" return
on all your input files?


a

On Sat, Mar 5, 2011 at 08:14, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Hi Vladimir,
> Yes, I specified all the file names.
> I also re-ran it including the full path in the filelist, but it still gave
> me the same error.
> I re-ran it without a filelist (just listed all filenames in the command),
> but it failed.
>
> Hi Alex,
> Yes, I have writing permission and that there is ample free space (over
> 120GB) in my current location.
> I copied all of my input file to a different location, made sure I had the
> correct permission and ample space, and re-ran mincaverage, but failed
> again.
>
> Another tidbit:
> The output file is created (3.2MB), but when I open it in register, it is
> just a black image.
>
>
> Thanks.
>
>
> Best,
> Lisa
>
>
> On Fri, Mar 4, 2011 at 12:44 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>
>> Hi Lisa,
>>
>> On the off-chance that this is the problem - are you sure you have
>> write access and free disk space in the location where you are trying
>> to write the output file?
>>
>> -- Alex
>>
>> On Fri, Mar 4, 2011 at 3:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>> >
>> > Hi Andrew,
>> >
>> > I double checked each minc file (displayed them in register) and they all
>> > seemed to be fine...
>> >
>> > Don't know if this helps at all..., but here are some more information:
>> >
>> > 1. A correction to what I wrote earlier:
>> >
>> > > I am trying to run mincaverage on 43 minc files, all which have been N3
>> > > intensity nonuniformity normalized, neck portion cropped off,
>> mincnorm-ed,
>> > > *and linearly (9parameter) registered to a standard template*.
>> >
>> >
>> > 2. I am using the -filelist option. I have a .txt file with each file
>> name
>> > listed on separate lines. Is this the correct format for the filelist?
>> >
>> > 3. The version I am using:
>> >
>> > > > mincaverage -version
>> > > program: 2.1.00
>> > > libminc: 2.1.00
>> > > netcdf : 4.1.1 of May 15 2010 04:10:51 $
>> > > HDF5 ? : 1.8.4
>> >
>> >
>> >
>> > Thanks.
>> >
>> >
>> > Best,
>> > Lisa
>> >
>> > On Fri, Mar 4, 2011 at 11:52 AM, Andrew Wood <andrew at biospective.com>
>> wrote:
>> >
>> > > Hi Lisa,
>> > >
>> > > Is there any chance that the problem is with your input minc files? I
>> just
>> > > gave minc average a few good minc volumes plus a filename that didn't
>> exist
>> > > and I got back your error message.
>> > >
>> > > Andrew
>> > >
>> > >
>> > > On Fri, Mar 4, 2011 at 2:23 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
>> wrote:
>> > >
>> > > > Hi Jared,
>> > > >
>> > > > I tried re-running mincaverage with the -clobber extention.
>> > > > I also ran it using a totally new output filename too, but it still
>> gives
>> > > > me
>> > > > the same error message.
>> > > >
>> > > > Thanks.
>> > > >
>> > > >
>> > > > Best,
>> > > > Lisa
>> > > >
>> > > >
>> > > >
>> > > > On Fri, Mar 4, 2011 at 11:05 AM, Jared Rowley <
>> jared.rowley at gmail.com
>> > > > >wrote:
>> > > >
>> > > > > Hi Lisa,
>> > > > >
>> > > > > I think you need to to do mincaverage -clobber.
>> > > > >
>> > > > > My guess is that the output.mnc already exists and you need to do
>> > > > -clobber
>> > > > > to overwrite it.
>> > > > >
>> > > > > Jared
>> > > > >
>> > > > >
>> > > > > On Fri, Mar 4, 2011 at 2:00 PM, Lisa F. Akiyama <lrisa87 at uw.edu>
>> > > wrote:
>> > > > >
>> > > > > > Hello,
>> > > > > >
>> > > > > > I am trying to run mincaverage on 43 minc files, all which have
>> been
>> > > N3
>> > > > > > intensity nonuniformity normalized, neck portion cropped off, and
>> > > > > > mincnorm-ed.
>> > > > > > The following is the error that I receive:
>> > > > > >
>> > > > > > Processing:........................miicv_attach: MINC package
>> entry
>> > > > point
>> > > > > > > *ncvarid: ncid -1: NetCDF: Not a valid ID*
>> > > > > >
>> > > > > >
>> > > > > > When I run mincaverage on individual files and on subsets of the
>> 43
>> > > > > files,
>> > > > > > mincaverage runs fine.
>> > > > > > What is the issue?
>> > > > > >
>> > > > > > Thank you in advance.
>> > > > > >
>> > > > > >
>> > > > > > Best,
>> > > > > > Lisa
>> > > > > > _______________________________________________
>> > > > > > MINC-users at bic.mni.mcgill.ca
>> > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> > > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > > --
>> > > > > Jared Rowley
>> > > > > Translational Neuroimaging Laboratory
>> > > > > McGill Centre for Studies in Aging
>> > > > > Douglas Hospital Research Center
>> > > > > McGill University
>> > > > > 6825 LaSalle Blvd.
>> > > > > Montreal, QC Canada
>> > > > > H4H 1R3
>> > > > > _______________________________________________
>> > > > > MINC-users at bic.mni.mcgill.ca
>> > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> > > > >
>> > > > _______________________________________________
>> > > > MINC-users at bic.mni.mcgill.ca
>> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> > > >
>> > > _______________________________________________
>> > > MINC-users at bic.mni.mcgill.ca
>> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> > >
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From claude at bic.mni.mcgill.ca  Sat Mar  5 11:37:06 2011
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Sat, 5 Mar 2011 11:37:06 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTinq_cWMO+LcP8nw1rK+6Z9Z3gp7dFJi5d3JPgMj@mail.gmail.com>
Message-ID: <201103051637.p25Gb6cg001716@cassio.bic.mni.mcgill.ca>

Andrew,

> I think this bug might be related to one I have seen as of late (only
> on Ubuntu Maverick and the latest Debian release). In combination with
> various phases of the moon you get this self same error. Even
> something as simple as changing the input files order can make it go
> away. I have noticed it more with register than anything else but
> still haven't seen anything all that consistent yet to track it down.
> :(

That's the Coriolis force effect. Why don't you try to run your
job on a computer in the northern hemisphere?

Lisa: if you can systematically reproduce your bug, then that would
be a starting point for us to debug the code. Have you tested mincaverage
on a different number of input files, like 2,3,4,..? Just for fun, set
the shell environment variable VOLUME_CACHE_THRESHOLD=-1. Caching should
have been disabled in minc 2.1.00, but just in case.


Claude

From lrisa87 at uw.edu  Sat Mar  5 19:18:04 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Sat, 5 Mar 2011 16:18:04 -0800
Subject: [MINC-users] mincaverage error
In-Reply-To: <201103051637.p25Gb6cg001716@cassio.bic.mni.mcgill.ca>
References: <AANLkTinq_cWMO+LcP8nw1rK+6Z9Z3gp7dFJi5d3JPgMj@mail.gmail.com>
	<201103051637.p25Gb6cg001716@cassio.bic.mni.mcgill.ca>
Message-ID: <AANLkTi=P1pCT5xF2y_4NuEEB7euUU0HW5_kuQPcdJesh@mail.gmail.com>

Andrew,

I tried running the filelists with several different file orders, but
unfortunately the same error kept on occurring.


Claude,
I set the shell environment as you instructed, and ran a bunch of
minaverages on different subsets of all the files I have.
I have two sets of data - one from site S (28 files) and another from site I
(15 files) (a total of 43 files).

When I mincaveraged site S files one by one (2, 3, 4, 5...), no errors came
up and output files were created just fine.
When I mincaveraged site I files one by one (2, 3, 4, 5...), also no errors
came up and output files were created correctly.
When I mincaverated all site S files (28) and one file from site I (one of
the 15 files; tested all 15) (a total of 29 files being averaged), the error
came up for all trials and the output files were black images when displayed
in register.
When I took a few files from both site S and site I so that the total number
of files was 29, mincaverage gave me that error (I have not tested this for
all possible pairings).
But when I mincaveraged a few files from site S and a few from site I (I
have not tested this for all possible pairings - total number of files used
was not 29 in all trials), it seems like the output files are created fine
without any errors.

As far as I can tell, it seems like the site S and site I files have slight
differences in their headers.
When I view their headers using MIPAV, all seem to be the same except for
the 'Begin' values in the variable information section (below is an example
from a site I file):

Variable information:
> Name: rootvariable VSize: 4 Type: NC_INT  *Begin: 4512*
>   Attributes:
> Name: varid Value: MINC standard variable
>  Name: vartype Value: group________
> Name: version Value: MINC Version    1.0
> Name: parent Value:
>  Name: children Value: image
> processing
>   Variable value: -2147483647
> Name: xspace VSize: 4 Type: NC_INT  *Begin: 4516*
>   Attributes:
> Name: varid Value: MINC standard variable
> Name: vartype Value: dimension____
>  Name: version Value: MINC Version    1.0
> Name: comments Value: X increases from patient left to right
>  Name: spacing Value: regular__
> Name: alignment Value: centre
> Name: step Value: 1.0
>  Name: start Value: -96.0
> Name: direction_cosines Value: 1.0 0.0 0.0
> Name: units Value: mm
>  Name: spacetype Value: native____
>   Variable value: 0
> Name: yspace VSize: 4 Type: NC_INT  *Begin: 4520*
>   Attributes:
> Name: varid Value: MINC standard variable
> Name: vartype Value: dimension____
>  Name: version Value: MINC Version    1.0
> Name: comments Value: Y increases from patient posterior to anterior
>  Name: spacing Value: regular__
> Name: alignment Value: centre
> Name: step Value: 1.0
>  Name: start Value: -134.0
> Name: direction_cosines Value: 0.0 1.0 0.0
> Name: units Value: mm
>  Name: spacetype Value: native____
>   Variable value: 0


I'm not sure if all I've written above makes any sense at all or if it even
helps in trying to debug this odd error that I am seeing.
Please let me know if I should test all possible pairings for all of the
functions that I've carried out if that helps.

Thank you.


Best,
Lisa


On Sat, Mar 5, 2011 at 8:37 AM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:

> Andrew,
>
> > I think this bug might be related to one I have seen as of late (only
> > on Ubuntu Maverick and the latest Debian release). In combination with
> > various phases of the moon you get this self same error. Even
> > something as simple as changing the input files order can make it go
> > away. I have noticed it more with register than anything else but
> > still haven't seen anything all that consistent yet to track it down.
> > :(
>
> That's the Coriolis force effect. Why don't you try to run your
> job on a computer in the northern hemisphere?
>
> Lisa: if you can systematically reproduce your bug, then that would
> be a starting point for us to debug the code. Have you tested mincaverage
> on a different number of input files, like 2,3,4,..? Just for fun, set
> the shell environment variable VOLUME_CACHE_THRESHOLD=-1. Caching should
> have been disabled in minc 2.1.00, but just in case.
>
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From zijdenbos at gmail.com  Sat Mar  5 20:10:44 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sat, 5 Mar 2011 20:10:44 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTi=P1pCT5xF2y_4NuEEB7euUU0HW5_kuQPcdJesh@mail.gmail.com>
References: <AANLkTinq_cWMO+LcP8nw1rK+6Z9Z3gp7dFJi5d3JPgMj@mail.gmail.com>
	<201103051637.p25Gb6cg001716@cassio.bic.mni.mcgill.ca>
	<AANLkTi=P1pCT5xF2y_4NuEEB7euUU0HW5_kuQPcdJesh@mail.gmail.com>
Message-ID: <AANLkTinzBTLo09dQp5EDAzQb4+R09S_HtFsMs8X_8AYg@mail.gmail.com>

Hi Lisa,

It looks like your files are not all sampled the same way; they
certainly have different coordinate axes it seems. Are they basically
native images, or did they all go through a mincresample step with the
same target (-like option)? Were they registered? mincaverage does  a
voxel-by-voxel averaging, meaning that the voxels do need to line up
across all volumes. You could check this using mincinfo; for the
averaging to work the output of mincinfo in terms of dimension
specifications should be the same across all volumes.

If this is indeed the problem, then I do wonder why mincaverage didn't
give a more meaningful error message.

If your images were not previously registered and resampled to the
same space, there wouldn't be much point in averaging them, as you
would average across the orientation and positional variability you
would have across sites/acquisitions. You'd probably end up with a
fuzzy/funny blob.

If you do want to register them without prior registration, you could
still get this to work by simply resampling all volumes to one of
them, e.g.,

mincresample -like <file1.mnc> <file2.mnc> <file2_resampled.mnc>

and then average across file1.mnc and all your resampled files. Better
would be to resample like above but with a transformation that maps
each brain to a common target.

-- A

On Sat, Mar 5, 2011 at 7:18 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Andrew,
>
> I tried running the filelists with several different file orders, but
> unfortunately the same error kept on occurring.
>
>
> Claude,
> I set the shell environment as you instructed, and ran a bunch of
> minaverages on different subsets of all the files I have.
> I have two sets of data - one from site S (28 files) and another from site I
> (15 files) (a total of 43 files).
>
> When I mincaveraged site S files one by one (2, 3, 4, 5...), no errors came
> up and output files were created just fine.
> When I mincaveraged site I files one by one (2, 3, 4, 5...), also no errors
> came up and output files were created correctly.
> When I mincaverated all site S files (28) and one file from site I (one of
> the 15 files; tested all 15) (a total of 29 files being averaged), the error
> came up for all trials and the output files were black images when displayed
> in register.
> When I took a few files from both site S and site I so that the total number
> of files was 29, mincaverage gave me that error (I have not tested this for
> all possible pairings).
> But when I mincaveraged a few files from site S and a few from site I (I
> have not tested this for all possible pairings - total number of files used
> was not 29 in all trials), it seems like the output files are created fine
> without any errors.
>
> As far as I can tell, it seems like the site S and site I files have slight
> differences in their headers.
> When I view their headers using MIPAV, all seem to be the same except for
> the 'Begin' values in the variable information section (below is an example
> from a site I file):
>
> Variable information:
>> Name: rootvariable VSize: 4 Type: NC_INT ?*Begin: 4512*
>> ? Attributes:
>> Name: varid Value: MINC standard variable
>> ?Name: vartype Value: group________
>> Name: version Value: MINC Version ? ?1.0
>> Name: parent Value:
>> ?Name: children Value: image
>> processing
>> ? Variable value: -2147483647
>> Name: xspace VSize: 4 Type: NC_INT ?*Begin: 4516*
>> ? Attributes:
>> Name: varid Value: MINC standard variable
>> Name: vartype Value: dimension____
>> ?Name: version Value: MINC Version ? ?1.0
>> Name: comments Value: X increases from patient left to right
>> ?Name: spacing Value: regular__
>> Name: alignment Value: centre
>> Name: step Value: 1.0
>> ?Name: start Value: -96.0
>> Name: direction_cosines Value: 1.0 0.0 0.0
>> Name: units Value: mm
>> ?Name: spacetype Value: native____
>> ? Variable value: 0
>> Name: yspace VSize: 4 Type: NC_INT ?*Begin: 4520*
>> ? Attributes:
>> Name: varid Value: MINC standard variable
>> Name: vartype Value: dimension____
>> ?Name: version Value: MINC Version ? ?1.0
>> Name: comments Value: Y increases from patient posterior to anterior
>> ?Name: spacing Value: regular__
>> Name: alignment Value: centre
>> Name: step Value: 1.0
>> ?Name: start Value: -134.0
>> Name: direction_cosines Value: 0.0 1.0 0.0
>> Name: units Value: mm
>> ?Name: spacetype Value: native____
>> ? Variable value: 0
>
>
> I'm not sure if all I've written above makes any sense at all or if it even
> helps in trying to debug this odd error that I am seeing.
> Please let me know if I should test all possible pairings for all of the
> functions that I've carried out if that helps.
>
> Thank you.
>
>
> Best,
> Lisa
>
>
> On Sat, Mar 5, 2011 at 8:37 AM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:
>
>> Andrew,
>>
>> > I think this bug might be related to one I have seen as of late (only
>> > on Ubuntu Maverick and the latest Debian release). In combination with
>> > various phases of the moon you get this self same error. Even
>> > something as simple as changing the input files order can make it go
>> > away. I have noticed it more with register than anything else but
>> > still haven't seen anything all that consistent yet to track it down.
>> > :(
>>
>> That's the Coriolis force effect. Why don't you try to run your
>> job on a computer in the northern hemisphere?
>>
>> Lisa: if you can systematically reproduce your bug, then that would
>> be a starting point for us to debug the code. Have you tested mincaverage
>> on a different number of input files, like 2,3,4,..? Just for fun, set
>> the shell environment variable VOLUME_CACHE_THRESHOLD=-1. Caching should
>> have been disabled in minc 2.1.00, but just in case.
>>
>>
>> Claude
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From claude at bic.mni.mcgill.ca  Sat Mar  5 23:45:08 2011
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Sat, 5 Mar 2011 23:45:08 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTinzBTLo09dQp5EDAzQb4+R09S_HtFsMs8X_8AYg@mail.gmail.com>
Message-ID: <201103060445.p264j8Vh010925@cassio.bic.mni.mcgill.ca>

Hi,

I thought about the resampling issue too, as suggested by Alex,
but after doing a mincaverage -help:

 -check_dimensions:      Check that dimension info matches across files (default).
 -nocheck_dimensions:    Do not check dimension info.

It seems that the default is to check dimensions! Maybe the check
is wrong...

Lisa, since you don't get an error when averaging images from the
same site, can you keep adding more images from the same site?
For example, S1+S2+...+SN+S1+S2+... Does adding more images make
it blow up? I want you to repeat images of the same site, not mixed
sites. 

mincinfo and mincheader will give you information about the orientation
of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
direction cosines, storage format. Alex's suggestion to resample
like a template file makes a lot of sense.

When you manage to obtain an output, does it make sense when you 
look at it in register/Display?

Claude

From lrisa87 at uw.edu  Mon Mar  7 14:04:05 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Mon, 7 Mar 2011 11:04:05 -0800
Subject: [MINC-users] mincaverage error
In-Reply-To: <201103060445.p264j8Vh010925@cassio.bic.mni.mcgill.ca>
References: <AANLkTinzBTLo09dQp5EDAzQb4+R09S_HtFsMs8X_8AYg@mail.gmail.com>
	<201103060445.p264j8Vh010925@cassio.bic.mni.mcgill.ca>
Message-ID: <AANLkTimAx7kqkgmj6uLyGKVMsbYpPMnw3M59LbN=cEkd@mail.gmail.com>

Alex Z.,

Here's a list of pre-processing I performed on each site S and site I files
before putting them through mincaverage:
1) N3 intensity nonuniformity correction
2) mincnorm so that the range would be 0-100
3) Linear registration of subject images to standard template: bestlinreg
using Vladimir Fonov's NIHPD-BIC model for 00-02 year age range (range
0-100) as the target. I also created a brain mask image and specified as the
target_mask that in the command. Used -lsq9.
    When I look at the header of the files, they all have a stamp mentioning
that the files went through mincresample with -like NIHPD-BIC template.
    I've check each individual's resampled image and they all seem fairly
well registered. (There were a few images that didn't do so well, but after
creating the subject specific brainmask and re-running bestlinreg on these
individuals, the outcomes were good)

I just ran mincinfo on all files: They all have the same dimension lengths,
steps and start values.

I'm not sure whether I should run the following as you suggested earlier
since I've registered them to a standard template already and also because
they have the same dimensions.

If you do want to register them without prior registration, you could
> still get this to work by simply resampling all volumes to one of
> them, e.g.,
> mincresample -like <file1.mnc> <file2.mnc> <file2_resampled.mnc>


Claude,

mincinfo and mincheader will give you information about the orientation

of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,

direction cosines, storage format.


It seems like all files have very similar headers. Regardless of which site
the scan came from, they had the same dimension length, step, start,
direction cosine, and units (mm) for x, y, and z.
I've attached mincinfo and mincheader outputs for S1 and I1 to this email
for your reference.

 For example, S1+S2+...+SN+S1+S2+... Does adding more images make

it blow up? I want you to repeat images of the same site, not mixed

sites.


I ran the following trials:

1) mincaverage -normalize -filelist all-S-site-files.txt Savg.mnc  ===> OK;
looks fine

2) mincaverage -normalize -filelist all-I-site-files.txt Iavg.mnc  ===> OK;
looks fine

3) mincaverage -normalize -filelist Savg.mnc-and-all-S-site-files.txt ===>
ERROR; miicv_attach: MINC package entry point
ncvarid: ncid -1: NetCDF: Not a valid ID

3a) mincaverage -normalize -filelist Savg.mnc-and-one-S-site-file.txt ===>
OK.

3b) mincaverage -normalize -filelist Savg.mnc-and-27(out of 28
total)-S-site_files.txt ===> OK. Same size, looks identical to original
Savg.mnc
      However, when I ran Savg.mnc-and-27-S-site-files (removed a different
subject image than previously), error message "
      ncvarid: ncid -1: NetCDF: Not a valid ID" appeared.  Haven't tested
for all possible pairings.


4) mincaverage -normalize -filelist Iavg.mnc-and-all-I-site-files.txt ===>
OK; looks fine, same size and looks identical to original Iavg.mnc


4a) mincaverage -normalize -filelist Iavg.mnc-and-14(out of 15
total)-I-site-files.txt (tried this with removing different subjects each
time although I haven't tested all possible pairings) ===> OK; looks good,
same size, and looks identical to original Iavg.mnc



It appears that there is something sketchy with the site S files rather than
the site I files.

Thank you.


Best,
Lisa


On Sat, Mar 5, 2011 at 8:45 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:

> Hi,
>
> I thought about the resampling issue too, as suggested by Alex,
> but after doing a mincaverage -help:
>
>  -check_dimensions:      Check that dimension info matches across files
> (default).
>  -nocheck_dimensions:    Do not check dimension info.
>
> It seems that the default is to check dimensions! Maybe the check
> is wrong...
>
> Lisa, since you don't get an error when averaging images from the
> same site, can you keep adding more images from the same site?
> For example, S1+S2+...+SN+S1+S2+... Does adding more images make
> it blow up? I want you to repeat images of the same site, not mixed
> sites.
>
> mincinfo and mincheader will give you information about the orientation
> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
> direction cosines, storage format. Alex's suggestion to resample
> like a template file makes a lot of sense.
>
> When you manage to obtain an output, does it make sense when you
> look at it in register/Display?
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
-------------- next part --------------
#################3mincinfo I1 (SEA0092)##########3

image: signed__ float 0 to 100
image dimensions: xspace yspace zspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    xspace                    195            1          -96
    yspace                    233            1         -134
    zspace                    159            1          -72



#############33mincheader I1###############
dimensions:
	xspace = 195 ;
	yspace = 233 ;
	zspace = 159 ;
variables:
	int rootvariable ;
		rootvariable:varid = "MINC standard variable" ;
		rootvariable:vartype = "group________" ;
		rootvariable:version = "MINC Version    1.0" ;
		rootvariable:parent = "" ;
		rootvariable:children = "image\n",
			"processing" ;
	int xspace ;
		xspace:varid = "MINC standard variable" ;
		xspace:vartype = "dimension____" ;
		xspace:version = "MINC Version    1.0" ;
		xspace:comments = "X increases from patient left to right" ;
		xspace:spacing = "regular__" ;
		xspace:alignment = "centre" ;
		xspace:step = 1. ;
		xspace:start = -96. ;
		xspace:direction_cosines = 1., 0., 0. ;
		xspace:units = "mm" ;
		xspace:spacetype = "native____" ;
	int yspace ;
		yspace:varid = "MINC standard variable" ;
		yspace:vartype = "dimension____" ;
		yspace:version = "MINC Version    1.0" ;
		yspace:comments = "Y increases from patient posterior to anterior" ;
		yspace:spacing = "regular__" ;
		yspace:alignment = "centre" ;
		yspace:step = 1. ;
		yspace:start = -134. ;
		yspace:direction_cosines = 0., 1., 0. ;
		yspace:units = "mm" ;
		yspace:spacetype = "native____" ;
	int zspace ;
		zspace:varid = "MINC standard variable" ;
		zspace:vartype = "dimension____" ;
		zspace:version = "MINC Version    1.0" ;
		zspace:comments = "Z increases from patient inferior to superior" ;
		zspace:spacing = "regular__" ;
		zspace:alignment = "centre" ;
		zspace:step = 1. ;
		zspace:start = -72. ;
		zspace:direction_cosines = 0., 0., 1. ;
		zspace:units = "mm" ;
		zspace:spacetype = "native____" ;
	double image-max(xspace) ;
		image-max:varid = "MINC standard variable" ;
		image-max:vartype = "var_attribute" ;
		image-max:version = "MINC Version    1.0" ;
		image-max:_FillValue = 1. ;
		image-max:parent = "image" ;
	double image-min(xspace) ;
		image-min:varid = "MINC standard variable" ;
		image-min:vartype = "var_attribute" ;
		image-min:version = "MINC Version    1.0" ;
		image-min:_FillValue = 0. ;
		image-min:parent = "image" ;
	int processing ;
		processing:parent = "rootvariable" ;
		processing:transformation0-filename = "SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm" ;
		processing:transformation0-filedata = "MNI Transform File\n",
			"%Wed Mar  2 17:21:31 2011>>> minctracc -clobber -xcorr -lsq9 -step 4 4 4 -simplex 2 -tol 0.004 -transformation /tmp/bestlinreg.pl-sl6JOF_9/SSEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm_3.xfm -model_mask ../nihpd_asym_00-02_t1w_brainmask.mnc /tmp/bestlinreg.pl-sl6JOF_9/SSEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm_4_dxyz.mnc /tmp/bestlinreg.pl-sl6JOF_9/Tnihpd_asym_00-02_t1w_4_dxyz.mnc /tmp/bestlinreg.pl-sl6JOF_9/SSEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm_4.xfm\n",
			"%(Package mni_autoreg 0.99.6, compiled by @harold (x86_64-unknown-linux-gnu) on Thu Jan 20 17:08:53 EST 2011)\n",
			"\n",
			"Transform_Type = Linear;\n",
			"Linear_Transform =\n",
			" 0.886912822723389 0.269598573446274 0.0238081403076649 -2.6237313747406\n",
			" -0.293741941452026 0.990325748920441 -0.271627128124237 -3.88510131835938\n",
			" -0.0957735255360603 0.231416314840317 0.947292149066925 -33.9751396179199;\n",
			"" ;
	float image(xspace, yspace, zspace) ;
		image:parent = "rootvariable" ;
		image:varid = "MINC standard variable" ;
		image:vartype = "group________" ;
		image:version = "MINC Version    1.0" ;
		image:image-max = "--->image-max" ;
		image:image-min = "--->image-min" ;
		image:complete = "true_" ;
		image:valid_range = 0.f, 100.f ;
		image:signtype = "signed__" ;

// global attributes:
		:ident = "todd:neptune-ubuntu:2011.03.02.17.21.34:2157:1" ;
		:history = "/usr/local/bic/bin/nu_correct SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout.mnc SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu.mnc\n",
			"Fri Feb 25 17:12:07 2011>>> minccalc -clobber -expression ((A[0] < 0.136172323) ? 0.0 : (A[0] > 401.7866021) ? 1.0 : (A[0]-0.136172323)/401.650429777) * 100 + 0; SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu.mnc SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm.mnc\n",
			"Wed Mar  2 17:21:34 2011>>> mincresample -clobber -like ../nihpd_asym_00-02_t1w.mnc -transformation SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.xfm SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm.mnc SEA0092_6mo_May2009_t1mpr_flipped-MNI152maskedout_nu_mincnorm-reg_nihpd_bestlinreg.mnc\n",
			"" ;
data:

 rootvariable = _ ;

 xspace = 0 ;

 yspace = 0 ;

 zspace = 0 ;

 image-max = 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 0.947396136382664, 2.42943418526572, 
    3.54712807798542, 5.43007380506798, 5.24310234752484, 5.34829036556262, 
    6.67209047055415, 10.9288733599668, 36.3487172599864, 84.8257225260093, 
    86.2320458650952, 90.3107790048268, 92.2324197538925, 94.4303746139242, 
    96.9602554939775, 96.8229717281455, 99.4185221494169, 99.3028232343371, 
    95.476047313064, 98.4255065946472, 96.6541113780925, 96.2440155508314, 
    95.325919366911, 97.5437208419121, 98.8889750341048, 99.6204374013019, 
    98.7399874243647, 97.4958232829498, 99.3923948702791, 99.7868374144113, 
    97.8121961832795, 96.5177085762091, 96.7953910055525, 98.6316597357256, 
    97.9282868455072, 98.0283044621664, 97.1196919634517, 98.5740097319334, 
    97.2217874433856, 96.2067240535846, 96.6066800776357, 96.9111508415941, 
    97.722676894639, 95.8158241034866, 96.6164974642248, 95.842644229338, 
    97.8234382249037, 95.142019165114, 98.7558462433008, 96.8567822834201, 
    94.4411746711171, 95.5269437288598, 94.4053363201693, 95.2683228963663, 
    96.8755942915174, 94.5648617855763, 95.2961733007075, 94.6672412578908, 
    95.5333153334278, 95.5588387998097, 95.7181933978884, 95.291576669733, 
    93.9703407365886, 97.6117804010904, 97.8813425222601, 92.8648519011405, 
    96.7612560713554, 98.7097134523909, 95.0144032274814, 97.8932007660336, 
    97.1219070847972, 93.9673501663108, 98.570064369599, 98.6346160250637, 
    97.6427544638386, 96.5268292662264, 96.1117424933994, 95.7841816373158, 
    95.4984849750389, 99.8054726310361, 98.9702733679704, 97.3082051035661, 
    96.8274130793568, 98.5531583853512, 98.0989370432797, 98.6487713857531, 
    99.365122813149, 98.7167349832031, 97.0260366549247, 97.5701973996575, 
    96.4080303281864, 97.2090986210998, 95.7935528188491, 98.8743078605843, 
    95.8149198309595, 94.3582954014065, 96.1299116322933, 97.5014546825681, 
    98.1822037203252, 96.4361661001698, 96.1891188778678, 98.2764253443323, 
    98.6383014165164, 98.3532371837748, 97.9850191314124, 95.7594893304802, 
    95.5377338007302, 97.4838081314802, 98.4664580900451, 99.6746324150443, 
    98.36076392894, 98.8901044035188, 98.4092890653164, 99.5249301842105, 
    99.99660375537, 99.7408373777891, 99.3233241861749, 99.5521028959736, 
    98.7816594609443, 98.9743221160359, 98.7226090870193, 100, 
    98.7184866641343, 97.5502477986922, 91.6209743283614, 96.7875721928541, 
    89.8002411071914, 89.4762705750763, 90.745842506823, 85.6993147347808, 
    90.3850492926194, 88.401299455667, 90.0115786773621, 85.0384803163856, 
    82.9575836413033, 65.5508104448483, 40.7643453389398, 15.3182288875258, 
    8.25609948865467, 7.55357639700481, 5.20630582965026, 3.4388455204862, 
    2.92469247968065, 2.06481643009108, 1.72675695938155, 0.0296052310782467, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36 ;

 image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0 ;

 processing = 0 ;
}
-------------- next part --------------
###########3mincinfo S1 (15331)###############

image: signed__ float 0 to 99.98685455322265625
image dimensions: xspace yspace zspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    xspace                    195            1          -96
    yspace                    233            1         -134
    zspace                    159            1          -72


##############3mincheader S1###################
dimensions:
	xspace = 195 ;
	yspace = 233 ;
	zspace = 159 ;
variables:
	int rootvariable ;
		rootvariable:varid = "MINC standard variable" ;
		rootvariable:vartype = "group________" ;
		rootvariable:version = "MINC Version    1.0" ;
		rootvariable:parent = "" ;
		rootvariable:children = "image\n",
			"processing" ;
	int xspace ;
		xspace:varid = "MINC standard variable" ;
		xspace:vartype = "dimension____" ;
		xspace:version = "MINC Version    1.0" ;
		xspace:comments = "X increases from patient left to right" ;
		xspace:spacing = "regular__" ;
		xspace:alignment = "centre" ;
		xspace:step = 1. ;
		xspace:start = -96. ;
		xspace:direction_cosines = 1., 0., 0. ;
		xspace:units = "mm" ;
		xspace:spacetype = "native____" ;
	int yspace ;
		yspace:varid = "MINC standard variable" ;
		yspace:vartype = "dimension____" ;
		yspace:version = "MINC Version    1.0" ;
		yspace:comments = "Y increases from patient posterior to anterior" ;
		yspace:spacing = "regular__" ;
		yspace:alignment = "centre" ;
		yspace:step = 1. ;
		yspace:start = -134. ;
		yspace:direction_cosines = 0., 1., 0. ;
		yspace:units = "mm" ;
		yspace:spacetype = "native____" ;
	int zspace ;
		zspace:varid = "MINC standard variable" ;
		zspace:vartype = "dimension____" ;
		zspace:version = "MINC Version    1.0" ;
		zspace:comments = "Z increases from patient inferior to superior" ;
		zspace:spacing = "regular__" ;
		zspace:alignment = "centre" ;
		zspace:step = 1. ;
		zspace:start = -72. ;
		zspace:direction_cosines = 0., 0., 1. ;
		zspace:units = "mm" ;
		zspace:spacetype = "native____" ;
	double image-max(xspace) ;
		image-max:varid = "MINC standard variable" ;
		image-max:vartype = "var_attribute" ;
		image-max:version = "MINC Version    1.0" ;
		image-max:_FillValue = 1. ;
		image-max:parent = "image" ;
	double image-min(xspace) ;
		image-min:varid = "MINC standard variable" ;
		image-min:vartype = "var_attribute" ;
		image-min:version = "MINC Version    1.0" ;
		image-min:_FillValue = 0. ;
		image-min:parent = "image" ;
	int processing ;
		processing:parent = "rootvariable" ;
		processing:transformation0-filename = "15331_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm" ;
		processing:transformation0-filedata = "MNI Transform File\n",
			"%Wed Mar  2 16:49:19 2011>>> minctracc -clobber -xcorr -lsq9 -step 4 4 4 -simplex 2 -tol 0.004 -transformation /tmp/bestlinreg.pl-fGFwUogf/S15331_001_MNI152maskedout_RAS_nu_mincnorm_3.xfm -model_mask ../nihpd_asym_00-02_t1w_brainmask.mnc /tmp/bestlinreg.pl-fGFwUogf/S15331_001_MNI152maskedout_RAS_nu_mincnorm_4_dxyz.mnc /tmp/bestlinreg.pl-fGFwUogf/Tnihpd_asym_00-02_t1w_4_dxyz.mnc /tmp/bestlinreg.pl-fGFwUogf/S15331_001_MNI152maskedout_RAS_nu_mincnorm_4.xfm\n",
			"%(Package mni_autoreg 0.99.6, compiled by @harold (x86_64-unknown-linux-gnu) on Thu Jan 20 17:08:53 EST 2011)\n",
			"\n",
			"Transform_Type = Linear;\n",
			"Linear_Transform =\n",
			" 1.07767593860626 0.184373259544373 0.0388876646757126 -3.00531005859375\n",
			" -0.168469712138176 0.921877026557922 0.297942489385605 -25.8111553192139\n",
			" 0.0183407459408045 -0.314893305301666 0.984695911407471 -10.4866342544556;\n",
			"" ;
	float image(xspace, yspace, zspace) ;
		image:parent = "rootvariable" ;
		image:varid = "MINC standard variable" ;
		image:vartype = "group________" ;
		image:version = "MINC Version    1.0" ;
		image:image-max = "--->image-max" ;
		image:image-min = "--->image-min" ;
		image:complete = "true_" ;
		image:valid_range = 0.f, 99.98685f ;
		image:signtype = "signed__" ;

// global attributes:
		:ident = "todd:neptune-ubuntu:2011.03.02.16.49.21:29928:1" ;
		:history = "/usr/local/bic/bin/nu_correct 15331_001_MNI152maskedout_RAS.mnc 15331_001_MNI152maskedout_RAS_nu.mnc\n",
			"Fri Feb 25 16:36:02 2011>>> minccalc -clobber -expression ((A[0] < 0.06380040559) ? 0.0 : (A[0] > 212.3628689) ? 1.0 : (A[0]-0.06380040559)/212.29906849441) * 100 + 0; 15331_001_MNI152maskedout_RAS_nu.mnc 15331_001_MNI152maskedout_RAS_nu_mincnorm.mnc\n",
			"Wed Mar  2 16:49:21 2011>>> mincresample -clobber -like ../nihpd_asym_00-02_t1w.mnc -transformation 15331_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.xfm 15331_001_MNI152maskedout_RAS_nu_mincnorm.mnc 15331_001_MNI152maskedout_RAS_nu_mincnorm-reg_nihpd_bestlinreg.mnc\n",
			"" ;
data:

 rootvariable = _ ;

 xspace = 0 ;

 yspace = 0 ;

 zspace = 0 ;

 image-max = 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.55469995539387, 6.33278886872083, 
    7.08308779408386, 8.86992227099348, 10.0161254301613, 10.1063879633967, 
    9.48942328803537, 19.8007739180369, 34.9949195463732, 44.587315545732, 
    59.6727530927446, 67.8497415191959, 68.3777632419512, 68.3461183747152, 
    73.3401866234652, 82.0885380612748, 78.8167148211461, 81.6043962955538, 
    87.6754354482819, 97.1659142415208, 90.1723563282406, 92.830070881478, 
    92.3353922984508, 95.0155322175335, 91.7019877333157, 93.6280024052765, 
    91.9018386560253, 92.2711697637928, 91.7294393322935, 92.1258102269573, 
    93.1567008765145, 93.9216206234875, 95.395966463057, 97.0959197745939, 
    91.2857219602329, 95.6205628442334, 96.4288475297023, 97.3768152177156, 
    97.5070650992748, 98.2629042061438, 99.1613677412349, 99.920397643351, 
    98.9481327622059, 98.1498584123454, 98.0328367486221, 98.801371297815, 
    97.9458213453987, 98.4836113469063, 94.850136143576, 96.3528957638941, 
    97.8468222404527, 96.3608324713172, 98.4886336442623, 97.7390676708002, 
    97.8493204962215, 98.7674502509632, 99.1334132600559, 99.936125091776, 
    99.5079141291886, 98.5686790263636, 99.7553862906256, 99.5896646247167, 
    97.6736304764061, 98.8131802431595, 99.1876780074735, 95.1991552228365, 
    97.3600799657159, 99.1537450040254, 99.6140053377204, 99.96884865558, 
    99.7346980872053, 99.4991527919376, 98.6221460384765, 99.3317505544238, 
    97.6546510374259, 96.2776072159455, 99.1532397509971, 98.3701703701902, 
    99.5213426462694, 99.3576558905812, 99.7432477221928, 98.9225705012906, 
    99.9506184966044, 98.690124962187, 99.6832216555423, 99.2496726584962, 
    99.1764946232698, 98.9882610742132, 99.5767827183409, 99.5079132229667, 
    99.1237208545437, 95.4622146886691, 99.2798644867955, 97.9766814701808, 
    99.0225723284731, 98.7423804377, 99.9868559628781, 99.9573671869341, 
    99.1275257606629, 99.8237183465494, 97.2335798210977, 98.7680607817248, 
    99.0005423555967, 97.4951834371533, 98.0941653645331, 97.581775141011, 
    98.7766374023007, 96.5869536973738, 98.4462937279818, 97.9143756848135, 
    98.2622596617922, 97.5680616066733, 98.665279385981, 98.8028279477938, 
    98.1632608887789, 97.0244172925731, 97.7018388143887, 98.0124595606233, 
    94.8111963676539, 94.0691560377755, 94.1555053607994, 95.7659643407836, 
    90.2671105016657, 88.9464678908923, 84.264669651766, 84.5725445106959, 
    87.4207798285377, 86.3488673832154, 81.8324836278584, 83.0463574775275, 
    77.3924010101098, 80.067629100354, 85.777696664326, 72.1519773550943, 
    85.4475809352519, 80.8048699589283, 61.2998376211863, 19.3499895593531, 
    3.61940727868719, 3.18118661218518, 1.66890657744288, 0.0122273915139385, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36, 1.17549435082229e-36, 
    1.17549435082229e-36, 1.17549435082229e-36 ;

 image-min = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 
    0, 0, 0, 0, 0, 0 ;

 processing = 0 ;
}

From lrisa87 at uw.edu  Mon Mar  7 16:17:55 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Mon, 7 Mar 2011 13:17:55 -0800
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTimAx7kqkgmj6uLyGKVMsbYpPMnw3M59LbN=cEkd@mail.gmail.com>
References: <AANLkTinzBTLo09dQp5EDAzQb4+R09S_HtFsMs8X_8AYg@mail.gmail.com>
	<201103060445.p264j8Vh010925@cassio.bic.mni.mcgill.ca>
	<AANLkTimAx7kqkgmj6uLyGKVMsbYpPMnw3M59LbN=cEkd@mail.gmail.com>
Message-ID: <AANLkTim0iPcFoJL0KcLLfWYUnLg2BX188hapmFfSAgna@mail.gmail.com>

Hi again,

Some update:

I was just able to add each file one by one to create a sum image, and was
able to divide this by the total #N value (constant) using mincmath.
Then, I ran mincnorm.
Is this equivalent/close enough to what mincaverage -normalize does?

Thanks.


Best,
Lisa
 ______________________________




On Mon, Mar 7, 2011 at 11:04 AM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:

> Alex Z.,
>
> Here's a list of pre-processing I performed on each site S and site I files
> before putting them through mincaverage:
> 1) N3 intensity nonuniformity correction
> 2) mincnorm so that the range would be 0-100
> 3) Linear registration of subject images to standard template: bestlinreg
> using Vladimir Fonov's NIHPD-BIC model for 00-02 year age range (range
> 0-100) as the target. I also created a brain mask image and specified as the
> target_mask that in the command. Used -lsq9.
>     When I look at the header of the files, they all have a stamp
> mentioning that the files went through mincresample with -like NIHPD-BIC
> template.
>     I've check each individual's resampled image and they all seem fairly
> well registered. (There were a few images that didn't do so well, but after
> creating the subject specific brainmask and re-running bestlinreg on these
> individuals, the outcomes were good)
>
> I just ran mincinfo on all files: They all have the same dimension lengths,
> steps and start values.
>
> I'm not sure whether I should run the following as you suggested earlier
> since I've registered them to a standard template already and also because
> they have the same dimensions.
>
>  If you do want to register them without prior registration, you could
>> still get this to work by simply resampling all volumes to one of
>> them, e.g.,
>> mincresample -like <file1.mnc> <file2.mnc> <file2_resampled.mnc>
>
>
> Claude,
>
> mincinfo and mincheader will give you information about the orientation
>
> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
>
> direction cosines, storage format.
>
>
> It seems like all files have very similar headers. Regardless of which site
> the scan came from, they had the same dimension length, step, start,
> direction cosine, and units (mm) for x, y, and z.
> I've attached mincinfo and mincheader outputs for S1 and I1 to this email
> for your reference.
>
>  For example, S1+S2+...+SN+S1+S2+... Does adding more images make
>
> it blow up? I want you to repeat images of the same site, not mixed
>
> sites.
>
>
> I ran the following trials:
>
> 1) mincaverage -normalize -filelist all-S-site-files.txt Savg.mnc  ===> OK;
> looks fine
>
> 2) mincaverage -normalize -filelist all-I-site-files.txt Iavg.mnc  ===> OK;
> looks fine
>
> 3) mincaverage -normalize -filelist Savg.mnc-and-all-S-site-files.txt ===>
> ERROR; miicv_attach: MINC package entry point
>  ncvarid: ncid -1: NetCDF: Not a valid ID
>
> 3a) mincaverage -normalize -filelist Savg.mnc-and-one-S-site-file.txt ===>
> OK.
>
> 3b) mincaverage -normalize -filelist Savg.mnc-and-27(out of 28
> total)-S-site_files.txt ===> OK. Same size, looks identical to original
> Savg.mnc
>       However, when I ran Savg.mnc-and-27-S-site-files (removed a different
> subject image than previously), error message "
>       ncvarid: ncid -1: NetCDF: Not a valid ID" appeared.  Haven't tested
> for all possible pairings.
>
>
> 4) mincaverage -normalize -filelist Iavg.mnc-and-all-I-site-files.txt ===>
> OK; looks fine, same size and looks identical to original Iavg.mnc
>
>
> 4a) mincaverage -normalize -filelist Iavg.mnc-and-14(out of 15
> total)-I-site-files.txt (tried this with removing different subjects each
> time although I haven't tested all possible pairings) ===> OK; looks good,
> same size, and looks identical to original Iavg.mnc
>
>
>
> It appears that there is something sketchy with the site S files rather
> than the site I files.
>
> Thank you.
>
>
> Best,
> Lisa
>
>
> On Sat, Mar 5, 2011 at 8:45 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:
>
>> Hi,
>>
>> I thought about the resampling issue too, as suggested by Alex,
>> but after doing a mincaverage -help:
>>
>>  -check_dimensions:      Check that dimension info matches across files
>> (default).
>>  -nocheck_dimensions:    Do not check dimension info.
>>
>> It seems that the default is to check dimensions! Maybe the check
>> is wrong...
>>
>> Lisa, since you don't get an error when averaging images from the
>> same site, can you keep adding more images from the same site?
>> For example, S1+S2+...+SN+S1+S2+... Does adding more images make
>> it blow up? I want you to repeat images of the same site, not mixed
>> sites.
>>
>> mincinfo and mincheader will give you information about the orientation
>> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
>> direction cosines, storage format. Alex's suggestion to resample
>> like a template file makes a lot of sense.
>>
>> When you manage to obtain an output, does it make sense when you
>> look at it in register/Display?
>>
>> Claude
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From zijdenbos at gmail.com  Tue Mar  8 09:06:17 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Tue, 8 Mar 2011 09:06:17 -0500
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTim0iPcFoJL0KcLLfWYUnLg2BX188hapmFfSAgna@mail.gmail.com>
References: <AANLkTinzBTLo09dQp5EDAzQb4+R09S_HtFsMs8X_8AYg@mail.gmail.com>
	<201103060445.p264j8Vh010925@cassio.bic.mni.mcgill.ca>
	<AANLkTimAx7kqkgmj6uLyGKVMsbYpPMnw3M59LbN=cEkd@mail.gmail.com>
	<AANLkTim0iPcFoJL0KcLLfWYUnLg2BX188hapmFfSAgna@mail.gmail.com>
Message-ID: <AANLkTinRu1u40tU1iUA1EJ0hZazz-emPCbvrymp5kTAd@mail.gmail.com>

Lisa A,

mincaverage -normalize will normalize each image to its mean prior to
averaging; which in my opinion is actually a poor way to normalize
them. I tend to normalize them explicitly prior to averaging with
something slightly smarter than a plain average across the image.

Now, I don't know what mincnorm is or does, but assuming it does some
sort of intensity normalization and you did run that on your images
prior to adding them, you should be ok. But either way you would want
to normalize them *before* averaging.

As for your mincaverage problem I am at a loss; but have you tried the
same thing with mincmath? In other words, does mincmath give the same
error when you add them all up in one call? (mincmath -float -add
<file1.mnc> <file2.mnc> <sum.mnc>) If it does I'd that points at a
generic problem in libminc; if not, it may be specific to mincaverage.
I would try to avoid adding images one by one, but if you do use a
float output type (like in the mincmath call above).

And here is a long shot: I noticed your images are at an
unconventional sampling lattice. This *should* really not pose any
problem, but on the off-chance that you ran into an odd bug, you may
want to run mincresample with '-like icbm_template_1.00mm.mnc'
instead of the template you used (you should have these template files
I believe). If (big if) that solves the problem that might give an
indication of where the problem lies.

-- A

On Mon, Mar 7, 2011 at 4:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Hi again,
>
> Some update:
>
> I was just able to add each file one by one to create a sum image, and was
> able to divide this by the total #N value (constant) using mincmath.
> Then, I ran mincnorm.
> Is this equivalent/close enough to what mincaverage -normalize does?
>
> Thanks.
>
>
> Best,
> Lisa
> ?______________________________
>
>
>
>
> On Mon, Mar 7, 2011 at 11:04 AM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
>
>> Alex Z.,
>>
>> Here's a list of pre-processing I performed on each site S and site I files
>> before putting them through mincaverage:
>> 1) N3 intensity nonuniformity correction
>> 2) mincnorm so that the range would be 0-100
>> 3) Linear registration of subject images to standard template: bestlinreg
>> using Vladimir Fonov's NIHPD-BIC model for 00-02 year age range (range
>> 0-100) as the target. I also created a brain mask image and specified as the
>> target_mask that in the command. Used -lsq9.
>> ? ? When I look at the header of the files, they all have a stamp
>> mentioning that the files went through mincresample with -like NIHPD-BIC
>> template.
>> ? ? I've check each individual's resampled image and they all seem fairly
>> well registered. (There were a few images that didn't do so well, but after
>> creating the subject specific brainmask and re-running bestlinreg on these
>> individuals, the outcomes were good)
>>
>> I just ran mincinfo on all files: They all have the same dimension lengths,
>> steps and start values.
>>
>> I'm not sure whether I should run the following as you suggested earlier
>> since I've registered them to a standard template already and also because
>> they have the same dimensions.
>>
>> ?If you do want to register them without prior registration, you could
>>> still get this to work by simply resampling all volumes to one of
>>> them, e.g.,
>>> mincresample -like <file1.mnc> <file2.mnc> <file2_resampled.mnc>
>>
>>
>> Claude,
>>
>> mincinfo and mincheader will give you information about the orientation
>>
>> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
>>
>> direction cosines, storage format.
>>
>>
>> It seems like all files have very similar headers. Regardless of which site
>> the scan came from, they had the same dimension length, step, start,
>> direction cosine, and units (mm) for x, y, and z.
>> I've attached mincinfo and mincheader outputs for S1 and I1 to this email
>> for your reference.
>>
>> ?For example, S1+S2+...+SN+S1+S2+... Does adding more images make
>>
>> it blow up? I want you to repeat images of the same site, not mixed
>>
>> sites.
>>
>>
>> I ran the following trials:
>>
>> 1) mincaverage -normalize -filelist all-S-site-files.txt Savg.mnc ?===> OK;
>> looks fine
>>
>> 2) mincaverage -normalize -filelist all-I-site-files.txt Iavg.mnc ?===> OK;
>> looks fine
>>
>> 3) mincaverage -normalize -filelist Savg.mnc-and-all-S-site-files.txt ===>
>> ERROR; miicv_attach: MINC package entry point
>> ?ncvarid: ncid -1: NetCDF: Not a valid ID
>>
>> 3a) mincaverage -normalize -filelist Savg.mnc-and-one-S-site-file.txt ===>
>> OK.
>>
>> 3b) mincaverage -normalize -filelist Savg.mnc-and-27(out of 28
>> total)-S-site_files.txt ===> OK. Same size, looks identical to original
>> Savg.mnc
>> ? ? ? However, when I ran Savg.mnc-and-27-S-site-files (removed a different
>> subject image than previously), error message "
>> ? ? ? ncvarid: ncid -1: NetCDF: Not a valid ID" appeared. ?Haven't tested
>> for all possible pairings.
>>
>>
>> 4) mincaverage -normalize -filelist Iavg.mnc-and-all-I-site-files.txt ===>
>> OK; looks fine, same size and looks identical to original Iavg.mnc
>>
>>
>> 4a) mincaverage -normalize -filelist Iavg.mnc-and-14(out of 15
>> total)-I-site-files.txt (tried this with removing different subjects each
>> time although I haven't tested all possible pairings) ===> OK; looks good,
>> same size, and looks identical to original Iavg.mnc
>>
>>
>>
>> It appears that there is something sketchy with the site S files rather
>> than the site I files.
>>
>> Thank you.
>>
>>
>> Best,
>> Lisa
>>
>>
>> On Sat, Mar 5, 2011 at 8:45 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>wrote:
>>
>>> Hi,
>>>
>>> I thought about the resampling issue too, as suggested by Alex,
>>> but after doing a mincaverage -help:
>>>
>>> ?-check_dimensions: ? ? ?Check that dimension info matches across files
>>> (default).
>>> ?-nocheck_dimensions: ? ?Do not check dimension info.
>>>
>>> It seems that the default is to check dimensions! Maybe the check
>>> is wrong...
>>>
>>> Lisa, since you don't get an error when averaging images from the
>>> same site, can you keep adding more images from the same site?
>>> For example, S1+S2+...+SN+S1+S2+... Does adding more images make
>>> it blow up? I want you to repeat images of the same site, not mixed
>>> sites.
>>>
>>> mincinfo and mincheader will give you information about the orientation
>>> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
>>> direction cosines, storage format. Alex's suggestion to resample
>>> like a template file makes a lot of sense.
>>>
>>> When you manage to obtain an output, does it make sense when you
>>> look at it in register/Display?
>>>
>>> Claude
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From lrisa87 at uw.edu  Tue Mar  8 13:26:07 2011
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Tue, 8 Mar 2011 10:26:07 -0800
Subject: [MINC-users] mincaverage error
In-Reply-To: <AANLkTinRu1u40tU1iUA1EJ0hZazz-emPCbvrymp5kTAd@mail.gmail.com>
References: <AANLkTinzBTLo09dQp5EDAzQb4+R09S_HtFsMs8X_8AYg@mail.gmail.com>
	<201103060445.p264j8Vh010925@cassio.bic.mni.mcgill.ca>
	<AANLkTimAx7kqkgmj6uLyGKVMsbYpPMnw3M59LbN=cEkd@mail.gmail.com>
	<AANLkTim0iPcFoJL0KcLLfWYUnLg2BX188hapmFfSAgna@mail.gmail.com>
	<AANLkTinRu1u40tU1iUA1EJ0hZazz-emPCbvrymp5kTAd@mail.gmail.com>
Message-ID: <AANLkTinSoCnQ53knJxocfNc9-SQ76oqWgkp0J3LDj10_@mail.gmail.com>

Hi Alex,

Yes, I used mincnorm for intensity normalization (normalized each file to
have a range of 0-100, which Fonov's template had) prior to
testing mincaverage.

 but have you tried the

same thing with mincmath? In other words, does mincmath give the same

error when you add them all up in one call? (mincmath -float -add

<file1.mnc> <file2.mnc> <sum.mnc>)


I tried that prior to adding each file one by one and dividing the sum image
by N, but got the same usual error.
I re-tried this using your suggested command with resampled images
(ran  mincresample
with '-like icbm_template_1.00mm.mnc'), but still got the same error...

I think my best bet for now would be to add images one by one, using the
float output type (which I didn't specify yesterday - I will re-run it),
and dividing it by N all using mincmath.

Thanks for all your explanations, tips, and suggestions.


Best,
Lisa

On Tue, Mar 8, 2011 at 6:06 AM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Lisa A,
>
> mincaverage -normalize will normalize each image to its mean prior to
> averaging; which in my opinion is actually a poor way to normalize
> them. I tend to normalize them explicitly prior to averaging with
> something slightly smarter than a plain average across the image.
>
> Now, I don't know what mincnorm is or does, but assuming it does some
> sort of intensity normalization and you did run that on your images
> prior to adding them, you should be ok. But either way you would want
> to normalize them *before* averaging.
>
> As for your mincaverage problem I am at a loss; but have you tried the
> same thing with mincmath? In other words, does mincmath give the same
> error when you add them all up in one call? (mincmath -float -add
> <file1.mnc> <file2.mnc> <sum.mnc>) If it does I'd that points at a
> generic problem in libminc; if not, it may be specific to mincaverage.
> I would try to avoid adding images one by one, but if you do use a
> float output type (like in the mincmath call above).
>
> And here is a long shot: I noticed your images are at an
> unconventional sampling lattice. This *should* really not pose any
> problem, but on the off-chance that you ran into an odd bug, you may
> want to run mincresample with '-like icbm_template_1.00mm.mnc'
> instead of the template you used (you should have these template files
> I believe). If (big if) that solves the problem that might give an
> indication of where the problem lies.
>
> -- A
>
> On Mon, Mar 7, 2011 at 4:17 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> > Hi again,
> >
> > Some update:
> >
> > I was just able to add each file one by one to create a sum image, and
> was
> > able to divide this by the total #N value (constant) using mincmath.
> > Then, I ran mincnorm.
> > Is this equivalent/close enough to what mincaverage -normalize does?
> >
> > Thanks.
> >
> >
> > Best,
> > Lisa
> >  ______________________________
> >
> >
> >
> >
> > On Mon, Mar 7, 2011 at 11:04 AM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> >
> >> Alex Z.,
> >>
> >> Here's a list of pre-processing I performed on each site S and site I
> files
> >> before putting them through mincaverage:
> >> 1) N3 intensity nonuniformity correction
> >> 2) mincnorm so that the range would be 0-100
> >> 3) Linear registration of subject images to standard template:
> bestlinreg
> >> using Vladimir Fonov's NIHPD-BIC model for 00-02 year age range (range
> >> 0-100) as the target. I also created a brain mask image and specified as
> the
> >> target_mask that in the command. Used -lsq9.
> >>     When I look at the header of the files, they all have a stamp
> >> mentioning that the files went through mincresample with -like NIHPD-BIC
> >> template.
> >>     I've check each individual's resampled image and they all seem
> fairly
> >> well registered. (There were a few images that didn't do so well, but
> after
> >> creating the subject specific brainmask and re-running bestlinreg on
> these
> >> individuals, the outcomes were good)
> >>
> >> I just ran mincinfo on all files: They all have the same dimension
> lengths,
> >> steps and start values.
> >>
> >> I'm not sure whether I should run the following as you suggested earlier
> >> since I've registered them to a standard template already and also
> because
> >> they have the same dimensions.
> >>
> >>  If you do want to register them without prior registration, you could
> >>> still get this to work by simply resampling all volumes to one of
> >>> them, e.g.,
> >>> mincresample -like <file1.mnc> <file2.mnc> <file2_resampled.mnc>
> >>
> >>
> >> Claude,
> >>
> >> mincinfo and mincheader will give you information about the orientation
> >>
> >> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
> >>
> >> direction cosines, storage format.
> >>
> >>
> >> It seems like all files have very similar headers. Regardless of which
> site
> >> the scan came from, they had the same dimension length, step, start,
> >> direction cosine, and units (mm) for x, y, and z.
> >> I've attached mincinfo and mincheader outputs for S1 and I1 to this
> email
> >> for your reference.
> >>
> >>  For example, S1+S2+...+SN+S1+S2+... Does adding more images make
> >>
> >> it blow up? I want you to repeat images of the same site, not mixed
> >>
> >> sites.
> >>
> >>
> >> I ran the following trials:
> >>
> >> 1) mincaverage -normalize -filelist all-S-site-files.txt Savg.mnc  ===>
> OK;
> >> looks fine
> >>
> >> 2) mincaverage -normalize -filelist all-I-site-files.txt Iavg.mnc  ===>
> OK;
> >> looks fine
> >>
> >> 3) mincaverage -normalize -filelist Savg.mnc-and-all-S-site-files.txt
> ===>
> >> ERROR; miicv_attach: MINC package entry point
> >>  ncvarid: ncid -1: NetCDF: Not a valid ID
> >>
> >> 3a) mincaverage -normalize -filelist Savg.mnc-and-one-S-site-file.txt
> ===>
> >> OK.
> >>
> >> 3b) mincaverage -normalize -filelist Savg.mnc-and-27(out of 28
> >> total)-S-site_files.txt ===> OK. Same size, looks identical to original
> >> Savg.mnc
> >>       However, when I ran Savg.mnc-and-27-S-site-files (removed a
> different
> >> subject image than previously), error message "
> >>       ncvarid: ncid -1: NetCDF: Not a valid ID" appeared.  Haven't
> tested
> >> for all possible pairings.
> >>
> >>
> >> 4) mincaverage -normalize -filelist Iavg.mnc-and-all-I-site-files.txt
> ===>
> >> OK; looks fine, same size and looks identical to original Iavg.mnc
> >>
> >>
> >> 4a) mincaverage -normalize -filelist Iavg.mnc-and-14(out of 15
> >> total)-I-site-files.txt (tried this with removing different subjects
> each
> >> time although I haven't tested all possible pairings) ===> OK; looks
> good,
> >> same size, and looks identical to original Iavg.mnc
> >>
> >>
> >>
> >> It appears that there is something sketchy with the site S files rather
> >> than the site I files.
> >>
> >> Thank you.
> >>
> >>
> >> Best,
> >> Lisa
> >>
> >>
> >> On Sat, Mar 5, 2011 at 8:45 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca
> >wrote:
> >>
> >>> Hi,
> >>>
> >>> I thought about the resampling issue too, as suggested by Alex,
> >>> but after doing a mincaverage -help:
> >>>
> >>>  -check_dimensions:      Check that dimension info matches across files
> >>> (default).
> >>>  -nocheck_dimensions:    Do not check dimension info.
> >>>
> >>> It seems that the default is to check dimensions! Maybe the check
> >>> is wrong...
> >>>
> >>> Lisa, since you don't get an error when averaging images from the
> >>> same site, can you keep adding more images from the same site?
> >>> For example, S1+S2+...+SN+S1+S2+... Does adding more images make
> >>> it blow up? I want you to repeat images of the same site, not mixed
> >>> sites.
> >>>
> >>> mincinfo and mincheader will give you information about the orientation
> >>> of the images. Watch for +ve vs -ve steps, voxel sizes, start coords,
> >>> direction cosines, storage format. Alex's suggestion to resample
> >>> like a template file makes a lot of sense.
> >>>
> >>> When you manage to obtain an output, does it make sense when you
> >>> look at it in register/Display?
> >>>
> >>> Claude
> >>> _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>
> >>
> >>
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.hendrikx at fcdonders.ru.nl  Sat Mar 12 09:00:39 2011
From: a.hendrikx at fcdonders.ru.nl (Hendrikx, A.A.E.M. (Anne))
Date: Sat, 12 Mar 2011 15:00:39 +0100 (CET)
Subject: [MINC-users] Watershed treshold and amygdala volume
Message-ID: <1259207840.204149.1299938439536.JavaMail.root@indus.zimbra.ru.nl>

Dear all,

We, members from the Donders Institute Nijmegen (The Netherlands), are using FreeSurfer to calculate amygdala volumes on MRI's. After a couple of tests we are suprised about the following:

We are wondering why the amygdala volume changes, after changing the watershed threshold. Besides, if we should nog change the ws-treshold, but manually remove remaining skull, the amygdala volume will not change. 

We don't understand this. Can anyone explane this to us? And besides, what consequences are there for the accuracy of the calculations?

Best wishes,

Anne Hendrikx

From pierre.bellec at criugm.qc.ca  Sat Mar 12 14:53:43 2011
From: pierre.bellec at criugm.qc.ca (Pierre Bellec)
Date: Sat, 12 Mar 2011 14:53:43 -0500
Subject: [MINC-users] compiling minc tools on ubuntu 10.10
Message-ID: <AANLkTimnUQrnADc3rvradVvs=aUMq+Ta8ank-1-Tsu5B@mail.gmail.com>

Dear minc-users,

I just wanted to share my experience compiling the minc tools on ubuntu
10.10 using Vlad's "big make" file. Overall, it works beatifully ! great
job. As there are no mincbundle available for 32 bits, I dived in the
compilation and only ran into a couple errors. First, the script is not
creating a couple of necessary folders. Second, there are a list of
requirement packages that I didn't have. Rather than reporting all of that
here, I took the liberty of editing the MINC wikibook section on "Installing
from sources" :
http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall

<http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall>I moved the
section Vlad wrote in the main installation section there. For those who
know about it, please review the dependency section, because I may have
installed too much stuff just in case (I am not sure for libxi-dev for
example, also the wiki intially mentioned that g++ is necessary only for old
N3, yet I needed it to compile 1.12.0 which seems to be the latest). Also, I
had to play a bit with the configuration of environment variables (PERL libs
weren't found following the wiki book tutorial). Please review that as well
here :
http://en.wikibooks.org/wiki/MINC/Tutorials/AddingPaths

<http://en.wikibooks.org/wiki/MINC/Tutorials/AddingPaths>Don't hesitate if
you have any suggestion/comment. Cheers,

Pierre Bellec, PhD
Chercheur adjoint
Centre de recherche de l'institut de G?riatrie de Montr?al
D?partement d'informatique et de recherche op?rationnelle
Universit? de Montr?al
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
(001)(514) 340 3540 #3367

From a.janke at gmail.com  Sun Mar 13 07:03:04 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Sun, 13 Mar 2011 21:03:04 +1000
Subject: [MINC-users] compiling minc tools on ubuntu 10.10
In-Reply-To: <AANLkTimnUQrnADc3rvradVvs=aUMq+Ta8ank-1-Tsu5B@mail.gmail.com>
References: <AANLkTimnUQrnADc3rvradVvs=aUMq+Ta8ank-1-Tsu5B@mail.gmail.com>
Message-ID: <AANLkTikkEHDtU=runD0XNftAKngmxebNmZzHF==ZUYoY@mail.gmail.com>

Hi Pierre,

Thanks for adding content! :) It all looks good, as for
pre-requisites, here is what I use when building the packages on
Ubuntu/Debian:

$ sudo apt-get install libnetcdf-dev libhdf5-serial-dev libnetpbm9-dev
fftw-dev \
   libgsl0-dev libgetopt-tabular-perl libxext-dev glutg3-dev libsoqt3-dev \
   libxmu-dev libxi-dev imagemagick libtext-format-perl libpcre++0 libpcre3 \
   libsimage-dev libpcre++-dev

Of course you may need more than this for vlads Makefile given that it
also builds his ITK stuff.

Thanks again,


a

From vladimir.fonov at gmail.com  Sun Mar 13 11:54:09 2011
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Sun, 13 Mar 2011 11:54:09 -0400
Subject: [MINC-users] compiling minc tools on ubuntu 10.10
In-Reply-To: <AANLkTikkEHDtU=runD0XNftAKngmxebNmZzHF==ZUYoY@mail.gmail.com>
References: <AANLkTimnUQrnADc3rvradVvs=aUMq+Ta8ank-1-Tsu5B@mail.gmail.com>
	<AANLkTikkEHDtU=runD0XNftAKngmxebNmZzHF==ZUYoY@mail.gmail.com>
Message-ID: <AANLkTim7GscTupTH=La4zgmdx9Tq7LN1z1Cgc9X4jP7k@mail.gmail.com>

Hello,


actually my makefile doesn't need netcdf, hdf5, netpbm and gsl. And it
compiles it's own version of cmake for  building ITK and EZminc

Note that  I updated the Makefile, so now it should create directories
automatically.

On Sun, Mar 13, 2011 at 7:03 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Pierre,
>
> Thanks for adding content! :) It all looks good, as for
> pre-requisites, here is what I use when building the packages on
> Ubuntu/Debian:
>
> $ sudo apt-get install libnetcdf-dev libhdf5-serial-dev libnetpbm9-dev
> fftw-dev \
> ? libgsl0-dev libgetopt-tabular-perl libxext-dev glutg3-dev libsoqt3-dev \
> ? libxmu-dev libxi-dev imagemagick libtext-format-perl libpcre++0 libpcre3 \
> ? libsimage-dev libpcre++-dev
>
> Of course you may need more than this for vlads Makefile given that it
> also builds his ITK stuff.
>
> Thanks again,
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Best regards,

?Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From a.janke at gmail.com  Mon Mar 14 07:54:34 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 14 Mar 2011 21:54:34 +1000
Subject: [MINC-users] Watershed treshold and amygdala volume
In-Reply-To: <1259207840.204149.1299938439536.JavaMail.root@indus.zimbra.ru.nl>
References: <1259207840.204149.1299938439536.JavaMail.root@indus.zimbra.ru.nl>
Message-ID: <AANLkTinjfDnvgBgMbZyXZtd1Zdx9Wute5Vm2pgVew4tP@mail.gmail.com>

Hi Hendrikx,

I am not that familiar with the details of freesurfer. Freesurfer does
use some MINC components internally though.

perhaps your question would be better asked on one of the freesurfer
mailing lists?

   http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport



-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883


On Sun, Mar 13, 2011 at 00:00, Hendrikx, A.A.E.M. (Anne)
<a.hendrikx at fcdonders.ru.nl> wrote:
> Dear all,
>
> We, members from the Donders Institute Nijmegen (The Netherlands), are using FreeSurfer to calculate amygdala volumes on MRI's. After a couple of tests we are suprised about the following:
>
> We are wondering why the amygdala volume changes, after changing the watershed threshold. Besides, if we should nog change the ws-treshold, but manually remove remaining skull, the amygdala volume will not change.
>
> We don't understand this. Can anyone explane this to us? And besides, what consequences are there for the accuracy of the calculations?
>
> Best wishes,
>
> Anne Hendrikx
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From giovanna_p at hotmail.com  Mon Mar 14 10:28:31 2011
From: giovanna_p at hotmail.com (Giovanna Pellecchia)
Date: Mon, 14 Mar 2011 10:28:31 -0400
Subject: [MINC-users] compiling minc tools on ubuntu 10.10 - expansion
In-Reply-To: <AANLkTikkEHDtU=runD0XNftAKngmxebNmZzHF==ZUYoY@mail.gmail.com>
References: <AANLkTimnUQrnADc3rvradVvs=aUMq+Ta8ank-1-Tsu5B@mail.gmail.com>
	<AANLkTikkEHDtU=runD0XNftAKngmxebNmZzHF==ZUYoY@mail.gmail.com>
Message-ID: <BLU0-SMTP917F244BBB80EE79E3B4E3F7CC0@phx.gbl>

Hi all,

regarding compilation from source, I invite those MINC users who have 
experience compiling on systems other than Ubuntu to take a look at the 
installation page:
http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall
and add a brief contribution for their systems, even if only to say it 
is not recommended ;-).

I had originally written the prerequisites (AKA dependencies) for Ubuntu 
8.10 on a different page 
(http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall/Additional_requirements, 
now an orphan page) to give it room to grow and include specific 
information for other OSs. Please provide some feedback in the talk page 
(http://en.wikibooks.org/wiki/Talk:MINC/Tutorials/SourceInstall)!

Thanks for your help!
Cheers,
Giovanna

Andrew Janke wrote:
> Hi Pierre,
>
> Thanks for adding content! :) It all looks good, as for
> pre-requisites, here is what I use when building the packages on
> Ubuntu/Debian:
>
> $ sudo apt-get install libnetcdf-dev libhdf5-serial-dev libnetpbm9-dev
> fftw-dev \
>    libgsl0-dev libgetopt-tabular-perl libxext-dev glutg3-dev libsoqt3-dev \
>    libxmu-dev libxi-dev imagemagick libtext-format-perl libpcre++0 libpcre3 \
>    libsimage-dev libpcre++-dev
>
> Of course you may need more than this for vlads Makefile given that it
> also builds his ITK stuff.
>
> Thanks again,
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>   

From lconcha at gmail.com  Mon Mar 14 20:10:37 2011
From: lconcha at gmail.com (Luis Concha)
Date: Mon, 14 Mar 2011 18:10:37 -0600
Subject: [MINC-users] build almost everything minc Makefile and git
	repository for EZminc
Message-ID: <AANLkTikib68GfOWqTfN6p_tqd41ExGe6jRcTXf5Q1DAc@mail.gmail.com>

Hello all.

I have successfully compiled the minc tools using Vlad's fantastic new
Makefile. Thanks to Pierre B. for updating the wiki and Vlad for
updating the file.

I am now trying to compile the tools for a cluster using Red Hat
Enterprise Linux AS release 4. I am getting the error of not having
permissions to write to /usr/local (of course I don't). I was my
understanding that this new makefile did not have to write anything
outside of the local user's directories. Perhaps I am mistaken, as I
see an INSTALLDIRS=site in the output. Is there a way around this?

The error occurs when installing Getopt-Tabular. Any clues? See below
for the tail of the make output.

Thanks a lot.

Luis




17:17:51 (247.94 KB/s) -
`/global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3.tar.gz'
saved [26453/26453]

cd /global/home/lconcha_g/lconcha/temp/src && tar zxf
/global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3.tar.gz
touch /global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3
cd /global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3 && \
perl ./Makefile.PL SITEPREFIX=/global/home/lconcha_g/lconcha/minc
INSTALLDIRS=site
INSTALLSITELIB=/global/home/lconcha_g/lconcha/minc/perl
INSTALLSITEBIN=/global/home/lconcha_g/lconcha/minc/bin \
	INSTALLSITEMAN1DIR=/global/home/lconcha_g/lconcha/minc
INSTALLSITEMAN3DIR=/global/home/lconcha_g/lconcha/minc && \
make && \
make install
Checking if your kit is complete...
Looks good
Writing Makefile for Getopt::Tabular
make[1]: Entering directory
`/global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3'
cp Tabular.pod blib/lib/Getopt/Tabular.pod
cp Tabular.pm blib/lib/Getopt/Tabular.pm
Manifying blib/man3/Getopt::Tabular.3pm
make[1]: Leaving directory
`/global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3'
make[1]: Entering directory
`/global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3'
Warning: You do not have permissions to install into
/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi at
/usr/lib/perl5/5.8.5/ExtUtils/Install.pm line 114.
Installing /global/home/lconcha_g/lconcha/minc/perl/Getopt/Tabular.pod
Installing /global/home/lconcha_g/lconcha/minc/perl/Getopt/Tabular.pm
Installing /global/home/lconcha_g/lconcha/minc/Getopt::Tabular.3pm
mkdir /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi/auto/Getopt:
Permission denied at /usr/lib/perl5/5.8.5/ExtUtils/Install.pm line 207
make[1]: *** [pure_site_install] Error 255
make[1]: Leaving directory
`/global/home/lconcha_g/lconcha/temp/src/Getopt-Tabular-0.3'
make: *** [/global/home/lconcha_g/lconcha/minc/perl/Getopt/Tabular.pm] Error 2

From a.janke at gmail.com  Mon Mar 14 23:01:59 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 15 Mar 2011 13:01:59 +1000
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <AANLkTikib68GfOWqTfN6p_tqd41ExGe6jRcTXf5Q1DAc@mail.gmail.com>
References: <AANLkTikib68GfOWqTfN6p_tqd41ExGe6jRcTXf5Q1DAc@mail.gmail.com>
Message-ID: <AANLkTi=fx7xonqyeATgZMuzZYR2GmbWB-wGbjF+5tT-Q@mail.gmail.com>

I think you will need to add PREFIX to the perl install. In the
Makefile the section looks like this:

$(getopt_tabular) : ${TEMP}/src/Getopt-Tabular-$(GETOPT_TABULAR_VER)
	cd ${TEMP}/src/Getopt-Tabular-$(GETOPT_TABULAR_VER) && \
	perl ./Makefile.PL PREFIX=$(PREFIX) SITEPREFIX=$(PREFIX) INSTALLDIRS=site \
                INSTALLSITELIB=$(PREFIX)/perl INSTALLSITEBIN=$(PREFIX)/bin \
		INSTALLSITEMAN1DIR=$(PREFIX) INSTALLSITEMAN3DIR=$(PREFIX) && \
	make && \
	make install
	touch $(getopt_tabular)

Note that I have added PREFIX=$(PREFIX)  I think the arguments you add
here depends on the way the module is made and the version of PERL.

Vlad, I was going to do an online commit for this on github but wasn't
quite game just yet...


-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883


On Tue, Mar 15, 2011 at 10:10, Luis Concha <lconcha at gmail.com> wrote:
> Hello all.
>
> I have successfully compiled the minc tools using Vlad's fantastic new
> Makefile. Thanks to Pierre B. for updating the wiki and Vlad for
> updating the file.

> The error occurs when installing Getopt-Tabular. Any clues? See below
> for the tail of the make output.

From lconcha at gmail.com  Tue Mar 15 15:40:32 2011
From: lconcha at gmail.com (Luis Concha)
Date: Tue, 15 Mar 2011 13:40:32 -0600
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
Message-ID: <AANLkTimKfT6AHUiygfnyGNWBWrb0pLu22v-Tgx3WvEe=@mail.gmail.com>

Hi Andrew and all.

> I think you will need to add PREFIX to the perl install. In the
> Andrew Janke

Thanks for the suggestion. I have tried it and I am still getting the
same error. I believe the root of it is how Makefile.PL is written,
which seems to be made by lib/ExtUtils/MakeMaker.pm. Of course, this
seems to depend on the perl version installed (5.8 in my case) and
only root can modify makemaker.pm.

I see that Makefile.PL sends out a few arguments to generate a
Makefile, After reading the Makefile, I see several calls to
/usr/lib64/perl5... (CCDLFLAGS, SITELIBEXP, SITEARCHEXP,
VENDORARCHEXP, VENDORLIBEXP, etc). I was wondering if I can overrride
these by sending the appropriate arguments through Makefile.PL. If
possible, then my ignorance will shine, as I have no clue what I
should provide instead.

Alternatively, should I compile my own version of perl from source, so
I have more control over MakeMaker.pm?

Thanks again.

Luis

From zijdenbos at gmail.com  Wed Mar 16 12:06:25 2011
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 16 Mar 2011 17:06:25 +0100
Subject: [MINC-users] HDF5 errors
Message-ID: <AANLkTikhjesHfwYnxHAjd74kQhrMFkAqMzY28gZ53Nvi@mail.gmail.com>

Hello all,

I just stumbled across a bunch of HDF5 runtime errors (see below). As
best I can tell these are due to a bogged-down NFS server; the files
the process needs are definitely there, but may take a while to get.
If I restart the exact same process, chances are high it completes
without error. I have so far only come across these only in xfmconcat
(with nonlinear deformations) and minc_displacement.

The main problem is that the errors are not caught; the process exits
gracefully and leaves a seemingly good output MINC file behind;
however upon inspection, the file is only partially written. The only
way to actually find the error is to catch it during some explicit
verification, or by grepping for 'HDF5' in the log files.

Does anybody have any thoughts about this or has seen this before? I
would say the the MINC library (miicv_get?) should catch this somehow
and throw an error causing the process to fail, but clearly that is
currently not happening.

These are locally-built executables based on MINC 2.1, HDF5 1.8.5.

-- Alex

HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
  #000: H5Dio.c line 174 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 404 in H5D_read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1724 in H5D_chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2737 in H5D_chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1116 in H5Z_pipeline(): filter returned failure during read
    major: Data filters
    minor: Read failed
  #005: H5Zdeflate.c line 122 in H5Z_filter_deflate(): inflate() failed
    major: Data filters
    minor: Unable to initialize object
(from miicv_get): Can't read dataset /minc-2.0/image/0/image

From lconcha at gmail.com  Wed Mar 16 15:46:29 2011
From: lconcha at gmail.com (Luis Concha)
Date: Wed, 16 Mar 2011 13:46:29 -0600
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
Message-ID: <AANLkTi=2k6ALGfBEA8k9pSGsg_9eO+9ESXu2Zsntr6_=@mail.gmail.com>

Hello all.

Replying to my own post is far from exciting, but I'm doing it so that
the solution I found to my compilation problem is of help to anyone in
the same situation.

The solution to compile everything using Vlad's big Makefile was to
install ActiveState Perl in my own directories, and adding it to the
PATH before the system's built in perl installation (using the
install.sh from the ActiveState Perl distribution). After that, make
all compiled everything without any further problems.

Minc tools on the cluster, here I go.

Thanks to all for helping out!

Luis


On Wed, Mar 16, 2011 at 10:00 AM,  <minc-users-request at bic.mni.mcgill.ca> wrote:
> Send MINC-users mailing list submissions to
> ? ? ? ?minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
> ? ? ? ?http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
> ? ? ? ?minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
> ? ? ? ?minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
> Today's Topics:
>
> ? 1. Re: build almost everything minc Makefile and git repository
> ? ? ?for EZminc (Luis Concha)
>
>
> ---------- Forwarded message ----------
> From:?Luis Concha <lconcha at gmail.com>
> To:?minc-users at bic.mni.mcgill.ca
> Date:?Tue, 15 Mar 2011 13:40:32 -0600
> Subject:?Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
> Hi Andrew and all.
>
>> I think you will need to add PREFIX to the perl install. In the
>> Andrew Janke
>
> Thanks for the suggestion. I have tried it and I am still getting the
> same error. I believe the root of it is how Makefile.PL is written,
> which seems to be made by lib/ExtUtils/MakeMaker.pm. Of course, this
> seems to depend on the perl version installed (5.8 in my case) and
> only root can modify makemaker.pm.
>
> I see that Makefile.PL sends out a few arguments to generate a
> Makefile, After reading the Makefile, I see several calls to
> /usr/lib64/perl5... (CCDLFLAGS, SITELIBEXP, SITEARCHEXP,
> VENDORARCHEXP, VENDORLIBEXP, etc). I was wondering if I can overrride
> these by sending the appropriate arguments through Makefile.PL. If
> possible, then my ignorance will shine, as I have no clue what I
> should provide instead.
>
> Alternatively, should I compile my own version of perl from source, so
> I have more control over MakeMaker.pm?
>
> Thanks again.
>
> Luis
>
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From a.janke at gmail.com  Thu Mar 17 07:02:53 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 17 Mar 2011 21:02:53 +1000
Subject: [MINC-users] HDF5 errors
In-Reply-To: <AANLkTikhjesHfwYnxHAjd74kQhrMFkAqMzY28gZ53Nvi@mail.gmail.com>
References: <AANLkTikhjesHfwYnxHAjd74kQhrMFkAqMzY28gZ53Nvi@mail.gmail.com>
Message-ID: <AANLkTikv-LMj-fEDPW3+3W3w4vcBaRAweOQ-NKFJsRsK@mail.gmail.com>

> I just stumbled across a bunch of HDF5 runtime errors (see below). As
> best I can tell these are due to a bogged-down NFS server; the files
> the process needs are definitely there, but may take a while to get.
> If I restart the exact same process, chances are high it completes
> without error. I have so far only come across these only in xfmconcat
> (with nonlinear deformations) and minc_displacement.

Does nfsstat show an error count during this?  If so I think your
problems are a bit more deep-seated than just MINC.



-- 
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883

From thomas.funck at mail.mcgill.ca  Thu Mar 17 10:09:20 2011
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Thu, 17 Mar 2011 14:09:20 +0000
Subject: [MINC-users] ecattominc and scale factors
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065C0E6@EXMBX2010-2.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065C0E6@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065C160@EXMBX2010-2.campus.MCGILL.CA>

Hi,

I am a grad student working the Jewish General for Dr. Thiel. When I convert ECAT7 files to MINC, the values of the MINC file do not match the original values of the ECAT7 file. I saw in the ECAT header that there are scale factors that are applied to the values of the ECAT file. However even when I multiply the values in the MINC file by the corresponding scale factors (using mincmath), the two files still don't match. Is there something I am doing wrong? Thanks for the help!

Best,

Thomas

From thomas.funck at mail.mcgill.ca  Thu Mar 17 15:09:24 2011
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Thu, 17 Mar 2011 19:09:24 +0000
Subject: [MINC-users] miopen_volume not opening file
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065C208@EXMBX2010-2.campus.MCGILL.CA>

Hi,

So this is my second problem of the day. I'm writing a program that requires reading .mnc files. However when I try to use miopen_volume it returns -1. I even tried running the first mini-program included in the MINC2 tutorials (code included below) and miopen_volume did not work here either. I'm assuming the code from the tutorial is correct and that there is some underlying problem with HDF5 or MINC2. I just reinstalled the latest versions of MINC2 (version 2.1) and HDF5 (version 1.8.6) on my Ubuntu system. I also ran "make check" on both before installing and they passed all the tests, so both libraries seem to be happy with the system. I really can't figure out what's going on because the programs and code should both be okay. Any ideas?

Best,

Thomas





#include <minc2.h>
#include <stdio.h>
 
int main(int argc, char **argv) {
  mihandle_t    minc_volume;
  double        voxel;
  int           result;
  unsigned long location[3];
 
  /* open the volume - first and only command line argument */
  result = miopen_volume(argv[1], MI2_OPEN_READ, &minc_volume);
  /* check for error on opening */
  if (result != MI_NOERROR) {
    fprintf(stderr, "Error opening input file: %d.\n", result);
  }
 
  return(0);
}

________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Thursday, March 17, 2011 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 68, Issue 18

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. HDF5 errors (Alex Zijdenbos)
   2. Re: build almost everything minc Makefile and git repository
      for EZminc (Luis Concha)
   3. Re: HDF5 errors (Andrew Janke)
   4. ecattominc and scale factors (Thomas Funck)


----------------------------------------------------------------------

Message: 1
Date: Wed, 16 Mar 2011 17:06:25 +0100
From: Alex Zijdenbos <zijdenbos at gmail.com>
Subject: [MINC-users] HDF5 errors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikhjesHfwYnxHAjd74kQhrMFkAqMzY28gZ53Nvi at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello all,

I just stumbled across a bunch of HDF5 runtime errors (see below). As
best I can tell these are due to a bogged-down NFS server; the files
the process needs are definitely there, but may take a while to get.
If I restart the exact same process, chances are high it completes
without error. I have so far only come across these only in xfmconcat
(with nonlinear deformations) and minc_displacement.

The main problem is that the errors are not caught; the process exits
gracefully and leaves a seemingly good output MINC file behind;
however upon inspection, the file is only partially written. The only
way to actually find the error is to catch it during some explicit
verification, or by grepping for 'HDF5' in the log files.

Does anybody have any thoughts about this or has seen this before? I
would say the the MINC library (miicv_get?) should catch this somehow
and throw an error causing the process to fail, but clearly that is
currently not happening.

These are locally-built executables based on MINC 2.1, HDF5 1.8.5.

-- Alex

HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
  #000: H5Dio.c line 174 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 404 in H5D_read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1724 in H5D_chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2737 in H5D_chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1116 in H5Z_pipeline(): filter returned failure during read
    major: Data filters
    minor: Read failed
  #005: H5Zdeflate.c line 122 in H5Z_filter_deflate(): inflate() failed
    major: Data filters
    minor: Unable to initialize object
(from miicv_get): Can't read dataset /minc-2.0/image/0/image


------------------------------

Message: 2
Date: Wed, 16 Mar 2011 13:46:29 -0600
From: Luis Concha <lconcha at gmail.com>
Subject: Re: [MINC-users] build almost everything minc Makefile and
        git repository for EZminc
To: minc-users at bic.mni.mcgill.ca
Message-ID:
        <AANLkTi=2k6ALGfBEA8k9pSGsg_9eO+9ESXu2Zsntr6_=@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello all.

Replying to my own post is far from exciting, but I'm doing it so that
the solution I found to my compilation problem is of help to anyone in
the same situation.

The solution to compile everything using Vlad's big Makefile was to
install ActiveState Perl in my own directories, and adding it to the
PATH before the system's built in perl installation (using the
install.sh from the ActiveState Perl distribution). After that, make
all compiled everything without any further problems.

Minc tools on the cluster, here I go.

Thanks to all for helping out!

Luis


On Wed, Mar 16, 2011 at 10:00 AM,  <minc-users-request at bic.mni.mcgill.ca> wrote:
> Send MINC-users mailing list submissions to
> ? ? ? ?minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
> ? ? ? ?http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
> ? ? ? ?minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
> ? ? ? ?minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
> Today's Topics:
>
> ? 1. Re: build almost everything minc Makefile and git repository
> ? ? ?for EZminc (Luis Concha)
>
>
> ---------- Forwarded message ----------
> From:?Luis Concha <lconcha at gmail.com>
> To:?minc-users at bic.mni.mcgill.ca
> Date:?Tue, 15 Mar 2011 13:40:32 -0600
> Subject:?Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
> Hi Andrew and all.
>
>> I think you will need to add PREFIX to the perl install. In the
>> Andrew Janke
>
> Thanks for the suggestion. I have tried it and I am still getting the
> same error. I believe the root of it is how Makefile.PL is written,
> which seems to be made by lib/ExtUtils/MakeMaker.pm. Of course, this
> seems to depend on the perl version installed (5.8 in my case) and
> only root can modify makemaker.pm.
>
> I see that Makefile.PL sends out a few arguments to generate a
> Makefile, After reading the Makefile, I see several calls to
> /usr/lib64/perl5... (CCDLFLAGS, SITELIBEXP, SITEARCHEXP,
> VENDORARCHEXP, VENDORLIBEXP, etc). I was wondering if I can overrride
> these by sending the appropriate arguments through Makefile.PL. If
> possible, then my ignorance will shine, as I have no clue what I
> should provide instead.
>
> Alternatively, should I compile my own version of perl from source, so
> I have more control over MakeMaker.pm?
>
> Thanks again.
>
> Luis
>
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>


------------------------------

Message: 3
Date: Thu, 17 Mar 2011 21:02:53 +1000
From: Andrew Janke <a.janke at gmail.com>
Subject: Re: [MINC-users] HDF5 errors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikv-LMj-fEDPW3+3W3w4vcBaRAweOQ-NKFJsRsK at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

> I just stumbled across a bunch of HDF5 runtime errors (see below). As
> best I can tell these are due to a bogged-down NFS server; the files
> the process needs are definitely there, but may take a while to get.
> If I restart the exact same process, chances are high it completes
> without error. I have so far only come across these only in xfmconcat
> (with nonlinear deformations) and minc_displacement.

Does nfsstat show an error count during this?  If so I think your
problems are a bit more deep-seated than just MINC.



--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883


------------------------------

Message: 4
Date: Thu, 17 Mar 2011 14:09:20 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
Subject: [MINC-users] ecattominc and scale factors
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065C160 at EXMBX2010-2.campus.MCGILL.CA>
Content-Type: text/plain; charset="us-ascii"

Hi,

I am a grad student working the Jewish General for Dr. Thiel. When I convert ECAT7 files to MINC, the values of the MINC file do not match the original values of the ECAT7 file. I saw in the ECAT header that there are scale factors that are applied to the values of the ECAT file. However even when I multiply the values in the MINC file by the corresponding scale factors (using mincmath), the two files still don't match. Is there something I am doing wrong? Thanks for the help!

Best,

Thomas


------------------------------

_______________________________________________
MINC-users mailing list
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


End of MINC-users Digest, Vol 68, Issue 18
******************************************

From peter.neelin at gmail.com  Thu Mar 17 15:25:44 2011
From: peter.neelin at gmail.com (Peter Neelin)
Date: Thu, 17 Mar 2011 15:25:44 -0400
Subject: [MINC-users] ecattominc and scale factors
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065C160@EXMBX2010-2.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065C0E6@EXMBX2010-2.campus.MCGILL.CA>
	<53F3FD0032C9CC4BA836E8F0FC289065C160@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <AANLkTi=PnGdY0cOgC_dAc6_Cj739GN5dLyFESCEuj3hA@mail.gmail.com>

On Thu, Mar 17, 2011 at 10:09 AM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:

> When I convert ECAT7 files to
> MINC, the values of the MINC file do not match the original values of the ECAT7 file. I saw in the
> ECAT header that there are scale factors that are applied to the values of the ECAT file. However
> even when I multiply the values in the MINC file by the corresponding scale factors (using
> mincmath), the two files still don't match. Is there something I am doing wrong?

By default, ecattominc will do decay correction if it has not already
been done. You can turn this off with -nodecay_correct - that would be
the quickest way to find out if this is the cause of the difference
between values.

Peter
-- 
Peter Neelin
(peter.neelin at gmail.com)

From nikelski at bic.mni.mcgill.ca  Thu Mar 17 17:09:37 2011
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Thu, 17 Mar 2011 14:09:37 -0700
Subject: [MINC-users] miopen_volume not opening file
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065C208@EXMBX2010-2.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065C208@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <AANLkTikiEAkq+PCW6G6-nP5K_TeFZ5TbaJtupcg-6p02@mail.gmail.com>

Hi Thomas,

  Could you provide the output of the following:

(1) mincinfo -version
(2) uname -a
(3) file my_test_minc_volume.mnc
(4) mincinfo my_test_minc_volume.mnc

  Which version of Ubuntu are you using?

-jim



On Thu, Mar 17, 2011 at 12:09 PM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:
> Hi,
>
> So this is my second problem of the day. I'm writing a program that requires reading .mnc files. However when I try to use miopen_volume it returns -1. I even tried running the first mini-program included in the MINC2 tutorials (code included below) and miopen_volume did not work here either. I'm assuming the code from the tutorial is correct and that there is some underlying problem with HDF5 or MINC2. I just reinstalled the latest versions of MINC2 (version 2.1) and HDF5 (version 1.8.6) on my Ubuntu system. I also ran "make check" on both before installing and they passed all the tests, so both libraries seem to be happy with the system. I really can't figure out what's going on because the programs and code should both be okay. Any ideas?
>
> Best,
>
> Thomas
>
>
>
>
>
> #include <minc2.h>
> #include <stdio.h>
>
> int main(int argc, char **argv) {
> ?mihandle_t ? ?minc_volume;
> ?double ? ? ? ?voxel;
> ?int ? ? ? ? ? result;
> ?unsigned long location[3];
>
> ?/* open the volume - first and only command line argument */
> ?result = miopen_volume(argv[1], MI2_OPEN_READ, &minc_volume);
> ?/* check for error on opening */
> ?if (result != MI_NOERROR) {
> ? ?fprintf(stderr, "Error opening input file: %d.\n", result);
> ?}
>
> ?return(0);
> }
>

-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University

From thomas.funck at mail.mcgill.ca  Fri Mar 18 15:54:39 2011
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Fri, 18 Mar 2011 19:54:39 +0000
Subject: [MINC-users] MINC-users Digest, Vol 68, Issue 19
In-Reply-To: <mailman.5.1300464002.14846.minc-users@bic.mni.mcgill.ca>
References: <mailman.5.1300464002.14846.minc-users@bic.mni.mcgill.ca>
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065C5B1@EXMBX2010-2.campus.MCGILL.CA>

Hi again,

I tried using the -nodecay_correct option but unfortunately that does not appear to have helped. Below is an ROI report from VINCI for the same ROI on four different images. As you can see the values in the ECAT file are much larger than the MINC files even if decay is not corrected. In file 3 tried multiplying the MINC file by the scale factor indicated in the ECAT header (approx. 2.43), but that didn't really help. I wasn't able to find any information online about how the scale factor is actually applied so I'm just guessing that it is multiplied.

Thomas


VINCI ROI Report:

(1) ECAT File - Frame 1 
#Name          Type     #Pixels       Average      Std.Dev.   [%]        Minimum       Maximum
 Roi2DEllipse  Ellipse      197  1.29479e+004  4.65448e+003  35.9  -8.28493e+002  1.96007e+004

(2) MINC - Frame 1 - Decay Not Corrected
#Name          Type     #Pixels       Average      Std.Dev.   [%]        Minimum       Maximum
 Roi2DEllipse  Ellipse      197  3.38301e+002  1.22103e+002  36.1  -2.61994e+001  5.07943e+002

(3)MINC - Frame 1 - Decay Not Corrected - Rescaled by Scale Factor 2.43
#Name          Type     #Pixels       Average      Std.Dev.   [%]        Minimum       Maximum
 Roi2DEllipse  Ellipse      197  8.22072e+002  2.96711e+002  36.1  -6.36647e+001  1.23430e+003

(4)MINC - Frame 1 - Decay Corrected
#Name          Type     #Pixels       Average      Std.Dev.   [%]        Minimum       Maximum
 Roi2DEllipse  Ellipse      197  3.49095e+002  1.25999e+002  36.1  -2.70353e+001  5.24149e+002


________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Friday, March 18, 2011 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 68, Issue 19

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. miopen_volume not opening file (Thomas Funck)
   2. Re: ecattominc and scale factors (Peter Neelin)
   3. Re: miopen_volume not opening file (EJ Nikelski)


----------------------------------------------------------------------

Message: 1
Date: Thu, 17 Mar 2011 19:09:24 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
Subject: [MINC-users] miopen_volume not opening file
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065C208 at EXMBX2010-2.campus.MCGILL.CA>
Content-Type: text/plain; charset="us-ascii"

Hi,

So this is my second problem of the day. I'm writing a program that requires reading .mnc files. However when I try to use miopen_volume it returns -1. I even tried running the first mini-program included in the MINC2 tutorials (code included below) and miopen_volume did not work here either. I'm assuming the code from the tutorial is correct and that there is some underlying problem with HDF5 or MINC2. I just reinstalled the latest versions of MINC2 (version 2.1) and HDF5 (version 1.8.6) on my Ubuntu system. I also ran "make check" on both before installing and they passed all the tests, so both libraries seem to be happy with the system. I really can't figure out what's going on because the programs and code should both be okay. Any ideas?

Best,

Thomas





#include <minc2.h>
#include <stdio.h>

int main(int argc, char **argv) {
  mihandle_t    minc_volume;
  double        voxel;
  int           result;
  unsigned long location[3];

  /* open the volume - first and only command line argument */
  result = miopen_volume(argv[1], MI2_OPEN_READ, &minc_volume);
  /* check for error on opening */
  if (result != MI_NOERROR) {
    fprintf(stderr, "Error opening input file: %d.\n", result);
  }

  return(0);
}

________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Thursday, March 17, 2011 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 68, Issue 18

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. HDF5 errors (Alex Zijdenbos)
   2. Re: build almost everything minc Makefile and git repository
      for EZminc (Luis Concha)
   3. Re: HDF5 errors (Andrew Janke)
   4. ecattominc and scale factors (Thomas Funck)


----------------------------------------------------------------------

Message: 1
Date: Wed, 16 Mar 2011 17:06:25 +0100
From: Alex Zijdenbos <zijdenbos at gmail.com>
Subject: [MINC-users] HDF5 errors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikhjesHfwYnxHAjd74kQhrMFkAqMzY28gZ53Nvi at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello all,

I just stumbled across a bunch of HDF5 runtime errors (see below). As
best I can tell these are due to a bogged-down NFS server; the files
the process needs are definitely there, but may take a while to get.
If I restart the exact same process, chances are high it completes
without error. I have so far only come across these only in xfmconcat
(with nonlinear deformations) and minc_displacement.

The main problem is that the errors are not caught; the process exits
gracefully and leaves a seemingly good output MINC file behind;
however upon inspection, the file is only partially written. The only
way to actually find the error is to catch it during some explicit
verification, or by grepping for 'HDF5' in the log files.

Does anybody have any thoughts about this or has seen this before? I
would say the the MINC library (miicv_get?) should catch this somehow
and throw an error causing the process to fail, but clearly that is
currently not happening.

These are locally-built executables based on MINC 2.1, HDF5 1.8.5.

-- Alex

HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
  #000: H5Dio.c line 174 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 404 in H5D_read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1724 in H5D_chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2737 in H5D_chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1116 in H5Z_pipeline(): filter returned failure during read
    major: Data filters
    minor: Read failed
  #005: H5Zdeflate.c line 122 in H5Z_filter_deflate(): inflate() failed
    major: Data filters
    minor: Unable to initialize object
(from miicv_get): Can't read dataset /minc-2.0/image/0/image


------------------------------

Message: 2
Date: Wed, 16 Mar 2011 13:46:29 -0600
From: Luis Concha <lconcha at gmail.com>
Subject: Re: [MINC-users] build almost everything minc Makefile and
        git repository for EZminc
To: minc-users at bic.mni.mcgill.ca
Message-ID:
        <AANLkTi=2k6ALGfBEA8k9pSGsg_9eO+9ESXu2Zsntr6_=@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello all.

Replying to my own post is far from exciting, but I'm doing it so that
the solution I found to my compilation problem is of help to anyone in
the same situation.

The solution to compile everything using Vlad's big Makefile was to
install ActiveState Perl in my own directories, and adding it to the
PATH before the system's built in perl installation (using the
install.sh from the ActiveState Perl distribution). After that, make
all compiled everything without any further problems.

Minc tools on the cluster, here I go.

Thanks to all for helping out!

Luis


On Wed, Mar 16, 2011 at 10:00 AM,  <minc-users-request at bic.mni.mcgill.ca> wrote:
> Send MINC-users mailing list submissions to
> ? ? ? ?minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
> ? ? ? ?http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
> ? ? ? ?minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
> ? ? ? ?minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
> Today's Topics:
>
> ? 1. Re: build almost everything minc Makefile and git repository
> ? ? ?for EZminc (Luis Concha)
>
>
> ---------- Forwarded message ----------
> From:?Luis Concha <lconcha at gmail.com>
> To:?minc-users at bic.mni.mcgill.ca
> Date:?Tue, 15 Mar 2011 13:40:32 -0600
> Subject:?Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
> Hi Andrew and all.
>
>> I think you will need to add PREFIX to the perl install. In the
>> Andrew Janke
>
> Thanks for the suggestion. I have tried it and I am still getting the
> same error. I believe the root of it is how Makefile.PL is written,
> which seems to be made by lib/ExtUtils/MakeMaker.pm. Of course, this
> seems to depend on the perl version installed (5.8 in my case) and
> only root can modify makemaker.pm.
>
> I see that Makefile.PL sends out a few arguments to generate a
> Makefile, After reading the Makefile, I see several calls to
> /usr/lib64/perl5... (CCDLFLAGS, SITELIBEXP, SITEARCHEXP,
> VENDORARCHEXP, VENDORLIBEXP, etc). I was wondering if I can overrride
> these by sending the appropriate arguments through Makefile.PL. If
> possible, then my ignorance will shine, as I have no clue what I
> should provide instead.
>
> Alternatively, should I compile my own version of perl from source, so
> I have more control over MakeMaker.pm?
>
> Thanks again.
>
> Luis
>
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>


------------------------------

Message: 3
Date: Thu, 17 Mar 2011 21:02:53 +1000
From: Andrew Janke <a.janke at gmail.com>
Subject: Re: [MINC-users] HDF5 errors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikv-LMj-fEDPW3+3W3w4vcBaRAweOQ-NKFJsRsK at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

> I just stumbled across a bunch of HDF5 runtime errors (see below). As
> best I can tell these are due to a bogged-down NFS server; the files
> the process needs are definitely there, but may take a while to get.
> If I restart the exact same process, chances are high it completes
> without error. I have so far only come across these only in xfmconcat
> (with nonlinear deformations) and minc_displacement.

Does nfsstat show an error count during this?  If so I think your
problems are a bit more deep-seated than just MINC.



--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883


------------------------------

Message: 4
Date: Thu, 17 Mar 2011 14:09:20 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
Subject: [MINC-users] ecattominc and scale factors
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065C160 at EXMBX2010-2.campus.MCGILL.CA>
Content-Type: text/plain; charset="us-ascii"

Hi,

I am a grad student working the Jewish General for Dr. Thiel. When I convert ECAT7 files to MINC, the values of the MINC file do not match the original values of the ECAT7 file. I saw in the ECAT header that there are scale factors that are applied to the values of the ECAT file. However even when I multiply the values in the MINC file by the corresponding scale factors (using mincmath), the two files still don't match. Is there something I am doing wrong? Thanks for the help!

Best,

Thomas


------------------------------

_______________________________________________
MINC-users mailing list
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


End of MINC-users Digest, Vol 68, Issue 18
******************************************


------------------------------

Message: 2
Date: Thu, 17 Mar 2011 15:25:44 -0400
From: Peter Neelin <peter.neelin at gmail.com>
Subject: Re: [MINC-users] ecattominc and scale factors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTi=PnGdY0cOgC_dAc6_Cj739GN5dLyFESCEuj3hA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Thu, Mar 17, 2011 at 10:09 AM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:

> When I convert ECAT7 files to
> MINC, the values of the MINC file do not match the original values of the ECAT7 file. I saw in the
> ECAT header that there are scale factors that are applied to the values of the ECAT file. However
> even when I multiply the values in the MINC file by the corresponding scale factors (using
> mincmath), the two files still don't match. Is there something I am doing wrong?

By default, ecattominc will do decay correction if it has not already
been done. You can turn this off with -nodecay_correct - that would be
the quickest way to find out if this is the cause of the difference
between values.

Peter
--
Peter Neelin
(peter.neelin at gmail.com)


------------------------------

Message: 3
Date: Thu, 17 Mar 2011 14:09:37 -0700
From: EJ Nikelski <nikelski at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] miopen_volume not opening file
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikiEAkq+PCW6G6-nP5K_TeFZ5TbaJtupcg-6p02 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Thomas,

  Could you provide the output of the following:

(1) mincinfo -version
(2) uname -a
(3) file my_test_minc_volume.mnc
(4) mincinfo my_test_minc_volume.mnc

  Which version of Ubuntu are you using?

-jim



On Thu, Mar 17, 2011 at 12:09 PM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:
> Hi,
>
> So this is my second problem of the day. I'm writing a program that requires reading .mnc files. However when I try to use miopen_volume it returns -1. I even tried running the first mini-program included in the MINC2 tutorials (code included below) and miopen_volume did not work here either. I'm assuming the code from the tutorial is correct and that there is some underlying problem with HDF5 or MINC2. I just reinstalled the latest versions of MINC2 (version 2.1) and HDF5 (version 1.8.6) on my Ubuntu system. I also ran "make check" on both before installing and they passed all the tests, so both libraries seem to be happy with the system. I really can't figure out what's going on because the programs and code should both be okay. Any ideas?
>
> Best,
>
> Thomas
>
>
>
>
>
> #include <minc2.h>
> #include <stdio.h>
>
> int main(int argc, char **argv) {
> ?mihandle_t ? ?minc_volume;
> ?double ? ? ? ?voxel;
> ?int ? ? ? ? ? result;
> ?unsigned long location[3];
>
> ?/* open the volume - first and only command line argument */
> ?result = miopen_volume(argv[1], MI2_OPEN_READ, &minc_volume);
> ?/* check for error on opening */
> ?if (result != MI_NOERROR) {
> ? ?fprintf(stderr, "Error opening input file: %d.\n", result);
> ?}
>
> ?return(0);
> }
>

--
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University


------------------------------

_______________________________________________
MINC-users mailing list
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


End of MINC-users Digest, Vol 68, Issue 19
******************************************

From thomas.funck at mail.mcgill.ca  Fri Mar 18 16:09:29 2011
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Fri, 18 Mar 2011 20:09:29 +0000
Subject: [MINC-users] MINC-users Digest, Vol 68, Issue 19
In-Reply-To: <mailman.5.1300464002.14846.minc-users@bic.mni.mcgill.ca>
References: <mailman.5.1300464002.14846.minc-users@bic.mni.mcgill.ca>
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065C5D2@EXMBX2010-2.campus.MCGILL.CA>

Thanks Jim, I did the file command and realized that the file was NetCDF
Hi Jim,

Thanks for the suggestions, using "file mymincfile.mnc" actually solved my problem. I recently upgraded MINC versions and forgot that I had to convert the old NetCDF based files to HDF5.

Thanks again,

Thomas

________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Friday, March 18, 2011 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 68, Issue 19

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. miopen_volume not opening file (Thomas Funck)
   2. Re: ecattominc and scale factors (Peter Neelin)
   3. Re: miopen_volume not opening file (EJ Nikelski)


----------------------------------------------------------------------

Message: 1
Date: Thu, 17 Mar 2011 19:09:24 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
Subject: [MINC-users] miopen_volume not opening file
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065C208 at EXMBX2010-2.campus.MCGILL.CA>
Content-Type: text/plain; charset="us-ascii"

Hi,

So this is my second problem of the day. I'm writing a program that requires reading .mnc files. However when I try to use miopen_volume it returns -1. I even tried running the first mini-program included in the MINC2 tutorials (code included below) and miopen_volume did not work here either. I'm assuming the code from the tutorial is correct and that there is some underlying problem with HDF5 or MINC2. I just reinstalled the latest versions of MINC2 (version 2.1) and HDF5 (version 1.8.6) on my Ubuntu system. I also ran "make check" on both before installing and they passed all the tests, so both libraries seem to be happy with the system. I really can't figure out what's going on because the programs and code should both be okay. Any ideas?

Best,

Thomas





#include <minc2.h>
#include <stdio.h>

int main(int argc, char **argv) {
  mihandle_t    minc_volume;
  double        voxel;
  int           result;
  unsigned long location[3];

  /* open the volume - first and only command line argument */
  result = miopen_volume(argv[1], MI2_OPEN_READ, &minc_volume);
  /* check for error on opening */
  if (result != MI_NOERROR) {
    fprintf(stderr, "Error opening input file: %d.\n", result);
  }

  return(0);
}

________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Thursday, March 17, 2011 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 68, Issue 18

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. HDF5 errors (Alex Zijdenbos)
   2. Re: build almost everything minc Makefile and git repository
      for EZminc (Luis Concha)
   3. Re: HDF5 errors (Andrew Janke)
   4. ecattominc and scale factors (Thomas Funck)


----------------------------------------------------------------------

Message: 1
Date: Wed, 16 Mar 2011 17:06:25 +0100
From: Alex Zijdenbos <zijdenbos at gmail.com>
Subject: [MINC-users] HDF5 errors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikhjesHfwYnxHAjd74kQhrMFkAqMzY28gZ53Nvi at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello all,

I just stumbled across a bunch of HDF5 runtime errors (see below). As
best I can tell these are due to a bogged-down NFS server; the files
the process needs are definitely there, but may take a while to get.
If I restart the exact same process, chances are high it completes
without error. I have so far only come across these only in xfmconcat
(with nonlinear deformations) and minc_displacement.

The main problem is that the errors are not caught; the process exits
gracefully and leaves a seemingly good output MINC file behind;
however upon inspection, the file is only partially written. The only
way to actually find the error is to catch it during some explicit
verification, or by grepping for 'HDF5' in the log files.

Does anybody have any thoughts about this or has seen this before? I
would say the the MINC library (miicv_get?) should catch this somehow
and throw an error causing the process to fail, but clearly that is
currently not happening.

These are locally-built executables based on MINC 2.1, HDF5 1.8.5.

-- Alex

HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
  #000: H5Dio.c line 174 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 404 in H5D_read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1724 in H5D_chunk_read(): unable to read raw data chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2737 in H5D_chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1116 in H5Z_pipeline(): filter returned failure during read
    major: Data filters
    minor: Read failed
  #005: H5Zdeflate.c line 122 in H5Z_filter_deflate(): inflate() failed
    major: Data filters
    minor: Unable to initialize object
(from miicv_get): Can't read dataset /minc-2.0/image/0/image


------------------------------

Message: 2
Date: Wed, 16 Mar 2011 13:46:29 -0600
From: Luis Concha <lconcha at gmail.com>
Subject: Re: [MINC-users] build almost everything minc Makefile and
        git repository for EZminc
To: minc-users at bic.mni.mcgill.ca
Message-ID:
        <AANLkTi=2k6ALGfBEA8k9pSGsg_9eO+9ESXu2Zsntr6_=@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hello all.

Replying to my own post is far from exciting, but I'm doing it so that
the solution I found to my compilation problem is of help to anyone in
the same situation.

The solution to compile everything using Vlad's big Makefile was to
install ActiveState Perl in my own directories, and adding it to the
PATH before the system's built in perl installation (using the
install.sh from the ActiveState Perl distribution). After that, make
all compiled everything without any further problems.

Minc tools on the cluster, here I go.

Thanks to all for helping out!

Luis


On Wed, Mar 16, 2011 at 10:00 AM,  <minc-users-request at bic.mni.mcgill.ca> wrote:
> Send MINC-users mailing list submissions to
> ? ? ? ?minc-users at bic.mni.mcgill.ca
>
> To subscribe or unsubscribe via the World Wide Web, visit
> ? ? ? ?http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> or, via email, send a message with subject or body 'help' to
> ? ? ? ?minc-users-request at bic.mni.mcgill.ca
>
> You can reach the person managing the list at
> ? ? ? ?minc-users-owner at bic.mni.mcgill.ca
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of MINC-users digest..."
>
> Today's Topics:
>
> ? 1. Re: build almost everything minc Makefile and git repository
> ? ? ?for EZminc (Luis Concha)
>
>
> ---------- Forwarded message ----------
> From:?Luis Concha <lconcha at gmail.com>
> To:?minc-users at bic.mni.mcgill.ca
> Date:?Tue, 15 Mar 2011 13:40:32 -0600
> Subject:?Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
> Hi Andrew and all.
>
>> I think you will need to add PREFIX to the perl install. In the
>> Andrew Janke
>
> Thanks for the suggestion. I have tried it and I am still getting the
> same error. I believe the root of it is how Makefile.PL is written,
> which seems to be made by lib/ExtUtils/MakeMaker.pm. Of course, this
> seems to depend on the perl version installed (5.8 in my case) and
> only root can modify makemaker.pm.
>
> I see that Makefile.PL sends out a few arguments to generate a
> Makefile, After reading the Makefile, I see several calls to
> /usr/lib64/perl5... (CCDLFLAGS, SITELIBEXP, SITEARCHEXP,
> VENDORARCHEXP, VENDORLIBEXP, etc). I was wondering if I can overrride
> these by sending the appropriate arguments through Makefile.PL. If
> possible, then my ignorance will shine, as I have no clue what I
> should provide instead.
>
> Alternatively, should I compile my own version of perl from source, so
> I have more control over MakeMaker.pm?
>
> Thanks again.
>
> Luis
>
>
> _______________________________________________
> MINC-users mailing list
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>


------------------------------

Message: 3
Date: Thu, 17 Mar 2011 21:02:53 +1000
From: Andrew Janke <a.janke at gmail.com>
Subject: Re: [MINC-users] HDF5 errors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikv-LMj-fEDPW3+3W3w4vcBaRAweOQ-NKFJsRsK at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

> I just stumbled across a bunch of HDF5 runtime errors (see below). As
> best I can tell these are due to a bogged-down NFS server; the files
> the process needs are definitely there, but may take a while to get.
> If I restart the exact same process, chances are high it completes
> without error. I have so far only come across these only in xfmconcat
> (with nonlinear deformations) and minc_displacement.

Does nfsstat show an error count during this?  If so I think your
problems are a bit more deep-seated than just MINC.



--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Brisbane->Australia    +61 (402) 700 883


------------------------------

Message: 4
Date: Thu, 17 Mar 2011 14:09:20 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
Subject: [MINC-users] ecattominc and scale factors
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065C160 at EXMBX2010-2.campus.MCGILL.CA>
Content-Type: text/plain; charset="us-ascii"

Hi,

I am a grad student working the Jewish General for Dr. Thiel. When I convert ECAT7 files to MINC, the values of the MINC file do not match the original values of the ECAT7 file. I saw in the ECAT header that there are scale factors that are applied to the values of the ECAT file. However even when I multiply the values in the MINC file by the corresponding scale factors (using mincmath), the two files still don't match. Is there something I am doing wrong? Thanks for the help!

Best,

Thomas


------------------------------

_______________________________________________
MINC-users mailing list
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


End of MINC-users Digest, Vol 68, Issue 18
******************************************


------------------------------

Message: 2
Date: Thu, 17 Mar 2011 15:25:44 -0400
From: Peter Neelin <peter.neelin at gmail.com>
Subject: Re: [MINC-users] ecattominc and scale factors
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTi=PnGdY0cOgC_dAc6_Cj739GN5dLyFESCEuj3hA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

On Thu, Mar 17, 2011 at 10:09 AM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:

> When I convert ECAT7 files to
> MINC, the values of the MINC file do not match the original values of the ECAT7 file. I saw in the
> ECAT header that there are scale factors that are applied to the values of the ECAT file. However
> even when I multiply the values in the MINC file by the corresponding scale factors (using
> mincmath), the two files still don't match. Is there something I am doing wrong?

By default, ecattominc will do decay correction if it has not already
been done. You can turn this off with -nodecay_correct - that would be
the quickest way to find out if this is the cause of the difference
between values.

Peter
--
Peter Neelin
(peter.neelin at gmail.com)


------------------------------

Message: 3
Date: Thu, 17 Mar 2011 14:09:37 -0700
From: EJ Nikelski <nikelski at bic.mni.mcgill.ca>
Subject: Re: [MINC-users] miopen_volume not opening file
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
        <AANLkTikiEAkq+PCW6G6-nP5K_TeFZ5TbaJtupcg-6p02 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Thomas,

  Could you provide the output of the following:

(1) mincinfo -version
(2) uname -a
(3) file my_test_minc_volume.mnc
(4) mincinfo my_test_minc_volume.mnc

  Which version of Ubuntu are you using?

-jim



On Thu, Mar 17, 2011 at 12:09 PM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:
> Hi,
>
> So this is my second problem of the day. I'm writing a program that requires reading .mnc files. However when I try to use miopen_volume it returns -1. I even tried running the first mini-program included in the MINC2 tutorials (code included below) and miopen_volume did not work here either. I'm assuming the code from the tutorial is correct and that there is some underlying problem with HDF5 or MINC2. I just reinstalled the latest versions of MINC2 (version 2.1) and HDF5 (version 1.8.6) on my Ubuntu system. I also ran "make check" on both before installing and they passed all the tests, so both libraries seem to be happy with the system. I really can't figure out what's going on because the programs and code should both be okay. Any ideas?
>
> Best,
>
> Thomas
>
>
>
>
>
> #include <minc2.h>
> #include <stdio.h>
>
> int main(int argc, char **argv) {
> ?mihandle_t ? ?minc_volume;
> ?double ? ? ? ?voxel;
> ?int ? ? ? ? ? result;
> ?unsigned long location[3];
>
> ?/* open the volume - first and only command line argument */
> ?result = miopen_volume(argv[1], MI2_OPEN_READ, &minc_volume);
> ?/* check for error on opening */
> ?if (result != MI_NOERROR) {
> ? ?fprintf(stderr, "Error opening input file: %d.\n", result);
> ?}
>
> ?return(0);
> }
>

--
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University


------------------------------

_______________________________________________
MINC-users mailing list
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


End of MINC-users Digest, Vol 68, Issue 19
******************************************

From peter.neelin at gmail.com  Sat Mar 19 00:49:14 2011
From: peter.neelin at gmail.com (Peter Neelin)
Date: Sat, 19 Mar 2011 00:49:14 -0400
Subject: [MINC-users] MINC-users Digest, Vol 68, Issue 19
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065C5B1@EXMBX2010-2.campus.MCGILL.CA>
References: <mailman.5.1300464002.14846.minc-users@bic.mni.mcgill.ca>
	<53F3FD0032C9CC4BA836E8F0FC289065C5B1@EXMBX2010-2.campus.MCGILL.CA>
Message-ID: <AANLkTi=UTrVdsmWtR5YWvaE1xgFmh-+h9o0PYm9dTVv4@mail.gmail.com>

On Fri, Mar 18, 2011 at 3:54 PM, Thomas Funck
<thomas.funck at mail.mcgill.ca> wrote:
> (1) ECAT File - Frame 1
> #Name ? ? ? ? ?Type ? ? #Pixels ? ? ? Average
> ?Roi2DEllipse ?Ellipse ? ? ?197 ?1.29479e+004

> (4)MINC - Frame 1 - Decay Corrected
> #Name ? ? ? ? ?Type ? ? #Pixels ? ? ? Average
> ?Roi2DEllipse ?Ellipse ? ? ?197 ?3.49095e+002

Oh right, I forgot (it has been 15 years - yikes!), ecattominc
converts to nCi/cc instead of the Bq/cc used by the ECAT software.
This is just due to MNI PET unit practice at the time that it was
written.

  12947.9 / 37 = 349.943

Run mincheader and you should see the units (attribute of the image
variable, I think).

Peter
-- 
Peter Neelin
(peter.neelin at gmail.com)

From asnedden at nd.edu  Thu Mar 24 19:27:38 2011
From: asnedden at nd.edu (Ali Snedden)
Date: Thu, 24 Mar 2011 19:27:38 -0400
Subject: [MINC-users] X11 forwarding for Display
Message-ID: <AANLkTik6usM5HrPk_oJhCZzc97jWZPH_c1VEM_doNBp1@mail.gmail.com>

Hello,

I was having difficulty with X11 forwarding when trying to use Display
from one mac machine
to another mac machine. I can get xedit and xterm to work, but not
Display.  I had noticed in the documentation for Display that it
states that you can build "with X window system", which I assumed was
X forwarding.  So, I built Display with the "--with-x" and
"--with-minc2" options

Here are my relevant settings:
On my local mac machine:
environmental variable DISPLAY is set to /tmp/launch-RuXg5G/org.x:0
and X11forwarding is yes in my /etc/sshd_config file

On my remote mac machine:
environmental variable DISPLAY is localhost:10.0
and X11forwarding is yes in my /etc/sshd_config file

Also on my remote machine, I am running Display-1.4.2 and Minc 2.0.18.
 Both machines, are running MacOSX 10.6.*  .

So after i've ssh'd into my remote mac, and I run "Display
somefile.mnc", I get the following error:

Display[24131] <Error>: kCGErrorFailure: Set a breakpoint @
CGErrorBreakpoint() to catch errors as they are logged.
xp_init: error: not initialized
error: invalid pixel format attribute
Abort trap

If you have any advice, I'd much appreciate it.  Thank you for your time.

Sincerely,
Ali

From a.janke at gmail.com  Fri Mar 25 08:11:20 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 25 Mar 2011 22:11:20 +1000
Subject: [MINC-users] X11 forwarding for Display
In-Reply-To: <AANLkTik6usM5HrPk_oJhCZzc97jWZPH_c1VEM_doNBp1@mail.gmail.com>
References: <AANLkTik6usM5HrPk_oJhCZzc97jWZPH_c1VEM_doNBp1@mail.gmail.com>
Message-ID: <AANLkTimtDEzz-Kb9h_dhDEB4QmCJJAMOxV3DTEwM2pbp@mail.gmail.com>

Hi Ali,


> I was having difficulty with X11 forwarding when trying to use Display
> from one mac machine
> to another mac machine. I can get xedit and xterm to work, but not
> Display. ?I had noticed in the documentation for Display that it
> states that you can build "with X window system", which I assumed was
> X forwarding. ?So, I built Display with the "--with-x" and
> "--with-minc2" options

This should all be fine.

> Here are my relevant settings:
> On my local mac machine:
> environmental variable DISPLAY is set to /tmp/launch-RuXg5G/org.x:0
> and X11forwarding is yes in my /etc/sshd_config file

My understanding is that DISPLAY on the local machine should still be

spencer:~$ echo $DISPLAY
:0.0

But perhaps this is a linux vs OSX difference. In any case you
shouldn't have to modify the setting if ssh is working correctly.

> On my remote mac machine:
> environmental variable DISPLAY is localhost:10.0
> and X11forwarding is yes in my /etc/sshd_config file

Do you also have:

X11DisplayOffset 10

set?

> Display[24131] <Error>: kCGErrorFailure: Set a breakpoint @
> CGErrorBreakpoint() to catch errors as they are logged.
> xp_init: error: not initialized
> error: invalid pixel format attribute
> Abort trap

I can't make much sense of this error, I take it you are running
ssh/Display from an X11 xterm window and not using the Mac "Terminal"
Application?


a

From asnedden at nd.edu  Fri Mar 25 10:41:41 2011
From: asnedden at nd.edu (Ali Snedden)
Date: Fri, 25 Mar 2011 10:41:41 -0400
Subject: [MINC-users] X11 forwarding for Display
In-Reply-To: <AANLkTimtDEzz-Kb9h_dhDEB4QmCJJAMOxV3DTEwM2pbp@mail.gmail.com>
References: <AANLkTik6usM5HrPk_oJhCZzc97jWZPH_c1VEM_doNBp1@mail.gmail.com>
	<AANLkTimtDEzz-Kb9h_dhDEB4QmCJJAMOxV3DTEwM2pbp@mail.gmail.com>
Message-ID: <AANLkTikSKxqWwhJ+NLSPS14FuLFDiuq-ESGiBB0rcwbD@mail.gmail.com>

Hi,

Yes I am running it in xterm.  I originally did not have,
X11DisplayOffset 10 in my /etc/sshd_config file, but I have now set it
on both my local and my remote machines.

I can still get xedit, xterm, and xeyes to all forward to my local
machine.  Unfortunately,  I still get the same error when trying to
"Display somefile.mnc".

I have fooled around with the DISPLAY variable some on my local
machine, setting  it to :0.0 . If I do this then X forwarding does not
work and I cannot get it xedit, xterm, or xeyes to forward.  I get the
error "connect /tmp/.X11-unix/X0: Connection refused".
So, I'm pretty sure that my original DISPLAY variable setting is
correct.  FYI, I think the DISPLAY variable is automatically set on
Mac OSX, (i.e. I don't explicitly set it in either my .bash_profile or
my .bashrc files).

Thanks for your time,
Sincerely,
Ali

On Fri, Mar 25, 2011 at 8:11 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Ali,
>
>
>> I was having difficulty with X11 forwarding when trying to use Display
>> from one mac machine
>> to another mac machine. I can get xedit and xterm to work, but not
>> Display. ?I had noticed in the documentation for Display that it
>> states that you can build "with X window system", which I assumed was
>> X forwarding. ?So, I built Display with the "--with-x" and
>> "--with-minc2" options
>
> This should all be fine.
>
>> Here are my relevant settings:
>> On my local mac machine:
>> environmental variable DISPLAY is set to /tmp/launch-RuXg5G/org.x:0
>> and X11forwarding is yes in my /etc/sshd_config file
>
> My understanding is that DISPLAY on the local machine should still be
>
> spencer:~$ echo $DISPLAY
> :0.0
>
> But perhaps this is a linux vs OSX difference. In any case you
> shouldn't have to modify the setting if ssh is working correctly.
>
>> On my remote mac machine:
>> environmental variable DISPLAY is localhost:10.0
>> and X11forwarding is yes in my /etc/sshd_config file
>
> Do you also have:
>
> X11DisplayOffset 10
>
> set?
>
>> Display[24131] <Error>: kCGErrorFailure: Set a breakpoint @
>> CGErrorBreakpoint() to catch errors as they are logged.
>> xp_init: error: not initialized
>> error: invalid pixel format attribute
>> Abort trap
>
> I can't make much sense of this error, I take it you are running
> ssh/Display from an X11 xterm window and not using the Mac "Terminal"
> Application?
>
>
> a
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From MKeaser at umaryland.edu  Mon Mar 28 13:48:21 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Mon, 28 Mar 2011 13:48:21 -0400
Subject: [MINC-users] build almost everything minc Makefile and
	git	repository for EZminc
In-Reply-To: <4D715D1D.1090404@gmail.com>
References: <4D715D1D.1090404@gmail.com>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>

Vladmir,

I installed most of the minc packages with the makefile you provided. However, I am having trouble installing Register and Display. I am using Ubuntu 10.04

I tried the command "make visual" and I get this message:

make: *** No rule to make target `visual'.  Stop.

At that point, i just tried to install Register and Display separately with the make command, and went into the respective directories to try and configure it. Each time i tried to configure with this line in Register,

./configure --prefix=/usr/local/minc -with-build-path=/usr/local/minc --with-minc2 --with-x  && \ make clean && \ make -j4 && \ make install 

 I get this error message: configure: error: cannot find required library bicpl

On my system it says bicpl is located in: /usr/local/minc/src/bicpl-1.4.6/Include/bicpl

I added that to the configure line, in it still says it cannot find it.

I'm kind of stuck right now and lost. Any help would greatly be appreciated.

Thanks,

Michael







________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
Sent: Friday, March 04, 2011 4:43 PM
To: MINC users mailing list
Subject: [MINC-users] build almost everything minc Makefile and git     repository for EZminc

Hello Everybody,

in an effort to simplify minc installation I have made publicly
available a "build almost everything minc" makefile:

https://github.com/vfonov/EZminc/raw/master/build_quarantine/Makefile

The main purpose of it is to build most of the publicly available minc
tools inside a quarantine with minimum dependencies on the system
libraries. So, everything is compiled statically.

Following packages are built by default:

netcdf-4.0.1 hdf5-1.8.6 minc-2.1.00 bicpl-1.4.6 ebtks-1.6.4
oobicpl-0.4.4 N3-1.12.0 classify-1.1.0 conglomerate-1.6.6
mni_autoreg-0.99.6 mni_perllib-0.08 mincblob-1.2.1 mincmorph-1.4
ray_trace-1.0.3 glim_image-1.2 InsightToolkit-3.20.0 fftw-3.2.2
cmake-2.8.4 gsl-1.14 Getopt-Tabular-0.3 ezminc-r83 netpbm-10.35.74


following packages may also be built if needed:

Register-1.4.0 Display-1.5.0
fltk-1.3.x-r7725 vtk-5.6.1

To use:

make PREFIX=<location of your quarantine> TEMP=<location where packages
will be built> PARALLEL_BUILD=-j<number of CPUs available> all

Also, as you can notice I have created a clone of EZminc repository on
the github:  https://github.com/vfonov/EZminc , hopefully it will be
easier to use it this way.


--
Best regards,
  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From lconcha at gmail.com  Mon Mar 28 14:18:51 2011
From: lconcha at gmail.com (Luis Concha)
Date: Mon, 28 Mar 2011 12:18:51 -0600
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>
References: <4D715D1D.1090404@gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>
Message-ID: <AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>

Hi Michael.

I noticed that, too. I saw that the option make visual is not included
in the makefile, although it is on the help for it. All I did was add
a line:
visual : $(register) $(Display).

Regarding bicp, use make bicpl first, then make visual.

I hope this helps.

Luis



On Mon, Mar 28, 2011 at 11:48 AM, Keaser, Michael L
<MKeaser at umaryland.edu> wrote:
> Vladmir,
>
> I installed most of the minc packages with the makefile you provided. However, I am having trouble installing Register and Display. I am using Ubuntu 10.04
>
> I tried the command "make visual" and I get this message:
>
> make: *** No rule to make target `visual'. ?Stop.
>
> At that point, i just tried to install Register and Display separately with the make command, and went into the respective directories to try and configure it. Each time i tried to configure with this line in Register,
>
> ./configure --prefix=/usr/local/minc -with-build-path=/usr/local/minc --with-minc2 --with-x ?&& \ make clean && \ make -j4 && \ make install
>
> ?I get this error message: configure: error: cannot find required library bicpl
>
> On my system it says bicpl is located in: /usr/local/minc/src/bicpl-1.4.6/Include/bicpl
>
> I added that to the configure line, in it still says it cannot find it.
>
> I'm kind of stuck right now and lost. Any help would greatly be appreciated.
>
> Thanks,
>
> Michael
>
>
>
>
>
>
>
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
> Sent: Friday, March 04, 2011 4:43 PM
> To: MINC users mailing list
> Subject: [MINC-users] build almost everything minc Makefile and git ? ? repository for EZminc
>
> Hello Everybody,
>
> in an effort to simplify minc installation I have made publicly
> available a "build almost everything minc" makefile:
>
> https://github.com/vfonov/EZminc/raw/master/build_quarantine/Makefile
>
> The main purpose of it is to build most of the publicly available minc
> tools inside a quarantine with minimum dependencies on the system
> libraries. So, everything is compiled statically.
>
> Following packages are built by default:
>
> netcdf-4.0.1 hdf5-1.8.6 minc-2.1.00 bicpl-1.4.6 ebtks-1.6.4
> oobicpl-0.4.4 N3-1.12.0 classify-1.1.0 conglomerate-1.6.6
> mni_autoreg-0.99.6 mni_perllib-0.08 mincblob-1.2.1 mincmorph-1.4
> ray_trace-1.0.3 glim_image-1.2 InsightToolkit-3.20.0 fftw-3.2.2
> cmake-2.8.4 gsl-1.14 Getopt-Tabular-0.3 ezminc-r83 netpbm-10.35.74
>
>
> following packages may also be built if needed:
>
> Register-1.4.0 Display-1.5.0
> fltk-1.3.x-r7725 vtk-5.6.1
>
> To use:
>
> make PREFIX=<location of your quarantine> TEMP=<location where packages
> will be built> PARALLEL_BUILD=-j<number of CPUs available> all
>
> Also, as you can notice I have created a clone of EZminc repository on
> the github: ?https://github.com/vfonov/EZminc , hopefully it will be
> easier to use it this way.
>
>
> --
> Best regards,
> ?Vladimir S. FONOV ~ v.s.fonov ?<at> ilmarin.info
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From MKeaser at umaryland.edu  Mon Mar 28 14:54:03 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Mon, 28 Mar 2011 14:54:03 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>
References: <4D715D1D.1090404@gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>,
	<AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AC@UMBEXMBX2.campus.umaryland.edu>

Luis,

I tried your suggestions, and that seemed to work for register, but not Display. I tried configuring Display separately and it is still an issue. I don't see it in the bin directory with the other commands  like register, mincblob, etc.

Also, with register, I get this error message every time i try to use it:

Xlib:  extension "GLX" missing on display ":0.0".
freeglut (no_program_name): OpenGL GLX extension not supported by display ':0.0'

Have you seen an error like  this before?

Thanks,

Michael
________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Luis Concha [lconcha at gmail.com]
Sent: Monday, March 28, 2011 2:18 PM
To: MINC users mailing list
Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc

Hi Michael.

I noticed that, too. I saw that the option make visual is not included
in the makefile, although it is on the help for it. All I did was add
a line:
visual : $(register) $(Display).

Regarding bicp, use make bicpl first, then make visual.

I hope this helps.

Luis



On Mon, Mar 28, 2011 at 11:48 AM, Keaser, Michael L
<MKeaser at umaryland.edu> wrote:
> Vladmir,
>
> I installed most of the minc packages with the makefile you provided. However, I am having trouble installing Register and Display. I am using Ubuntu 10.04
>
> I tried the command "make visual" and I get this message:
>
> make: *** No rule to make target `visual'.  Stop.
>
> At that point, i just tried to install Register and Display separately with the make command, and went into the respective directories to try and configure it. Each time i tried to configure with this line in Register,
>
> ./configure --prefix=/usr/local/minc -with-build-path=/usr/local/minc --with-minc2 --with-x  && \ make clean && \ make -j4 && \ make install
>
>  I get this error message: configure: error: cannot find required library bicpl
>
> On my system it says bicpl is located in: /usr/local/minc/src/bicpl-1.4.6/Include/bicpl
>
> I added that to the configure line, in it still says it cannot find it.
>
> I'm kind of stuck right now and lost. Any help would greatly be appreciated.
>
> Thanks,
>
> Michael
>
>
>
>
>
>
>
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
> Sent: Friday, March 04, 2011 4:43 PM
> To: MINC users mailing list
> Subject: [MINC-users] build almost everything minc Makefile and git     repository for EZminc
>
> Hello Everybody,
>
> in an effort to simplify minc installation I have made publicly
> available a "build almost everything minc" makefile:
>
> https://github.com/vfonov/EZminc/raw/master/build_quarantine/Makefile
>
> The main purpose of it is to build most of the publicly available minc
> tools inside a quarantine with minimum dependencies on the system
> libraries. So, everything is compiled statically.
>
> Following packages are built by default:
>
> netcdf-4.0.1 hdf5-1.8.6 minc-2.1.00 bicpl-1.4.6 ebtks-1.6.4
> oobicpl-0.4.4 N3-1.12.0 classify-1.1.0 conglomerate-1.6.6
> mni_autoreg-0.99.6 mni_perllib-0.08 mincblob-1.2.1 mincmorph-1.4
> ray_trace-1.0.3 glim_image-1.2 InsightToolkit-3.20.0 fftw-3.2.2
> cmake-2.8.4 gsl-1.14 Getopt-Tabular-0.3 ezminc-r83 netpbm-10.35.74
>
>
> following packages may also be built if needed:
>
> Register-1.4.0 Display-1.5.0
> fltk-1.3.x-r7725 vtk-5.6.1
>
> To use:
>
> make PREFIX=<location of your quarantine> TEMP=<location where packages
> will be built> PARALLEL_BUILD=-j<number of CPUs available> all
>
> Also, as you can notice I have created a clone of EZminc repository on
> the github:  https://github.com/vfonov/EZminc , hopefully it will be
> easier to use it this way.
>
>
> --
> Best regards,
>  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From mishkind at gmail.com  Mon Mar 28 19:34:48 2011
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Mon, 28 Mar 2011 19:34:48 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AC@UMBEXMBX2.campus.umaryland.edu>
References: <4D715D1D.1090404@gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AC@UMBEXMBX2.campus.umaryland.edu>
Message-ID: <AANLkTikkJqq6-5vqjjh4XXS9weKGP+UMx8p116Vsjz-d@mail.gmail.com>

Hi,
I've had the same problem with Display/register on my ubuntu 10.10 32-blt build.

The first time around I tried this, but did not get register or Display:
make all PREFIX=/usr/local/bic TEMP=$HOME/temp

So I tried this and got register:
make register PREFIX=/usr/local/bic TEMP=$HOME/temp

But this didn't work for Display (ie. no executable).
make Display PREFIX=/usr/local/bic TEMP=$HOME/temp

Then I tried debugging:
Inside the source dir of Display-1.5.0
./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
--with-minc2 --with-x
make

Which runs to completion but does not produce an executable. Attached
is my config.log.

Micheal: I don't get that error with register. must be video card
specific or else fixed in 10.10.

mishkin




On Mon, Mar 28, 2011 at 2:54 PM, Keaser, Michael L
<MKeaser at umaryland.edu> wrote:
>
> Luis,
>
> I tried your suggestions, and that seemed to work for register, but not Display. I tried configuring Display separately and it is still an issue. I don't see it in the bin directory with the other commands ?like register, mincblob, etc.
>
> Also, with register, I get this error message every time i try to use it:
>
> Xlib: ?extension "GLX" missing on display ":0.0".
> freeglut (no_program_name): OpenGL GLX extension not supported by display ':0.0'
>
> Have you seen an error like ?this before?
>
> Thanks,
>
> Michael
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Luis Concha [lconcha at gmail.com]
> Sent: Monday, March 28, 2011 2:18 PM
> To: MINC users mailing list
> Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
>
> Hi Michael.
>
> I noticed that, too. I saw that the option make visual is not included
> in the makefile, although it is on the help for it. All I did was add
> a line:
> visual : $(register) $(Display).
>
> Regarding bicp, use make bicpl first, then make visual.
>
> I hope this helps.
>
> Luis
>
>
>
> On Mon, Mar 28, 2011 at 11:48 AM, Keaser, Michael L
> <MKeaser at umaryland.edu> wrote:
> > Vladmir,
> >
> > I installed most of the minc packages with the makefile you provided. However, I am having trouble installing Register and Display. I am using Ubuntu 10.04
> >
> > I tried the command "make visual" and I get this message:
> >
> > make: *** No rule to make target `visual'. ?Stop.
> >
> > At that point, i just tried to install Register and Display separately with the make command, and went into the respective directories to try and configure it. Each time i tried to configure with this line in Register,
> >
> > ./configure --prefix=/usr/local/minc -with-build-path=/usr/local/minc --with-minc2 --with-x ?&& \ make clean && \ make -j4 && \ make install
> >
> > ?I get this error message: configure: error: cannot find required library bicpl
> >
> > On my system it says bicpl is located in: /usr/local/minc/src/bicpl-1.4.6/Include/bicpl
> >
> > I added that to the configure line, in it still says it cannot find it.
> >
> > I'm kind of stuck right now and lost. Any help would greatly be appreciated.
> >
> > Thanks,
> >
> > Michael
> >
> >
> >
> >
> >
> >
> >
> > ________________________________________
> > From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
> > Sent: Friday, March 04, 2011 4:43 PM
> > To: MINC users mailing list
> > Subject: [MINC-users] build almost everything minc Makefile and git ? ? repository for EZminc
> >
> > Hello Everybody,
> >
> > in an effort to simplify minc installation I have made publicly
> > available a "build almost everything minc" makefile:
> >
> > https://github.com/vfonov/EZminc/raw/master/build_quarantine/Makefile
> >
> > The main purpose of it is to build most of the publicly available minc
> > tools inside a quarantine with minimum dependencies on the system
> > libraries. So, everything is compiled statically.
> >
> > Following packages are built by default:
> >
> > netcdf-4.0.1 hdf5-1.8.6 minc-2.1.00 bicpl-1.4.6 ebtks-1.6.4
> > oobicpl-0.4.4 N3-1.12.0 classify-1.1.0 conglomerate-1.6.6
> > mni_autoreg-0.99.6 mni_perllib-0.08 mincblob-1.2.1 mincmorph-1.4
> > ray_trace-1.0.3 glim_image-1.2 InsightToolkit-3.20.0 fftw-3.2.2
> > cmake-2.8.4 gsl-1.14 Getopt-Tabular-0.3 ezminc-r83 netpbm-10.35.74
> >
> >
> > following packages may also be built if needed:
> >
> > Register-1.4.0 Display-1.5.0
> > fltk-1.3.x-r7725 vtk-5.6.1
> >
> > To use:
> >
> > make PREFIX=<location of your quarantine> TEMP=<location where packages
> > will be built> PARALLEL_BUILD=-j<number of CPUs available> all
> >
> > Also, as you can notice I have created a clone of EZminc repository on
> > the github: ?https://github.com/vfonov/EZminc , hopefully it will be
> > easier to use it this way.
> >
> >
> > --
> > Best regards,
> > ?Vladimir S. FONOV ~ v.s.fonov ?<at> ilmarin.info
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From a.janke at gmail.com  Tue Mar 29 08:16:52 2011
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 29 Mar 2011 22:16:52 +1000
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <AANLkTikkJqq6-5vqjjh4XXS9weKGP+UMx8p116Vsjz-d@mail.gmail.com>
References: <4D715D1D.1090404@gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AC@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTikkJqq6-5vqjjh4XXS9weKGP+UMx8p116Vsjz-d@mail.gmail.com>
Message-ID: <AANLkTikeG=aYEP4k4weRZbAtB9r50Wekz7aw5+FHU=D7@mail.gmail.com>

If this is the same "bug" that I have been bitten by it's to do with
libtool and the way bicpl is linked (or not as the case often turns
out to be) with libnetpbm.

If you run make in the Display directory, copy and paste the last line
of the build (when Display is made) and then run it without the
libtool part.  turn

   $ libtool <blah> gcc <blah>

into

   $ gcc <blah>

and in most cases Display will be made.

YMMV but this is what I have seen but haven't got to the bottom of yet.

a

On Tue, Mar 29, 2011 at 09:34, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> Then I tried debugging:
> Inside the source dir of Display-1.5.0
> ./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
> --with-minc2 --with-x
> make

From MKeaser at umaryland.edu  Wed Mar 30 17:35:04 2011
From: MKeaser at umaryland.edu (Keaser, Michael L)
Date: Wed, 30 Mar 2011 17:35:04 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <AANLkTikkJqq6-5vqjjh4XXS9weKGP+UMx8p116Vsjz-d@mail.gmail.com>
References: <4D715D1D.1090404@gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>
	<AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AC@UMBEXMBX2.campus.umaryland.edu>,
	<AANLkTikkJqq6-5vqjjh4XXS9weKGP+UMx8p116Vsjz-d@mail.gmail.com>
Message-ID: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2C1@UMBEXMBX2.campus.umaryland.edu>

I'm wondering if the error message that i get when trying to use register

Xlib:  extension "GLX" missing on display ":0.0".
> freeglut (no_program_name): OpenGL GLX extension not supported by display ':0.0'

has something to do with the video card on my server. This the output that i get when i type "sudo lspci | grep VGA"

06:03.0 VGA compatible controller: Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a)

Maybe this is causing the conflict? Reading online it seems that glx extension requires a NVIDIA card, and my server only has a VGA? Could that be the problem? Anybody else experience this issue?


________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Mishkin Derakhshan [mishkind at gmail.com]
Sent: Monday, March 28, 2011 7:34 PM
To: MINC users mailing list
Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc

Hi,
I've had the same problem with Display/register on my ubuntu 10.10 32-blt build.

The first time around I tried this, but did not get register or Display:
make all PREFIX=/usr/local/bic TEMP=$HOME/temp

So I tried this and got register:
make register PREFIX=/usr/local/bic TEMP=$HOME/temp

But this didn't work for Display (ie. no executable).
make Display PREFIX=/usr/local/bic TEMP=$HOME/temp

Then I tried debugging:
Inside the source dir of Display-1.5.0
./configure --prefix=/usr/local/bic --with-build-path=/usr/local/bic
--with-minc2 --with-x
make

Which runs to completion but does not produce an executable. Attached
is my config.log.

Micheal: I don't get that error with register. must be video card
specific or else fixed in 10.10.

mishkin




On Mon, Mar 28, 2011 at 2:54 PM, Keaser, Michael L
<MKeaser at umaryland.edu> wrote:
>
> Luis,
>
> I tried your suggestions, and that seemed to work for register, but not Display. I tried configuring Display separately and it is still an issue. I don't see it in the bin directory with the other commands  like register, mincblob, etc.
>
> Also, with register, I get this error message every time i try to use it:
>
> Xlib:  extension "GLX" missing on display ":0.0".
> freeglut (no_program_name): OpenGL GLX extension not supported by display ':0.0'
>
> Have you seen an error like  this before?
>
> Thanks,
>
> Michael
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Luis Concha [lconcha at gmail.com]
> Sent: Monday, March 28, 2011 2:18 PM
> To: MINC users mailing list
> Subject: Re: [MINC-users] build almost everything minc Makefile and git repository for EZminc
>
> Hi Michael.
>
> I noticed that, too. I saw that the option make visual is not included
> in the makefile, although it is on the help for it. All I did was add
> a line:
> visual : $(register) $(Display).
>
> Regarding bicp, use make bicpl first, then make visual.
>
> I hope this helps.
>
> Luis
>
>
>
> On Mon, Mar 28, 2011 at 11:48 AM, Keaser, Michael L
> <MKeaser at umaryland.edu> wrote:
> > Vladmir,
> >
> > I installed most of the minc packages with the makefile you provided. However, I am having trouble installing Register and Display. I am using Ubuntu 10.04
> >
> > I tried the command "make visual" and I get this message:
> >
> > make: *** No rule to make target `visual'.  Stop.
> >
> > At that point, i just tried to install Register and Display separately with the make command, and went into the respective directories to try and configure it. Each time i tried to configure with this line in Register,
> >
> > ./configure --prefix=/usr/local/minc -with-build-path=/usr/local/minc --with-minc2 --with-x  && \ make clean && \ make -j4 && \ make install
> >
> >  I get this error message: configure: error: cannot find required library bicpl
> >
> > On my system it says bicpl is located in: /usr/local/minc/src/bicpl-1.4.6/Include/bicpl
> >
> > I added that to the configure line, in it still says it cannot find it.
> >
> > I'm kind of stuck right now and lost. Any help would greatly be appreciated.
> >
> > Thanks,
> >
> > Michael
> >
> >
> >
> >
> >
> >
> >
> > ________________________________________
> > From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Vladimir S. FONOV [vladimir.fonov at gmail.com]
> > Sent: Friday, March 04, 2011 4:43 PM
> > To: MINC users mailing list
> > Subject: [MINC-users] build almost everything minc Makefile and git     repository for EZminc
> >
> > Hello Everybody,
> >
> > in an effort to simplify minc installation I have made publicly
> > available a "build almost everything minc" makefile:
> >
> > https://github.com/vfonov/EZminc/raw/master/build_quarantine/Makefile
> >
> > The main purpose of it is to build most of the publicly available minc
> > tools inside a quarantine with minimum dependencies on the system
> > libraries. So, everything is compiled statically.
> >
> > Following packages are built by default:
> >
> > netcdf-4.0.1 hdf5-1.8.6 minc-2.1.00 bicpl-1.4.6 ebtks-1.6.4
> > oobicpl-0.4.4 N3-1.12.0 classify-1.1.0 conglomerate-1.6.6
> > mni_autoreg-0.99.6 mni_perllib-0.08 mincblob-1.2.1 mincmorph-1.4
> > ray_trace-1.0.3 glim_image-1.2 InsightToolkit-3.20.0 fftw-3.2.2
> > cmake-2.8.4 gsl-1.14 Getopt-Tabular-0.3 ezminc-r83 netpbm-10.35.74
> >
> >
> > following packages may also be built if needed:
> >
> > Register-1.4.0 Display-1.5.0
> > fltk-1.3.x-r7725 vtk-5.6.1
> >
> > To use:
> >
> > make PREFIX=<location of your quarantine> TEMP=<location where packages
> > will be built> PARALLEL_BUILD=-j<number of CPUs available> all
> >
> > Also, as you can notice I have created a clone of EZminc repository on
> > the github:  https://github.com/vfonov/EZminc , hopefully it will be
> > easier to use it this way.
> >
> >
> > --
> > Best regards,
> >  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From giovanna_p at hotmail.com  Thu Mar 31 10:40:53 2011
From: giovanna_p at hotmail.com (Giovanna Pellecchia)
Date: Thu, 31 Mar 2011 10:40:53 -0400
Subject: [MINC-users] build almost everything minc Makefile and git
 repository for EZminc
In-Reply-To: <00EF2C3B391AF84C8ED343F4469D4D56055F5BC2C1@UMBEXMBX2.campus.umaryland.edu>
References: <4D715D1D.1090404@gmail.com>	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AB@UMBEXMBX2.campus.umaryland.edu>	<AANLkTik1_N7tJRX2xJtEK8XL66uxrhMdY9Ti-Ac3piiB@mail.gmail.com>	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2AC@UMBEXMBX2.campus.umaryland.edu>,
	<AANLkTikkJqq6-5vqjjh4XXS9weKGP+UMx8p116Vsjz-d@mail.gmail.com>
	<00EF2C3B391AF84C8ED343F4469D4D56055F5BC2C1@UMBEXMBX2.campus.umaryland.edu>
Message-ID: <BLU0-SMTP1223A2E56D590B345ED5C35F7BF0@phx.gbl>

Keaser, Michael L wrote:
> I'm wondering if the error message that i get when trying to use register
>
> Xlib:  extension "GLX" missing on display ":0.0".
>   
>> freeglut (no_program_name): OpenGL GLX extension not supported by display ':0.0'
>>     
>
> has something to do with the video card on my server. This the output that i get when i type "sudo lspci | grep VGA"
>
> 06:03.0 VGA compatible controller: Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a)
>
> Maybe this is causing the conflict? Reading online it seems that glx extension requires a NVIDIA card, and my server only has a VGA? Could that be the problem? Anybody else experience this issue?
>
>   
My understanding is that NVIDIA provides its own glx extension during 
the driver installation:

locate nvidia | grep glx
/usr/lib/nvidia/libglx.so.xserver-xorg-core

(on a PC with Nvidia card), but the generic libglx should work for other 
cards. I do not have experience with Matrox, but ATI didn't give 
problems during installation. Sorry if this doesn't help much...

GP