From lrisa87 at uw.edu  Thu Apr  1 19:58:02 2010
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Thu, 1 Apr 2010 16:58:02 -0700
Subject: [MINC-users] "Not a netCDF file" error
Message-ID: <o2ne2890cba1004011658xd34d0d5cv89a75fa717d5cf8e@mail.gmail.com>

Hello,

I recently installed MINC.
(used mni-2006-11-15.tar.gz from http://packages.bic.mni.mcgill.ca/cygwin/)

I can get outputs using the "man" commands, e.g. *man mincinfo*.
However, when I try to run a certain tool like

> *mincinfo -image_info /usr/local/mni/data/ABC.mnc*

I get the follwing output:

> *ncopen: filename "/usr/local/mni/data/ABC.mnc": Not a netCDF file*

*miopen: MINC package entry point*


Does anyone know the solution to this issue?

Thank you in advance.


Best,
Lisa

From vladimir.fonov at gmail.com  Thu Apr  1 22:53:15 2010
From: vladimir.fonov at gmail.com (Vladimir Fonov)
Date: Thu, 1 Apr 2010 22:53:15 -0400
Subject: [MINC-users] "Not a netCDF file" error
In-Reply-To: <o2ne2890cba1004011658xd34d0d5cv89a75fa717d5cf8e@mail.gmail.com>
References: <o2ne2890cba1004011658xd34d0d5cv89a75fa717d5cf8e@mail.gmail.com>
Message-ID: <h2jfb3c4431004011953p91dace21i2a1ee57cb29857c2@mail.gmail.com>

Hello,

On Thu, Apr 1, 2010 at 7:58 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> I recently installed MINC.
> (used mni-2006-11-15.tar.gz from http://packages.bic.mni.mcgill.ca/cygwin/)
>
> I can get outputs using the "man" commands, e.g. *man mincinfo*.
> However, when I try to run a certain tool like
>
>> *mincinfo -image_info /usr/local/mni/data/ABC.mnc*
>
> I get the follwing output:
>
>> *ncopen: filename "/usr/local/mni/data/ABC.mnc": Not a netCDF file*
>
> *miopen: MINC package entry point*
>
>
> Does anyone know the solution to this issue?

This looks like you've got minc2 file , and the library that you
installed supports only minc1.

The easy way to check is to use file command, minc1 will be of type
"NetCDF Data Format data" and minc2 will show "Hierarchical Data
Format (version 5) data". You can convert between formats using
mincconvert command.

-- 
Best regards,
 Vladimir S. Fonov ~ v.s.fonov <@> ilmarin.info

From lrisa87 at uw.edu  Fri Apr  2 13:24:41 2010
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 2 Apr 2010 10:24:41 -0700
Subject: [MINC-users] "Not a netCDF file" error
In-Reply-To: <h2jfb3c4431004011953p91dace21i2a1ee57cb29857c2@mail.gmail.com>
References: <o2ne2890cba1004011658xd34d0d5cv89a75fa717d5cf8e@mail.gmail.com> 
	<h2jfb3c4431004011953p91dace21i2a1ee57cb29857c2@mail.gmail.com>
Message-ID: <x2ge2890cba1004021024u2e605a54hb199bca7f1ba6978@mail.gmail.com>

Hi Vladimir,

Thank you for your reply.
Yes, as you've suspected, my minc files were Minc2 files.
Since there isn't a newer version of the precompiled binaries for Cygwin
released on the website, I am trying to install minc-2.0.18.
However, after running the make command, I got the following error:
*make [2]: *** [voxeltoworld.exe] Error1*
*make [2]: leaving directory ''/usr/local/minc-2.0.18'*
*make [1]: *** [all-recursive] Error1*
*make [1]: leaving directory ''/usr/local/minc-2.0.18'*
*make: *** [all] Error2*
*
*
Any tips on how to resolve this problem?

Thanks.


Best,
Lisa


On Thu, Apr 1, 2010 at 7:53 PM, Vladimir Fonov <vladimir.fonov at gmail.com>wrote:

> Hello,
>
> On Thu, Apr 1, 2010 at 7:58 PM, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> > I recently installed MINC.
> > (used mni-2006-11-15.tar.gz from
> http://packages.bic.mni.mcgill.ca/cygwin/)
> >
> > I can get outputs using the "man" commands, e.g. *man mincinfo*.
> > However, when I try to run a certain tool like
> >
> >> *mincinfo -image_info /usr/local/mni/data/ABC.mnc*
> >
> > I get the follwing output:
> >
> >> *ncopen: filename "/usr/local/mni/data/ABC.mnc": Not a netCDF file*
> >
> > *miopen: MINC package entry point*
> >
> >
> > Does anyone know the solution to this issue?
>
> This looks like you've got minc2 file , and the library that you
> installed supports only minc1.
>
> The easy way to check is to use file command, minc1 will be of type
> "NetCDF Data Format data" and minc2 will show "Hierarchical Data
> Format (version 5) data". You can convert between formats using
> mincconvert command.
>
> --
> Best regards,
>  Vladimir S. Fonov ~ v.s.fonov <@> 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  Fri Apr  2 17:29:12 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 3 Apr 2010 08:29:12 +1100
Subject: [MINC-users] "Not a netCDF file" error
In-Reply-To: <x2ge2890cba1004021024u2e605a54hb199bca7f1ba6978@mail.gmail.com>
References: <o2ne2890cba1004011658xd34d0d5cv89a75fa717d5cf8e@mail.gmail.com> 
	<h2jfb3c4431004011953p91dace21i2a1ee57cb29857c2@mail.gmail.com> 
	<x2ge2890cba1004021024u2e605a54hb199bca7f1ba6978@mail.gmail.com>
Message-ID: <s2pd747ed51004021429haec78cbta3e21bb553d79cee@mail.gmail.com>

Hi Lisa,

I have almost finished a new MINC 2.x build for all the minc tools on
Cygwin. I will let you know ASAP when it is done so that you can use
this updated binary cygwin build.

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


On Sat, Apr 3, 2010 at 04:24, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> Hi Vladimir,
>
> Thank you for your reply.
> Yes, as you've suspected, my minc files were Minc2 files.
> Since there isn't a newer version of the precompiled binaries for Cygwin
> released on the website, I am trying to install minc-2.0.18.
> However, after running the make command, I got the following error:
> *make [2]: *** [voxeltoworld.exe] Error1*
> *make [2]: leaving directory ''/usr/local/minc-2.0.18'*
> *make [1]: *** [all-recursive] Error1*
> *make [1]: leaving directory ''/usr/local/minc-2.0.18'*
> *make: *** [all] Error2*

From lrisa87 at uw.edu  Fri Apr  2 17:41:04 2010
From: lrisa87 at uw.edu (Lisa F. Akiyama)
Date: Fri, 2 Apr 2010 14:41:04 -0700
Subject: [MINC-users] "Not a netCDF file" error
In-Reply-To: <s2pd747ed51004021429haec78cbta3e21bb553d79cee@mail.gmail.com>
References: <o2ne2890cba1004011658xd34d0d5cv89a75fa717d5cf8e@mail.gmail.com> 
	<h2jfb3c4431004011953p91dace21i2a1ee57cb29857c2@mail.gmail.com> 
	<x2ge2890cba1004021024u2e605a54hb199bca7f1ba6978@mail.gmail.com> 
	<s2pd747ed51004021429haec78cbta3e21bb553d79cee@mail.gmail.com>
Message-ID: <i2we2890cba1004021441g92a0abacs9ab1f6350038e127@mail.gmail.com>

Hi Andrew,

Thank you for your help!
Looking forward to the new precompiled version!


Best,
Lisa


On Fri, Apr 2, 2010 at 2:29 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Lisa,
>
> I have almost finished a new MINC 2.x build for all the minc tools on
> Cygwin. I will let you know ASAP when it is done so that you can use
> this updated binary cygwin build.
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>
>
> On Sat, Apr 3, 2010 at 04:24, Lisa F. Akiyama <lrisa87 at uw.edu> wrote:
> > Hi Vladimir,
> >
> > Thank you for your reply.
> > Yes, as you've suspected, my minc files were Minc2 files.
> > Since there isn't a newer version of the precompiled binaries for Cygwin
> > released on the website, I am trying to install minc-2.0.18.
> > However, after running the make command, I got the following error:
> > *make [2]: *** [voxeltoworld.exe] Error1*
> > *make [2]: leaving directory ''/usr/local/minc-2.0.18'*
> > *make [1]: *** [all-recursive] Error1*
> > *make [1]: leaving directory ''/usr/local/minc-2.0.18'*
> > *make: *** [all] Error2*
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From burt.crepeault at crulrg.ulaval.ca  Tue Apr  6 08:59:21 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Tue, 6 Apr 2010 08:59:21 -0400
Subject: [MINC-users] inormalize-2.0.18: Volume and model dimensions do not
	match!
In-Reply-To: <ac2a7d1f1003310922hf2c1f29i47ef582544c23265@mail.gmail.com>
References: <ac2a7d1f1003310922hf2c1f29i47ef582544c23265@mail.gmail.com>
Message-ID: <h2gac2a7d1f1004060559k98cb387alc0b8e5452ea3f5b8@mail.gmail.com>

Hi all,

I've recently built the latest MINC suite for OS X and am currently testing
everything. It appears that inormalize's behaviour has changed when using a
model file.

With version 2.0.09:

neon:install:# /opt/MEDICS/EX/etc/minc2/bin/inormalize -clobber -model
colin27.mnc 70.mnc 71.mnc
Reading volume
/Users/burt/Desktop/build/install/70.mnc...............................................................................................................................................................................................................................................................Done
Reading volume /Users/burt/Desktop/build/install/colin27.mncDone
Considering 7536640 voxels (100% of total)
Selected normalization: medianOfRatios
Converting
volume................................................................................................................................................................................................................................................................Done
Converting
volume.....................................................................................................................................................................................Done
Normalizing (0.365348, 0)
CPU time elapsed in inormalize: 1.184
SYS time elapsed in inormalize: 0.117
USR time elapsed in inormalize: 1.459

With version 2.0.18:

neon:install:# inormalize -clobber -model colin27.mnc 70.mnc 71.mnc
Reading volume
/Users/burt/Desktop/build/install/70.mnc...............................................................................................................................................................................................................................................................Done
Reading volume /Users/burt/Desktop/build/install/colin27.mncDone
Considering 7536640 voxels (100% of total)
Selected normalization: medianOfRatios
Volume and model dimensions do not match!

What has changed since version 2.0.09? The changelog doesn't seem to contain
the answer. Is there a reason why we can no longer normalize images whose
dimensions differ from the model? Here are the dimensions for both:

neon:install:# mincinfo 70.mnc colin27.mnc
file: 70.mnc
image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                    256      1.05469     -139.275
    yspace                    256      1.05469     -132.873
    xspace                    115          1.3     -79.0931


file: colin27.mnc
image: unsigned short 0 to 65535
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                    181            1          -72
    yspace                    217            1         -126
    xspace                    181            1          -90

Thanks,

Burt.


-------------
Burt Cr?peault
Centre de recherche de l'universit? Laval - Robert-Giffard
2601 de la Canardi?re, suite F-4400
Qu?bec QC G1J 2G3
418-663-5741, ext 6844

From davids at bic.mni.mcgill.ca  Mon Apr 12 13:02:34 2010
From: davids at bic.mni.mcgill.ca (David Seminowicz)
Date: Mon, 12 Apr 2010 13:02:34 -0400
Subject: [MINC-users] temporal filtering
In-Reply-To: <6fe841c71003241228w63f336c4xcdfec13713c504f9@mail.gmail.com>
References: <003701cac205$1df9b6d0$59ed2470$@mni.mcgill.ca>	
	<6fe841c71003161629w7f2de963k369e5fd3d75271b0@mail.gmail.com>
	<6fe841c71003241228w63f336c4xcdfec13713c504f9@mail.gmail.com>
Message-ID: <001201cada62$07292e70$157b8b50$@mni.mcgill.ca>

Hi Pierre and Michael, this is perfect - thanks!  dave

 

 

 

---------- Forwarded message ----------
From: Pierre Bellec <pierre.bellec at gmail.com>
Date: 2010/3/16
Subject: Re: [MINC-users] temporal filtering
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>


Dear David,

It seems that the response to your post I sent to the minc-users list a
couple of days ago got lost once again. Anyway, Michael kindly pointed at
the NIAK package which works in Matlab or Octave :
http://wiki.bic.mni.mcgill.ca/index.php/NeuroImagingAnalysisKit

To give a bit more details, it implements linear fitting of discrete cosine
(DC) basis. This approach is particularly well adapted to short signals with
poor sampling, e.g. fMRI time series, because it doesn't have marked edges
effect. Matlab also comes with a tool to design various types of filters
(see the signal processing toolbox), but methods such as Butterworth have to
be very carefully designed depending on the type of signals you are trying
to process. 


Back to the NIAK thing, you can directly filter signals in Matlab/Octave
using NIAK_FILTER_TSERIES or apply the filter on MINC or NIFTI 4D volumes
using NIAK_BRICK_TIME_FILTER. Type "help niak_brick_time_filter" on the
matlab/octave command line for more infos.

Hope this helps,

Pierre Bellec
Post-doctoral fellow
McConnel Brain Imaging Center, Webster 2B
Montreal Neurological Institute
3801 University Street         
Montreal, Quebec, Canada H3A 2B4
http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
tel:       (001)(514) 398 5220
fax:      (001)(514) 398 8948



2010/3/12 David Seminowicz <davids at bic.mni.mcgill.ca>

Does anyone have a (Matlab) script or know of good software for applying a


temporal filter (e.g. bandpass) to timecourse datasets?  Thanks, Dave



______________________
David A. Seminowicz, Ph.D.
Postdoctoral Fellow
Alan Edwards Centre for Research on Pain
McGill University
Rm M/19 Strathcona Anatomy & Dentistry
3640 University St.
Montreal, Quebec H3A 2B2



Ph: 514.398.1271
Fax: 514.398.7464



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

 

 


From burt.crepeault at crulrg.ulaval.ca  Tue Apr 13 11:06:42 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Tue, 13 Apr 2010 11:06:42 -0400
Subject: [MINC-users] inormalize-2.0.18: Volume and model dimensions do
	not match!
In-Reply-To: <h2gac2a7d1f1004060559k98cb387alc0b8e5452ea3f5b8@mail.gmail.com>
References: <ac2a7d1f1003310922hf2c1f29i47ef582544c23265@mail.gmail.com>
	<h2gac2a7d1f1004060559k98cb387alc0b8e5452ea3f5b8@mail.gmail.com>
Message-ID: <t2hac2a7d1f1004130806md80facc2od54fe267907104b4@mail.gmail.com>

Anyone?

Burt.



On Tue, Apr 6, 2010 at 08:59, Burt Cr?peault <
burt.crepeault at crulrg.ulaval.ca> wrote:

> Hi all,
>
> I've recently built the latest MINC suite for OS X and am currently testing
> everything. It appears that inormalize's behaviour has changed when using a
> model file.
>
> With version 2.0.09:
>
> neon:install:# /opt/MEDICS/EX/etc/minc2/bin/inormalize -clobber -model
> colin27.mnc 70.mnc 71.mnc
> Reading volume
> /Users/burt/Desktop/build/install/70.mnc...............................................................................................................................................................................................................................................................Done
> Reading volume /Users/burt/Desktop/build/install/colin27.mncDone
> Considering 7536640 voxels (100% of total)
> Selected normalization: medianOfRatios
> Converting
> volume................................................................................................................................................................................................................................................................Done
> Converting
> volume.....................................................................................................................................................................................Done
> Normalizing (0.365348, 0)
> CPU time elapsed in inormalize: 1.184
> SYS time elapsed in inormalize: 0.117
> USR time elapsed in inormalize: 1.459
>
> With version 2.0.18:
>
> neon:install:# inormalize -clobber -model colin27.mnc 70.mnc 71.mnc
> Reading volume
> /Users/burt/Desktop/build/install/70.mnc...............................................................................................................................................................................................................................................................Done
> Reading volume /Users/burt/Desktop/build/install/colin27.mncDone
> Considering 7536640 voxels (100% of total)
> Selected normalization: medianOfRatios
> Volume and model dimensions do not match!
>
> What has changed since version 2.0.09? The changelog doesn't seem to
> contain the answer. Is there a reason why we can no longer normalize images
> whose dimensions differ from the model? Here are the dimensions for both:
>
>
> neon:install:# mincinfo 70.mnc colin27.mnc
> file: 70.mnc
> image: unsigned short 0 to 65535
> image dimensions: zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     zspace                    256      1.05469     -139.275
>     yspace                    256      1.05469     -132.873
>     xspace                    115          1.3     -79.0931
>
>
> file: colin27.mnc
> image: unsigned short 0 to 65535
> image dimensions: zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     zspace                    181            1          -72
>     yspace                    217            1         -126
>     xspace                    181            1          -90
>
> Thanks,
>
> Burt.
>
>
> -------------
> Burt Cr?peault
> Centre de recherche de l'universit? Laval - Robert-Giffard
> 2601 de la Canardi?re, suite F-4400
> Qu?bec QC G1J 2G3
> 418-663-5741, ext 6844
>

From alex at bic.mni.mcgill.ca  Tue Apr 13 11:26:01 2010
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Tue, 13 Apr 2010 11:26:01 -0400
Subject: [MINC-users] inormalize-2.0.18: Volume and model dimensions do
	not match!
In-Reply-To: <t2hac2a7d1f1004130806md80facc2od54fe267907104b4@mail.gmail.com>
References: <ac2a7d1f1003310922hf2c1f29i47ef582544c23265@mail.gmail.com>
	<h2gac2a7d1f1004060559k98cb387alc0b8e5452ea3f5b8@mail.gmail.com>
	<t2hac2a7d1f1004130806md80facc2od54fe267907104b4@mail.gmail.com>
Message-ID: <x2je758a6651004130826ld5b40a0bt6b761a390a559e3b@mail.gmail.com>

Hi Burt,

Well, I am not sure why in your case the behaviour (or at least the
error message) has changed; but I am pretty sure that inormalize never
supported volumes and models with different dimensions, as it works
entirely in the voxel domain. I think the problem (perhaps now in the
past) has been that it silently "worked" anyways, but I think it is
unlikely that you actually got the results you were expecting.

Internally, it will pull out the voxels into a linear array (or
arrays) and then operate on those - so the only way it would actually
work correctly is if *all* input volumes are sampled on the same
lattice - at least in cases where it does some kind of voxel-by-voxel
operation such as medianOfRatios (for ratioOfMedians for instance it
probably won't matter, as it would not need to perform a
voxel-by-voxel operation).

If you can still reproduce this (looks like you are), I would try and
resample the volumes to the same lattice (mincresample -nearest -like)
and re-run the "old" inormalize you have; my guess is that the result
would be different.

Rule of thumb would be to always make sure your volumes are sampled
the same way (and inormalize *should* warn you if they are not, like
it now appears to do).

-- A

On Tue, Apr 13, 2010 at 11:06 AM, Burt Cr?peault
<burt.crepeault at crulrg.ulaval.ca> wrote:
> Anyone?
>
> Burt.
>
>
>
> On Tue, Apr 6, 2010 at 08:59, Burt Cr?peault <
> burt.crepeault at crulrg.ulaval.ca> wrote:
>
>> Hi all,
>>
>> I've recently built the latest MINC suite for OS X and am currently testing
>> everything. It appears that inormalize's behaviour has changed when using a
>> model file.
>>
>> With version 2.0.09:
>>
>> neon:install:# /opt/MEDICS/EX/etc/minc2/bin/inormalize -clobber -model
>> colin27.mnc 70.mnc 71.mnc
>> Reading volume
>> /Users/burt/Desktop/build/install/70.mnc...............................................................................................................................................................................................................................................................Done
>> Reading volume /Users/burt/Desktop/build/install/colin27.mncDone
>> Considering 7536640 voxels (100% of total)
>> Selected normalization: medianOfRatios
>> Converting
>> volume................................................................................................................................................................................................................................................................Done
>> Converting
>> volume.....................................................................................................................................................................................Done
>> Normalizing (0.365348, 0)
>> CPU time elapsed in inormalize: 1.184
>> SYS time elapsed in inormalize: 0.117
>> USR time elapsed in inormalize: 1.459
>>
>> With version 2.0.18:
>>
>> neon:install:# inormalize -clobber -model colin27.mnc 70.mnc 71.mnc
>> Reading volume
>> /Users/burt/Desktop/build/install/70.mnc...............................................................................................................................................................................................................................................................Done
>> Reading volume /Users/burt/Desktop/build/install/colin27.mncDone
>> Considering 7536640 voxels (100% of total)
>> Selected normalization: medianOfRatios
>> Volume and model dimensions do not match!
>>
>> What has changed since version 2.0.09? The changelog doesn't seem to
>> contain the answer. Is there a reason why we can no longer normalize images
>> whose dimensions differ from the model? Here are the dimensions for both:
>>
>>
>> neon:install:# mincinfo 70.mnc colin27.mnc
>> file: 70.mnc
>> image: unsigned short 0 to 65535
>> image dimensions: zspace yspace xspace
>> ? ? dimension name ? ? ? ? length ? ? ? ? step ? ? ? ?start
>> ? ? -------------- ? ? ? ? ------ ? ? ? ? ---- ? ? ? ?-----
>> ? ? zspace ? ? ? ? ? ? ? ? ? ?256 ? ? ?1.05469 ? ? -139.275
>> ? ? yspace ? ? ? ? ? ? ? ? ? ?256 ? ? ?1.05469 ? ? -132.873
>> ? ? xspace ? ? ? ? ? ? ? ? ? ?115 ? ? ? ? ?1.3 ? ? -79.0931
>>
>>
>> file: colin27.mnc
>> image: unsigned short 0 to 65535
>> image dimensions: zspace yspace xspace
>> ? ? dimension name ? ? ? ? length ? ? ? ? step ? ? ? ?start
>> ? ? -------------- ? ? ? ? ------ ? ? ? ? ---- ? ? ? ?-----
>> ? ? zspace ? ? ? ? ? ? ? ? ? ?181 ? ? ? ? ? ?1 ? ? ? ? ?-72
>> ? ? yspace ? ? ? ? ? ? ? ? ? ?217 ? ? ? ? ? ?1 ? ? ? ? -126
>> ? ? xspace ? ? ? ? ? ? ? ? ? ?181 ? ? ? ? ? ?1 ? ? ? ? ?-90
>>
>> Thanks,
>>
>> Burt.
>>
>>
>> -------------
>> Burt Cr?peault
>> Centre de recherche de l'universit? Laval - Robert-Giffard
>> 2601 de la Canardi?re, suite F-4400
>> Qu?bec QC G1J 2G3
>> 418-663-5741, ext 6844
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From mishkind at gmail.com  Fri Apr 16 18:33:06 2010
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Fri, 16 Apr 2010 18:33:06 -0400
Subject: [MINC-users] bicpl documentation
Message-ID: <w2u9c5abb61004161533u7edbdbd6qf25d3f2566b8d3f0@mail.gmail.com>

Hello,
There used to be some documentation on bicpl here:
http://www.bic.mni.mcgill.ca/software/bicpl/
If I recall it was created with doxygen.

i realize that the bicpl library has probably changed a lot so
a) is there a new online documentation source? if not:
b) is /libraries/bicpl/Documentation in cvs up to date? and if so
c) how do I use the files in  /libraries/bicpl/Documentation

thanks,
mishkin

From mishkind at gmail.com  Fri Apr 16 18:59:33 2010
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Fri, 16 Apr 2010 18:59:33 -0400
Subject: [MINC-users] bicpl documentation
In-Reply-To: <w2u9c5abb61004161533u7edbdbd6qf25d3f2566b8d3f0@mail.gmail.com>
References: <w2u9c5abb61004161533u7edbdbd6qf25d3f2566b8d3f0@mail.gmail.com>
Message-ID: <p2x9c5abb61004161559g1bbb34c6t7082e39a55b322d2@mail.gmail.com>

On Fri, Apr 16, 2010 at 6:33 PM, Mishkin Derakhshan <mishkind at gmail.com> wrote:
> Hello,
> There used to be some documentation on bicpl here:
> http://www.bic.mni.mcgill.ca/software/bicpl/
> If I recall it was created with doxygen.
>
> i realize that the bicpl library has probably changed a lot so
> a) is there a new online documentation source? if not:
> b) is /libraries/bicpl/Documentation in cvs up to date? and if so
> c) how do I use the files in ?/libraries/bicpl/Documentation

Thanks to ACV for helping me install doxygen and its dependencies and
getting c) to work.
For those interested:

sudo apt-get install graphviz libtool doxygen
cd /libraries/bicpl/
./autogen.sh
./configure --with-build-path=/usr/local/bic/ --with-minc2
cd Documentation/
make dox
firefox html/index.html

Now about a) and b)...

>
> thanks,
> mishkin
>

From tasso.zoidis at gmail.com  Sat Apr 24 09:11:24 2010
From: tasso.zoidis at gmail.com (Tasso)
Date: Sat, 24 Apr 2010 09:11:24 -0400
Subject: [MINC-users] Building minc 2.0.18 on Slackware 13.0
Message-ID: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com>

Hello,

I'm trying to build a minc2 version 2.0.18 installation package for
Slackware 13..0 because my roommate, who studies at McGill University
doing his PhD to become an orthophonist, will need minc2nii for his
research. I'm building him a laptop with all the software he will
need, like audacity, or praat. I have successfully installed hdf5
version 1.8.4 patch 1 and netcdf version 4.0.1. So when I run my build
script, I get the following error:

configure: WARNING: unrecognized options: --enable-minc2

This is the ./configure section of my script:

./configure \
 --prefix=/usr \
 --mandir=/usr/man \
 --libdir=/usr/lib${LIBDIRSUFFIX} \
 --docdir=/usr/doc/$PRGNAM-$VERSION \
 --localstatedir=/var \
 --sysconfdir=/etc \
 --includedir=/usr/local/include \
 --bindir=/usr/bin \
 --sbindir=/sbin \
 --with-build-path=/usr/local \
 --enable-minc2 \
--enable-static \
 --disable-shared \
 --build=$ARCH-slackware-linux

I would like to know if there is something I aint doing right... If
you need the complete source to the .SlackBuild script I can supply it
no problem.

Thanks,
Tasso

From vladimir.fonov at gmail.com  Sat Apr 24 16:51:04 2010
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Sat, 24 Apr 2010 16:51:04 -0400
Subject: [MINC-users] Building minc 2.0.18 on Slackware 13.0
In-Reply-To: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com>
References: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com>
Message-ID: <4BD359B8.8090109@gmail.com>

Hello,

Tasso wrote:
> version 1.8.4 patch 1 and netcdf version 4.0.1. So when I run my build
> script, I get the following error:
> 
> configure: WARNING: unrecognized options: --enable-minc2
> 
> This is the ./configure section of my script:

just remove --enable-minc2 from your configure section.


From tasso.zoidis at gmail.com  Sat Apr 24 17:31:22 2010
From: tasso.zoidis at gmail.com (Tasso)
Date: Sat, 24 Apr 2010 17:31:22 -0400
Subject: [MINC-users] Building minc 2.0.18 on Slackware 13.0
In-Reply-To: <4BD359B8.8090109@gmail.com>
References: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com>
	<4BD359B8.8090109@gmail.com>
Message-ID: <x2tee2e95971004241431ue91c4d0dibcc576a965e36ae7@mail.gmail.com>

Ok I did so and it wont compile.

It seems I need version 3.6.1 of netcdf and version 1.6.6 of hdf5. Is that true?



On Sat, Apr 24, 2010 at 4:51 PM, Vladimir S. Fonov
<vladimir.fonov at gmail.com> wrote:
> Hello,
>
> Tasso wrote:
>>
>> version 1.8.4 patch 1 and netcdf version 4.0.1. So when I run my build
>> script, I get the following error:
>>
>> configure: WARNING: unrecognized options: --enable-minc2
>>
>> This is the ./configure section of my script:
>
> just remove --enable-minc2 from your configure section.
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Sat Apr 24 18:39:14 2010
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Sat, 24 Apr 2010 18:39:14 -0400
Subject: [MINC-users] Building minc 2.0.18 on Slackware 13.0
In-Reply-To: <x2tee2e95971004241431ue91c4d0dibcc576a965e36ae7@mail.gmail.com>
References: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com>	<4BD359B8.8090109@gmail.com>
	<x2tee2e95971004241431ue91c4d0dibcc576a965e36ae7@mail.gmail.com>
Message-ID: <4BD37312.6020705@gmail.com>

Hello,

Tasso wrote:
> Ok I did so and it wont compile.
> 
> It seems I need version 3.6.1 of netcdf and version 1.6.6 of hdf5. Is that true?
Ahh, yes HDF5 version 1.6.10 and netcdf 3.6.3 definetly works. Hdf5 
1.8.x is expected to be supported in next minc version.

-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com

From pgravel at bic.mni.mcgill.ca  Wed Apr 28 22:14:51 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 28 Apr 2010 22:14:51 -0400 (EDT)
Subject: [MINC-users]  Skeleton for reading and writing a MINC file
In-Reply-To: <4BD37312.6020705@gmail.com>
References: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com>
	<4BD359B8.8090109@gmail.com>
	<x2tee2e95971004241431ue91c4d0dibcc576a965e36ae7@mail.gmail.com>
	<4BD37312.6020705@gmail.com>
Message-ID: <Pine.LNX.4.64.1004282210280.3746@grumio.bic.mni.mcgill.ca>

Dear All,

I would like to transfer certain matlab scripts (currently using emma 
tools) to c code, and I was wondering if anyone would have a skeleton c 
program to read and write a minc file (minc1 or minc2 whichever is 
better), or if there is a web site explaining how to do this...

Thanking you very much in advance!

Best Regards,

Paul


From a.janke at gmail.com  Wed Apr 28 22:19:58 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 29 Apr 2010 12:19:58 +1000
Subject: [MINC-users] Skeleton for reading and writing a MINC file
In-Reply-To: <Pine.LNX.4.64.1004282210280.3746@grumio.bic.mni.mcgill.ca>
References: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com> 
	<4BD359B8.8090109@gmail.com>
	<x2tee2e95971004241431ue91c4d0dibcc576a965e36ae7@mail.gmail.com>
	<4BD37312.6020705@gmail.com>
	<Pine.LNX.4.64.1004282210280.3746@grumio.bic.mni.mcgill.ca>
Message-ID: <p2rd747ed51004281919ib1099f08t563f6e735ce217f7@mail.gmail.com>

Hi Paul,

> I would like to transfer certain matlab scripts (currently using emma tools)
> to c code, and I was wondering if anyone would have a skeleton c program to
> read and write a minc file (minc1 or minc2 whichever is better), or if there
> is a web site explaining how to do this...

Have a look at the tutorials here:

   http://en.wikibooks.org/wiki/MINC/Tutorials

There are a few "hello world" type examples. Vladimir Fonov has also
written an EZMINC wrapper that might interest you:

   http://en.wikibooks.org/wiki/MINC/EZMINC

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

From waveflux at gmail.com  Wed Apr 28 22:32:02 2010
From: waveflux at gmail.com (Tom Tom)
Date: Wed, 28 Apr 2010 22:32:02 -0400
Subject: [MINC-users] Automatic way to flip brains?
Message-ID: <z2l33a8bd31004281932u838d2a34h1309e67ad88c61bc@mail.gmail.com>

Hi everyone,

I have a few minc files that have brains that are upside down so i'm
wondering if there is an automated way to flip them 180 degrees?

thanks in advance!
Tom Beaudry

From a.janke at gmail.com  Wed Apr 28 22:36:50 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 29 Apr 2010 12:36:50 +1000
Subject: [MINC-users] Automatic way to flip brains?
In-Reply-To: <z2l33a8bd31004281932u838d2a34h1309e67ad88c61bc@mail.gmail.com>
References: <z2l33a8bd31004281932u838d2a34h1309e67ad88c61bc@mail.gmail.com>
Message-ID: <r2ud747ed51004281936g79ca8b25m92e97a410be12cd8@mail.gmail.com>

Hi Tom

On Thu, Apr 29, 2010 at 12:32, Tom Tom <waveflux at gmail.com> wrote:
> I have a few minc files that have brains that are upside down so i'm
> wondering if there is an automated way to flip them 180 degrees?

I have a dirty little perl script to do this:

  http://mavis.anu.edu.au/scripts/volflip

Use it like this:

   $ volflip -z <in.mnc> <out.mnc>

Be careful when doing things like this that you don't mess with any
direction cosines in your volume. volflip will most certainly not do
what you expect if you wish to retain this information.


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

From waveflux at gmail.com  Wed Apr 28 22:48:34 2010
From: waveflux at gmail.com (Tom Tom)
Date: Wed, 28 Apr 2010 22:48:34 -0400
Subject: [MINC-users] Automatic way to flip brains?
In-Reply-To: <r2ud747ed51004281936g79ca8b25m92e97a410be12cd8@mail.gmail.com>
References: <z2l33a8bd31004281932u838d2a34h1309e67ad88c61bc@mail.gmail.com>
	<r2ud747ed51004281936g79ca8b25m92e97a410be12cd8@mail.gmail.com>
Message-ID: <s2u33a8bd31004281948h5022003bu73831149b9b4e27a@mail.gmail.com>

thanks a lot Andrew!

i'll give it a try :)

Tom

On Wed, Apr 28, 2010 at 10:36 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Tom
>
> On Thu, Apr 29, 2010 at 12:32, Tom Tom <waveflux at gmail.com> wrote:
>> I have a few minc files that have brains that are upside down so i'm
>> wondering if there is an automated way to flip them 180 degrees?
>
> I have a dirty little perl script to do this:
>
> ?http://mavis.anu.edu.au/scripts/volflip
>
> Use it like this:
>
> ? $ volflip -z <in.mnc> <out.mnc>
>
> Be careful when doing things like this that you don't mess with any
> direction cosines in your volume. volflip will most certainly not do
> what you expect if you wish to retain this information.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->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  Thu Apr 29 07:00:19 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 29 Apr 2010 21:00:19 +1000
Subject: [MINC-users] bicpl documentation
In-Reply-To: <p2x9c5abb61004161559g1bbb34c6t7082e39a55b322d2@mail.gmail.com>
References: <w2u9c5abb61004161533u7edbdbd6qf25d3f2566b8d3f0@mail.gmail.com> 
	<p2x9c5abb61004161559g1bbb34c6t7082e39a55b322d2@mail.gmail.com>
Message-ID: <q2pd747ed51004290400yaba8e153ya3024d04c2cfa002@mail.gmail.com>

>> a) is there a new online documentation source? if not:
>> b) is /libraries/bicpl/Documentation in cvs up to date? and if so

> Now about a) and b)...

a) I am moving (and updating) everything I find to here:

   http://en.wikibooks.org/wiki/MINC

b) As up to date as anything else


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

From pgravel at bic.mni.mcgill.ca  Thu Apr 29 14:39:26 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Thu, 29 Apr 2010 14:39:26 -0400 (EDT)
Subject: [MINC-users] Skeleton for reading and writing a MINC file
In-Reply-To: <p2rd747ed51004281919ib1099f08t563f6e735ce217f7@mail.gmail.com>
References: <h2zee2e95971004240611g33536490pdd8cbf4e196a6b22@mail.gmail.com>
	<4BD359B8.8090109@gmail.com>
	<x2tee2e95971004241431ue91c4d0dibcc576a965e36ae7@mail.gmail.com>
	<4BD37312.6020705@gmail.com>
	<Pine.LNX.4.64.1004282210280.3746@grumio.bic.mni.mcgill.ca>
	<p2rd747ed51004281919ib1099f08t563f6e735ce217f7@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1004291438230.17123@grumio.bic.mni.mcgill.ca>

Thanks Andrew!

I had a quick look at the links, and it seems to be just what I'm looking 
for; I shall give it a try!

Best,

Paul


On Thu, 29 Apr 2010, Andrew Janke wrote:

> Hi Paul,
>
>> I would like to transfer certain matlab scripts (currently using emma tools)
>> to c code, and I was wondering if anyone would have a skeleton c program to
>> read and write a minc file (minc1 or minc2 whichever is better), or if there
>> is a web site explaining how to do this...
>
> Have a look at the tutorials here:
>
>   http://en.wikibooks.org/wiki/MINC/Tutorials
>
> There are a few "hello world" type examples. Vladimir Fonov has also
> written an EZMINC wrapper that might interest you:
>
>   http://en.wikibooks.org/wiki/MINC/EZMINC
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From burt.crepeault at crulrg.ulaval.ca  Fri Apr 30 12:21:30 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Fri, 30 Apr 2010 12:21:30 -0400
Subject: [MINC-users] Building Register on Ubuntu
Message-ID: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>

Hi all,

I'm attempting to build version 1.3.6 of Register on Ubuntu 9.10.

I used:

./configure --prefix=$pti --with-build-path=$pti --with-minc2
--x-includes=/usr/include/X11 --x-libraries=/usr/lib/X11

When making, I get:

gcc  -g -O2  -L/Network/MEDICS/EX/etc/minc-2.0.18/lib -o tagtoxfm
tagtoxfm.o ParseArgv.o -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm
-lm  -lm
/Network/MEDICS/EX/etc/minc-2.0.18/lib/libbicpl.a(dgesvd.o): In function
`bicpl_dgesvd_':
/opt/build/source/bicpl-1.4.6/bicpl_clapack/dgesvd.c:235: undefined
reference to `bicpl_ilaenv_'
/opt/build/source/bicpl-1.4.6/bicpl_clapack/dgesvd.c:237: undefined
reference to `bicpl_lsame_'
[ lots more of that ]
collect2: ld returned 1 exit status
make[2]: *** [tagtoxfm] Error 1
make[2]: Leaving directory `/opt/build/source/Register-1.3.6/Tagtoxfm'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/opt/build/source/Register-1.3.6'
make: *** [all] Error 2

I built Display 1.4.2 with the same configure command and it worked;
minc-tools-2.0.18, ebtks-1.6.2 and bicpl-1.4.6 have all successfully been
built and installed in $pti (/Network/MEDICS/EX/etc/minc-2.0.18).

Burt.


-------------
Burt Cr?peault
Centre de recherche de l'universit? Laval - Robert-Giffard
2601 de la Canardi?re, suite F-4400
Qu?bec QC G1J 2G3
418-663-5741, ext 6844

From burt.crepeault at crulrg.ulaval.ca  Fri Apr 30 13:34:18 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Fri, 30 Apr 2010 13:34:18 -0400
Subject: [MINC-users] Building Register on Ubuntu
In-Reply-To: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
Message-ID: <w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>

Ok, forget it, my bad, I forgot to make distclean bicpl before building it
again (it has previously been built for OS X).

However, here's another one for N3:

./configure --prefix=$pti --with-build-path=$pti --with-minc2

make

[...]
g++  -g -O2  -L/Network/MEDICS/EX/etc/minc-2.0.18/lib -o evaluate_field
src/EvaluateField/evaluateField.o src/EvaluateField/evaluateFieldArgs.o
src/SplineSmooth/fieldIO.o libmincprog.a -lvolume_io2 -lminc2 -lhdf5 -lz
-lnetcdf -lm -lEBTKS     -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm
-lEBTKS
/Network/MEDICS/EX/etc/minc-2.0.18/lib/libEBTKS.a(Spline.o): In function
`RSpline::addDataPoint(float const*, double)':
/opt/build/source/ebtks-1.6.2/src/Spline.cc:346: undefined reference to
`Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double> const&)'
/opt/build/source/ebtks-1.6.2/src/Spline.cc:347: undefined reference to
`Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double> const&)'
/Network/MEDICS/EX/etc/minc-2.0.18/lib/libEBTKS.a(Spline.o): In function
`Mat<double>::operator-() const':
/opt/build/source/ebtks-1.6.2/./templates/Matrix.h:486: undefined reference
to `Mat<double>& operator-=<double, double>(Mat<double>&, Mat<double>
const&)'
/Network/MEDICS/EX/etc/minc-2.0.18/lib/libEBTKS.a(Spline.o): In function
`TPSpline::addDataPoint(float const*, double)':
/opt/build/source/ebtks-1.6.2/src/Spline.cc:547: undefined reference to
`Mat<double>& operator-=<double, double>(Mat<double>&, Mat<double> const&)'
/opt/build/source/ebtks-1.6.2/src/Spline.cc:550: undefined reference to
`Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double> const&)'
/opt/build/source/ebtks-1.6.2/src/Spline.cc:551: undefined reference to
`Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double> const&)'
/Network/MEDICS/EX/etc/minc-2.0.18/lib/libEBTKS.a(TBSpline.o): In function
`TBSpline::fit()':
/opt/build/source/ebtks-1.6.2/src/TBSpline.cc:303: undefined reference to
`Mat<double>& operator+=<double, double>(Mat<double>&, Mat<double> const&)'
collect2: ld returned 1 exit status
make[1]: *** [evaluate_field] Error 1
make[1]: Leaving directory `/opt/build/source/N3-1.11.0'
make: *** [all-recursive] Error 1

I made sure I built EBTKS correctly this time... ;)

Am I missing a library?

Burt.



On Fri, Apr 30, 2010 at 12:21, Burt Cr?peault <
burt.crepeault at crulrg.ulaval.ca> wrote:

> Hi all,
>
> I'm attempting to build version 1.3.6 of Register on Ubuntu 9.10.
>
> I used:
>
> ./configure --prefix=$pti --with-build-path=$pti --with-minc2
> --x-includes=/usr/include/X11 --x-libraries=/usr/lib/X11
>
> When making, I get:
>
> gcc  -g -O2  -L/Network/MEDICS/EX/etc/minc-2.0.18/lib -o tagtoxfm
> tagtoxfm.o ParseArgv.o -lbicpl -lvolume_io2 -lminc2 -lhdf5 -lz -lnetcdf -lm
> -lm  -lm
> /Network/MEDICS/EX/etc/minc-2.0.18/lib/libbicpl.a(dgesvd.o): In function
> `bicpl_dgesvd_':
> /opt/build/source/bicpl-1.4.6/bicpl_clapack/dgesvd.c:235: undefined
> reference to `bicpl_ilaenv_'
> /opt/build/source/bicpl-1.4.6/bicpl_clapack/dgesvd.c:237: undefined
> reference to `bicpl_lsame_'
> [ lots more of that ]
> collect2: ld returned 1 exit status
> make[2]: *** [tagtoxfm] Error 1
> make[2]: Leaving directory `/opt/build/source/Register-1.3.6/Tagtoxfm'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/opt/build/source/Register-1.3.6'
> make: *** [all] Error 2
>
> I built Display 1.4.2 with the same configure command and it worked;
> minc-tools-2.0.18, ebtks-1.6.2 and bicpl-1.4.6 have all successfully been
> built and installed in $pti (/Network/MEDICS/EX/etc/minc-2.0.18).
>
> Burt.
>
>
> -------------
> Burt Cr?peault
> Centre de recherche de l'universit? Laval - Robert-Giffard
> 2601 de la Canardi?re, suite F-4400
> Qu?bec QC G1J 2G3
> 418-663-5741, ext 6844
>
>