From a.janke at gmail.com  Sat May  1 07:16:48 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 1 May 2010 21:16:48 +1000
Subject: [MINC-users] Building Register on Ubuntu
In-Reply-To: <w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com> 
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>
Message-ID: <u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com>

Hi Burt,

> /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&)'

This is a problem with EBTKS and versions of g++ greater than 4.2.
You will have to either get the version of EBTKS from CVS or build
with an older version of g++ and then re-link N3 against this.


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

From vladimir.fonov at gmail.com  Sat May  1 15:47:24 2010
From: vladimir.fonov at gmail.com (Vladimir Fonov)
Date: Sat, 1 May 2010 15:47:24 -0400
Subject: [MINC-users] Building Register on Ubuntu
In-Reply-To: <u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com>
Message-ID: <h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>

Hello,

On Sat, May 1, 2010 at 7:16 AM, Andrew Janke <a.janke at gmail.com> wrote:
>> /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&)'
>
> This is a problem with EBTKS and versions of g++ greater than 4.2.
> You will have to either get the version of EBTKS from CVS or build
> with an older version of g++ and then re-link N3 against this.

It's also possible to try this (fixed) version of EBTKS:
http://www.bic.mni.mcgill.ca/~vfonov/software/ebtks-1.6.2.tar.gz


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

From pbellec at bic.mni.mcgill.ca  Mon May  3 22:16:00 2010
From: pbellec at bic.mni.mcgill.ca (Pierre Bellec)
Date: Mon, 3 May 2010 22:16:00 -0400
Subject: [MINC-users] crash related to a long history
Message-ID: <w2w6fe841c71005031916ib5700a66of0d42b7596dfa6ad@mail.gmail.com>

Dear minc-users,

I just ran into the following bug when trying to run the Feb-14-2008
quarantine of CIVET on a T1 minc volume. NU_CORRECT crashed with the
following error :
spawn: exec of minc_modify_header failed: Liste d'arguments trop longue

I checked the history of the file, and found that there was a single
dcm2minc command applied to ... over 3000 files ! Basically the history
looked like :
--- History of subject_mri.mnc ---
[01] Fri Apr 16 17:00:55 2010>>> /usr/local/bic/bin/dcm2mnc \
     /data/dicom/dicom-XXXX-subject_20091004.151045_15_1.dcm \
     /data/dicom/new \
     /data/output_men/
with XXXX going from 0000 to 1993, with every number up to 1220 or so
associated to two files (that rule stopped at something like 1222 which by
itself is a bit puzzling). Note that I modified the path and file name to
remove the name of the study/subject.

I cleared the history by doing :
$ minc_modify_header -sinsert :history='' subject_20091005_151045_16_mri.mnc
and that solved the problem. Voila.

Now I don't know if the "bug" can be attributed to the way dcm2mnc was
invoked (I didn't make the conversion myself so I can't comment much on
that), a limitation of NU_CORRECT or a limitation of the way CIVET modifies
the history. In any case I thought this issue might be of interest for the
MINC users community.

Best regards,

Pierre Bellec, PhD
Chercheur post-doctorant
Centre de recherche de l'institut de G?riatrie de Montr?al
4565, Chemin Queen-Mary
Montr?al (Qu?bec)
H3W 1W5
http://wiki.bic.mni.mcgill.ca/index.php/PierreBellec
tel:       (001)(514) 340 3540 #3367
fax:      (001)(514) 340 3530

From a.janke at gmail.com  Mon May  3 22:35:29 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 4 May 2010 12:35:29 +1000
Subject: [MINC-users] crash related to a long history
In-Reply-To: <w2w6fe841c71005031916ib5700a66of0d42b7596dfa6ad@mail.gmail.com>
References: <w2w6fe841c71005031916ib5700a66of0d42b7596dfa6ad@mail.gmail.com>
Message-ID: <q2gd747ed51005031935v5d4dcbffze488a01edc2cebac@mail.gmail.com>

Hi Pierre,

> I just ran into the following bug when trying to run the Feb-14-2008
> quarantine of CIVET on a T1 minc volume. NU_CORRECT crashed with the
> following error :
> spawn: exec of minc_modify_header failed: Liste d'arguments trop longue
>
> I cleared the history by doing :
> $ minc_modify_header -sinsert :history='' subject_20091005_151045_16_mri.mnc
> and that solved the problem. Voila.

Certainly this has been a problem with nu_correct in the past and you
are right, the only (easy) solution is to reduce the size of the
header. As I remember it is to do with how N3 sets up its output file
via "templating" the original MINC file. Mind you dcm2mnc is known for
making rather enormous headers...  I too have hit the same problem but
attack it with this:

   http://mavis.anu.edu.au/scripts/minc_de-dicomerise

So instead of the "scorched earth" approach this (attempts to) just
remove the dicom parts of a header.


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

From burt.crepeault at crulrg.ulaval.ca  Thu May  6 10:28:11 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Thu, 6 May 2010 10:28:11 -0400
Subject: [MINC-users] Building Register on Ubuntu
In-Reply-To: <h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com> 
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com> 
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com> 
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>
Message-ID: <y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com>

Thanks Vlad, that worked.

Andrew: for the future, what're your CVS connection params?

Burt.




On Sat, May 1, 2010 at 15:47, Vladimir Fonov <vladimir.fonov at gmail.com>wrote:

> Hello,
>
> On Sat, May 1, 2010 at 7:16 AM, Andrew Janke <a.janke at gmail.com> wrote:
> >> /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&)'
> >
> > This is a problem with EBTKS and versions of g++ greater than 4.2.
> > You will have to either get the version of EBTKS from CVS or build
> > with an older version of g++ and then re-link N3 against this.
>
> It's also possible to try this (fixed) version of EBTKS:
> http://www.bic.mni.mcgill.ca/~vfonov/software/ebtks-1.6.2.tar.gz<http://www.bic.mni.mcgill.ca/%7Evfonov/software/ebtks-1.6.2.tar.gz>
>
>
> --
> 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 pgravel at bic.mni.mcgill.ca  Wed May 12 11:26:49 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 12 May 2010 11:26:49 -0400 (EDT)
Subject: [MINC-users]  mincblur removes data:time variable
In-Reply-To: <y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com> 
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com> 
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>
	<y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca>

Dear All,

I am looking into having a csh script to blur a dynamic PET scan. To 
accomplish this, I extract each frame using mincreshape, then blur them 
using mincblur, then finally concatenate (over the time dimension) the 
blurred frames into a blurred dynamic PET. However, it seems that mincblur 
removes the data:time variable, thus resulting in a concatenated blurred 
dynamic PET without the proper frame start time information.
Is there a work around to get the proper time values reinserted in this 
blurred PET scan file?

Many thanks again!

Paul


From a.janke at gmail.com  Wed May 12 11:43:51 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 13 May 2010 01:43:51 +1000
Subject: [MINC-users] mincblur removes data:time variable
In-Reply-To: <Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com> 
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com> 
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com> 
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com> 
	<y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com> 
	<Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca>
Message-ID: <AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D@mail.gmail.com>

Hi Paul,

> I am looking into having a csh script to blur a dynamic PET scan. To
> accomplish this, I extract each frame using mincreshape, then blur them
> using mincblur, then finally concatenate (over the time dimension) the
> blurred frames into a blurred dynamic PET. However, it seems that mincblur
> removes the data:time variable, thus resulting in a concatenated blurred
> dynamic PET without the proper frame start time information.
> Is there a work around to get the proper time values reinserted in this
> blurred PET scan file?

I can only suggest that you first extract the values and then when you
put everything back together (with mincconcat) that you use the
-coordlist option with your extracted time points.


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

From anthonin at biospective.com  Wed May 12 11:48:43 2010
From: anthonin at biospective.com (Anthonin Reilhac)
Date: Wed, 12 May 2010 11:48:43 -0400
Subject: [MINC-users] mincblur removes data:time variable
In-Reply-To: <AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com>
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>
	<y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com>
	<Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca>
	<AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D@mail.gmail.com>
Message-ID: <AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5@mail.gmail.com>

Hi Paul,



I can only suggest that you first extract the values and then when you
> put everything back together (with mincconcat) that you use the
> -coordlist option with your extracted time points.
>
>
> This is what I usually do as well.
I had the same issue with the do_PET_realignement script in which I had to
work on individual frames and concatenate them back in a single dynamic PET
volume.


Anthonin

> --
> 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 pgravel at bic.mni.mcgill.ca  Wed May 12 11:54:05 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 12 May 2010 11:54:05 -0400 (EDT)
Subject: [MINC-users] mincblur removes data:time variable
In-Reply-To: <AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com>
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>
	<y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com>
	<Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca>
	<AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D@mail.gmail.com>
	<AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1005121153460.17382@grumio.bic.mni.mcgill.ca>

Thanks Anthonin and Andrew!

I will give it a try!

Best,

Paul


On Wed, 12 May 2010, Anthonin Reilhac wrote:

> Hi Paul,
>
>
>
> I can only suggest that you first extract the values and then when you
>> put everything back together (with mincconcat) that you use the
>> -coordlist option with your extracted time points.
>>
>>
>> This is what I usually do as well.
> I had the same issue with the do_PET_realignement script in which I had to
> work on individual frames and concatenate them back in a single dynamic PET
> volume.
>
>
> Anthonin
>
>> --
>> 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
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From nikelski at bic.mni.mcgill.ca  Wed May 12 12:30:14 2010
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Wed, 12 May 2010 09:30:14 -0700
Subject: [MINC-users] mincblur removes data:time variable
In-Reply-To: <Pine.LNX.4.64.1005121153460.17382@grumio.bic.mni.mcgill.ca>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com>
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>
	<y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com>
	<Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca>
	<AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D@mail.gmail.com>
	<AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5@mail.gmail.com>
	<Pine.LNX.4.64.1005121153460.17382@grumio.bic.mni.mcgill.ca>
Message-ID: <AANLkTil51sUW0OvUxCPadD3eUgEelFlsKKqZsss_DuW_@mail.gmail.com>

Hi Paul,

   I also ran across this a while ago and created a 4D blurring script
that saves the time info. It's called mincBlur4D ... seems to work
well. I'll try to attach to this e-mail, ... if no-go, I can send it
to you directly.

-Jim


On Wed, May 12, 2010 at 8:54 AM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> Thanks Anthonin and Andrew!
>
> I will give it a try!
>
> Best,
>
> Paul
>
>
> On Wed, 12 May 2010, Anthonin Reilhac wrote:
>
>> Hi Paul,
>>
>>
>>
>> I can only suggest that you first extract the values and then when you
>>>
>>> put everything back together (with mincconcat) that you use the
>>> -coordlist option with your extracted time points.
>>>
>>>
>>> This is what I usually do as well.
>>
>> I had the same issue with the do_PET_realignement script in which I had to
>> work on individual frames and concatenate them back in a single dynamic
>> PET
>> volume.
>>
>>
>> Anthonin
>>
>>> --
>>> 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
>>>
>> _______________________________________________
>> 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
>



-- 
=================================
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 pgravel at bic.mni.mcgill.ca  Wed May 12 12:42:01 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 12 May 2010 12:42:01 -0400 (EDT)
Subject: [MINC-users] mincblur removes data:time variable
In-Reply-To: <AANLkTil51sUW0OvUxCPadD3eUgEelFlsKKqZsss_DuW_@mail.gmail.com>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com>
	<w2uac2a7d1f1004301034xe09127fcu744a709d2a3cc4c7@mail.gmail.com>
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com>
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com>
	<y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com>
	<Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca>
	<AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D@mail.gmail.com>
	<AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5@mail.gmail.com>
	<Pine.LNX.4.64.1005121153460.17382@grumio.bic.mni.mcgill.ca>
	<AANLkTil51sUW0OvUxCPadD3eUgEelFlsKKqZsss_DuW_@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1005121241050.30692@grumio.bic.mni.mcgill.ca>

Hi Jim,

I guess it was a no-go!  If you don't mind I would definitely like to try 
your script.  Could you put it somewhere on the BIC server?

Best,

Paul


On Wed, 12 May 2010, EJ Nikelski wrote:

> Hi Paul,
>
>   I also ran across this a while ago and created a 4D blurring script
> that saves the time info. It's called mincBlur4D ... seems to work
> well. I'll try to attach to this e-mail, ... if no-go, I can send it
> to you directly.
>
> -Jim
>
>
> On Wed, May 12, 2010 at 8:54 AM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> Thanks Anthonin and Andrew!
>>
>> I will give it a try!
>>
>> Best,
>>
>> Paul
>>
>>
>> On Wed, 12 May 2010, Anthonin Reilhac wrote:
>>
>>> Hi Paul,
>>>
>>>
>>>
>>> I can only suggest that you first extract the values and then when you
>>>>
>>>> put everything back together (with mincconcat) that you use the
>>>> -coordlist option with your extracted time points.
>>>>
>>>>
>>>> This is what I usually do as well.
>>>
>>> I had the same issue with the do_PET_realignement script in which I had to
>>> work on individual frames and concatenate them back in a single dynamic
>>> PET
>>> volume.
>>>
>>>
>>> Anthonin
>>>
>>>> --
>>>> 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
>>>>
>>> _______________________________________________
>>> 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
>>
>
>
>
> -- 
> =================================
> 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 a.janke at gmail.com  Wed May 12 18:37:29 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 13 May 2010 08:37:29 +1000
Subject: [MINC-users] mincblur removes data:time variable
In-Reply-To: <Pine.LNX.4.64.1005121241050.30692@grumio.bic.mni.mcgill.ca>
References: <y2gac2a7d1f1004300921s96e1db33z1253e32ce1c3d48c@mail.gmail.com> 
	<u2yd747ed51005010416u12bd4d25uda5951c58681c5b3@mail.gmail.com> 
	<h2hfb3c4431005011247ie323969bz8ec280b6327e34ea@mail.gmail.com> 
	<y2zac2a7d1f1005060728u2065a5e2jae7eef61d946397@mail.gmail.com> 
	<Pine.LNX.4.64.1005121121210.9617@grumio.bic.mni.mcgill.ca> 
	<AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D@mail.gmail.com> 
	<AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5@mail.gmail.com> 
	<Pine.LNX.4.64.1005121153460.17382@grumio.bic.mni.mcgill.ca> 
	<AANLkTil51sUW0OvUxCPadD3eUgEelFlsKKqZsss_DuW_@mail.gmail.com> 
	<Pine.LNX.4.64.1005121241050.30692@grumio.bic.mni.mcgill.ca>
Message-ID: <AANLkTil74OvJ0fML-31UY43twEjZNu_JFNTp1nmegX1L@mail.gmail.com>

The mailing list strips attachments.

If you'd like to email it to me I can put it in the scripts directory
on packages.bic.mni.mcgill.ca or perhaps even include it in the
mincblur package (mni_autoreg).


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


On Thu, May 13, 2010 at 02:42, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> I guess it was a no-go! ?If you don't mind I would definitely like to try
> your script. ?Could you put it somewhere on the BIC server?

From rodell at pet.auh.dk  Thu May 13 10:17:32 2010
From: rodell at pet.auh.dk (Anders Rodell)
Date: Thu, 13 May 2010 16:17:32 +0200
Subject: [MINC-users] MINC-users Digest, Vol 58, Issue 5
In-Reply-To: <mailman.3.1273680002.4858.minc-users@bic.mni.mcgill.ca>
References: <mailman.3.1273680002.4858.minc-users@bic.mni.mcgill.ca>
Message-ID: <AANLkTinMIoJxj88FrsywhxpVdx661luPSs_KT3XEz7dH@mail.gmail.com>

Hi Paul

I might have a small perl script for doing the dynamic blurring of pet
scans, if you are interested ill send it to you and you could use some
of that for your csh script.

 best regards Anders

On Wed, May 12, 2010 at 6:00 PM,  <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. ?mincblur removes data:time variable (Paul GRAVEL)
> ? 2. Re: mincblur removes data:time variable (Andrew Janke)
> ? 3. Re: mincblur removes data:time variable (Anthonin Reilhac)
> ? 4. Re: mincblur removes data:time variable (Paul GRAVEL)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 12 May 2010 11:26:49 -0400 (EDT)
> From: Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> Subject: [MINC-users] ?mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Cc: Paul Gravel - McGill Account <paul.gravel2 at mail.mcgill.ca>
> Message-ID:
> ? ? ? ?<Pine.LNX.4.64.1005121121210.9617 at grumio.bic.mni.mcgill.ca>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Dear All,
>
> I am looking into having a csh script to blur a dynamic PET scan. To
> accomplish this, I extract each frame using mincreshape, then blur them
> using mincblur, then finally concatenate (over the time dimension) the
> blurred frames into a blurred dynamic PET. However, it seems that mincblur
> removes the data:time variable, thus resulting in a concatenated blurred
> dynamic PET without the proper frame start time information.
> Is there a work around to get the proper time values reinserted in this
> blurred PET scan file?
>
> Many thanks again!
>
> Paul
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 13 May 2010 01:43:51 +1000
> From: Andrew Janke <a.janke at gmail.com>
> Subject: Re: [MINC-users] mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
> ? ? ? ?<AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Paul,
>
>> I am looking into having a csh script to blur a dynamic PET scan. To
>> accomplish this, I extract each frame using mincreshape, then blur them
>> using mincblur, then finally concatenate (over the time dimension) the
>> blurred frames into a blurred dynamic PET. However, it seems that mincblur
>> removes the data:time variable, thus resulting in a concatenated blurred
>> dynamic PET without the proper frame start time information.
>> Is there a work around to get the proper time values reinserted in this
>> blurred PET scan file?
>
> I can only suggest that you first extract the values and then when you
> put everything back together (with mincconcat) that you use the
> -coordlist option with your extracted time points.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia ? ?+61 (402) 700 883
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 12 May 2010 11:48:43 -0400
> From: Anthonin Reilhac <anthonin at biospective.com>
> Subject: Re: [MINC-users] mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
> ? ? ? ?<AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Paul,
>
>
>
> I can only suggest that you first extract the values and then when you
>> put everything back together (with mincconcat) that you use the
>> -coordlist option with your extracted time points.
>>
>>
>> This is what I usually do as well.
> I had the same issue with the do_PET_realignement script in which I had to
> work on individual frames and concatenate them back in a single dynamic PET
> volume.
>
>
> Anthonin
>
>> --
>> 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
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 12 May 2010 11:54:05 -0400 (EDT)
> From: Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
> ? ? ? ?<Pine.LNX.4.64.1005121153460.17382 at grumio.bic.mni.mcgill.ca>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Thanks Anthonin and Andrew!
>
> I will give it a try!
>
> Best,
>
> Paul
>
>
> On Wed, 12 May 2010, Anthonin Reilhac wrote:
>
>> Hi Paul,
>>
>>
>>
>> I can only suggest that you first extract the values and then when you
>>> put everything back together (with mincconcat) that you use the
>>> -coordlist option with your extracted time points.
>>>
>>>
>>> This is what I usually do as well.
>> I had the same issue with the do_PET_realignement script in which I had to
>> work on individual frames and concatenate them back in a single dynamic PET
>> volume.
>>
>>
>> Anthonin
>>
>>> --
>>> 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
>>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
> ------------------------------
>
> _______________________________________________
> 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 58, Issue 5
> *****************************************
>



-- 
Anders Bertil Rodell M.Sc. C.S. PhD.
Aarhus PET Centre, Aarhus University Hospital,
Norrebrogade 44, 8000 Aarhus C,
phone work:   +45 89 49 40 97
mobile phone: +45 61 70 85 30
email: rodell at pet.auh.dk

From pgravel at bic.mni.mcgill.ca  Thu May 13 15:53:11 2010
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Thu, 13 May 2010 15:53:11 -0400 (EDT)
Subject: [MINC-users] MINC-users Digest, Vol 58, Issue 5
In-Reply-To: <AANLkTinMIoJxj88FrsywhxpVdx661luPSs_KT3XEz7dH@mail.gmail.com>
References: <mailman.3.1273680002.4858.minc-users@bic.mni.mcgill.ca>
	<AANLkTinMIoJxj88FrsywhxpVdx661luPSs_KT3XEz7dH@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1005131549090.15725@grumio.bic.mni.mcgill.ca>

Thanks all who replied to this email!

I actually implemented Andrew's and Anthonin's recommendations, and it 
does work. Nevertheless, thanks Anders and Jim for sharing your scripts!

Best,

Paul


On Thu, 13 May 2010, Anders Rodell wrote:

> Hi Paul
>
> I might have a small perl script for doing the dynamic blurring of pet
> scans, if you are interested ill send it to you and you could use some
> of that for your csh script.
>
> best regards Anders
>
> On Wed, May 12, 2010 at 6:00 PM,  <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. ?mincblur removes data:time variable (Paul GRAVEL)
>> ? 2. Re: mincblur removes data:time variable (Andrew Janke)
>> ? 3. Re: mincblur removes data:time variable (Anthonin Reilhac)
>> ? 4. Re: mincblur removes data:time variable (Paul GRAVEL)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 12 May 2010 11:26:49 -0400 (EDT)
>> From: Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>> Subject: [MINC-users] ?mincblur removes data:time variable
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Cc: Paul Gravel - McGill Account <paul.gravel2 at mail.mcgill.ca>
>> Message-ID:
>> ? ? ? ?<Pine.LNX.4.64.1005121121210.9617 at grumio.bic.mni.mcgill.ca>
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>> Dear All,
>>
>> I am looking into having a csh script to blur a dynamic PET scan. To
>> accomplish this, I extract each frame using mincreshape, then blur them
>> using mincblur, then finally concatenate (over the time dimension) the
>> blurred frames into a blurred dynamic PET. However, it seems that mincblur
>> removes the data:time variable, thus resulting in a concatenated blurred
>> dynamic PET without the proper frame start time information.
>> Is there a work around to get the proper time values reinserted in this
>> blurred PET scan file?
>>
>> Many thanks again!
>>
>> Paul
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 13 May 2010 01:43:51 +1000
>> From: Andrew Janke <a.janke at gmail.com>
>> Subject: Re: [MINC-users] mincblur removes data:time variable
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Message-ID:
>> ? ? ? ?<AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi Paul,
>>
>>> I am looking into having a csh script to blur a dynamic PET scan. To
>>> accomplish this, I extract each frame using mincreshape, then blur them
>>> using mincblur, then finally concatenate (over the time dimension) the
>>> blurred frames into a blurred dynamic PET. However, it seems that mincblur
>>> removes the data:time variable, thus resulting in a concatenated blurred
>>> dynamic PET without the proper frame start time information.
>>> Is there a work around to get the proper time values reinserted in this
>>> blurred PET scan file?
>>
>> I can only suggest that you first extract the values and then when you
>> put everything back together (with mincconcat) that you use the
>> -coordlist option with your extracted time points.
>>
>>
>> --
>> Andrew Janke
>> (a.janke at gmail.com || http://a.janke.googlepages.com/)
>> Canberra->Australia ? ?+61 (402) 700 883
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Wed, 12 May 2010 11:48:43 -0400
>> From: Anthonin Reilhac <anthonin at biospective.com>
>> Subject: Re: [MINC-users] mincblur removes data:time variable
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Message-ID:
>> ? ? ? ?<AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5 at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi Paul,
>>
>>
>>
>> I can only suggest that you first extract the values and then when you
>>> put everything back together (with mincconcat) that you use the
>>> -coordlist option with your extracted time points.
>>>
>>>
>>> This is what I usually do as well.
>> I had the same issue with the do_PET_realignement script in which I had to
>> work on individual frames and concatenate them back in a single dynamic PET
>> volume.
>>
>>
>> Anthonin
>>
>>> --
>>> 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
>>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Wed, 12 May 2010 11:54:05 -0400 (EDT)
>> From: Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>> Subject: Re: [MINC-users] mincblur removes data:time variable
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Message-ID:
>> ? ? ? ?<Pine.LNX.4.64.1005121153460.17382 at grumio.bic.mni.mcgill.ca>
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>> Thanks Anthonin and Andrew!
>>
>> I will give it a try!
>>
>> Best,
>>
>> Paul
>>
>>
>> On Wed, 12 May 2010, Anthonin Reilhac wrote:
>>
>>> Hi Paul,
>>>
>>>
>>>
>>> I can only suggest that you first extract the values and then when you
>>>> put everything back together (with mincconcat) that you use the
>>>> -coordlist option with your extracted time points.
>>>>
>>>>
>>>> This is what I usually do as well.
>>> I had the same issue with the do_PET_realignement script in which I had to
>>> work on individual frames and concatenate them back in a single dynamic PET
>>> volume.
>>>
>>>
>>> Anthonin
>>>
>>>> --
>>>> 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
>>>>
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> 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 58, Issue 5
>> *****************************************
>>
>
>
>
> -- 
> Anders Bertil Rodell M.Sc. C.S. PhD.
> Aarhus PET Centre, Aarhus University Hospital,
> Norrebrogade 44, 8000 Aarhus C,
> phone work:   +45 89 49 40 97
> mobile phone: +45 61 70 85 30
> email: rodell at pet.auh.dk
> _______________________________________________
> 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 May 14 14:20:37 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Fri, 14 May 2010 14:20:37 -0400
Subject: [MINC-users] Pink Register
Message-ID: <AANLkTinukK8JlKf-TNz0xvxBXMhldn2Wfc-zqm6AYF7n@mail.gmail.com>

Hi all,

I just noticed after building Register-1.3.6 on OS X 64-bits that the user
interface's colors are off: the whole window is in shades of pink and red,
including the voxel area. Any idea why this is? This is what I used to
configure the build:

./configure LDFLAGS="-dylib_file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib"
CFLAGS="-O2 -arch x86_64 -m64 -isysroot /Developer/SDKs/MacOSX10.5.sdk
-mmacosx-version-min=10.5" CXXFLAGS="-O2 -arch x86_64 -m64 -isysroot
/Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5" --prefix=$pti
--with-build-path=$pti --with-minc2 --with-apple-opengl-framework

I got plenty of this kind of warning during the configure, don't know if
it's related:

config.status: creating User_interface/input/Makefile
config.status: WARNING:  User_interface/input/Makefile.in seems to ignore
the --datarootdir setting
config.status: creating User_interface/layout/Makefile
config.status: WARNING:  User_interface/layout/Makefile.in seems to ignore
the --datarootdir setting
config.status: creating User_interface/main/Makefile
config.status: WARNING:  User_interface/main/Makefile.in seems to ignore the
--datarootdir setting


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 nikelski at bic.mni.mcgill.ca  Fri May 14 15:18:46 2010
From: nikelski at bic.mni.mcgill.ca (EJ Nikelski)
Date: Fri, 14 May 2010 12:18:46 -0700
Subject: [MINC-users] Pink Register
In-Reply-To: <AANLkTinukK8JlKf-TNz0xvxBXMhldn2Wfc-zqm6AYF7n@mail.gmail.com>
References: <AANLkTinukK8JlKf-TNz0xvxBXMhldn2Wfc-zqm6AYF7n@mail.gmail.com>
Message-ID: <AANLkTilJW_t50tRVWE8UOMVNtE9Gipd_Xc1ucsgBmilI@mail.gmail.com>

Hi Burt,

   What, you don't like a colorful display? :)  I suspect that you're
encountering the same problem that I had a few months ago. Bottom line
- it's a problem with minc-2.0.17/18.  Claude solved my problem by
having me build against the cvs version (2.0.19).  I've included the
e-mail that was sent out to the list at the time.

-jim


Hi mincy list,

  OK, we have a solution.  Claude provided me with a version of
minc-2.0.19 from cvs head, which fixes my problem.  So, for any of you
Mac users who are *not* experiencing this problem because your tools
were built on top of minc-2.0.16 (or less), hold off rebuilding until
minc-2.0.19 gets released.  Perhaps we can hope for a Christmas
release of minc?

-Jim



On Tue, Dec 8, 2009 at 8:26 PM, EJ Nikelski <nikelski at bic.mni.mcgill.ca> wrote:
- Hide quoted text -
> Hi all,
>
>   I'm currently rebuilding my minc tools under OS X (10.5.8) in
> preparation for a cold and windy winter.  All of the bits and pieces
> build without much complaint, but whenever I launch Register or
> Display, all of the windows have a distinct pink-ish, purple-ish hue.
> Festive yes! ... but not what I really need right now.
>
>  Any ideas?  I thought that it might be due to recent changes in the
> bicpl, however rebuilding with older bicpl versions makes no
> difference.  Has anyone seen this before?
>
> -Jim
>
> --
> =================================
> 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
>



--
=================================
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

On Fri, May 14, 2010 at 11:20 AM, Burt Cr?peault
<burt.crepeault at crulrg.ulaval.ca> wrote:
> Hi all,
>
> I just noticed after building Register-1.3.6 on OS X 64-bits that the user
> interface's colors are off: the whole window is in shades of pink and red,
> including the voxel area. Any idea why this is? This is what I used to
> configure the build:
>
> ./configure LDFLAGS="-dylib_file
> /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib"
> CFLAGS="-O2 -arch x86_64 -m64 -isysroot /Developer/SDKs/MacOSX10.5.sdk
> -mmacosx-version-min=10.5" CXXFLAGS="-O2 -arch x86_64 -m64 -isysroot
> /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5" --prefix=$pti
> --with-build-path=$pti --with-minc2 --with-apple-opengl-framework
>
> I got plenty of this kind of warning during the configure, don't know if
> it's related:
>
> config.status: creating User_interface/input/Makefile
> config.status: WARNING: ?User_interface/input/Makefile.in seems to ignore
> the --datarootdir setting
> config.status: creating User_interface/layout/Makefile
> config.status: WARNING: ?User_interface/layout/Makefile.in seems to ignore
> the --datarootdir setting
> config.status: creating User_interface/main/Makefile
> config.status: WARNING: ?User_interface/main/Makefile.in seems to ignore the
> --datarootdir setting
>
>
> 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
>



-- 
=================================
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 alex at bic.mni.mcgill.ca  Sun May 16 13:32:16 2010
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Sun, 16 May 2010 13:32:16 -0400
Subject: [MINC-users] mincblur and single slices
Message-ID: <AANLkTinDZ2QHvI1w-p8mA5qlFhm6gzHSJgPjEr9LaXvl@mail.gmail.com>

I ran into a number of mincblur oddities when dealing with
single-slice minc volumes. For example, I have a single-slice image
that, when blurred with:

   mincblur -no_apodize -dim 2 -fwhm 1 <in.mnc> <out>

generates the expected result; However, when I happened to convert the
datatype of that same slice from byte to short ran the same mincblur
call, the result suffered from a wraparound effect. See the image at

   http://dl.dropbox.com/u/5709165/mincblur/test_blur.jpg

with the underlying data in

   http://dl.dropbox.com/u/5709165/mincblur/test_blur.tar.gz

I have also seen such wraparound effects appear as a function of image
dimensions (regardless of data type). So from what I can tell mincblur
is broken when it comes to dealing with single-slice data; but broken
in a somewhat unpredictable way because in certain circumstances it
will actually do the right thing (as in the 'byte' example I gave).
Padding the image with a slice above and below will make the problem
from this example go away; but again, I am not sure how the failures
depend on the number of slices added.

Is anybody familiar enough with the innards of mincblur to address
this issue? Ideally it would be fixed such as to allow proper 2D
blurring on single-slice volumes; but barring that, it would be good
if at least it generated an error as opposed to silently and
unpredictably doing the right or wrong thing.

Thanks,

-- Alex

From burt.crepeault at crulrg.ulaval.ca  Mon May 17 11:48:15 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Mon, 17 May 2010 11:48:15 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
Message-ID: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com>

Hi all,

Can't wait to get this OS X 64-bit build going... Man this is tough...
(sigh)

Ok, so this time, it's nu_correct that doesn't run, giving an Assertion
failed at line 32 in file templates/Pool.cc:

neon:Darwin:# nu_correct -clobber -verbose -mapping_dir
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/  -iterations 100
-shrink 3 -fwhm 0.1 -distance 100
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.\[mnc.rsh\]\[mnc.dns\].Br.80_p2.mnc.gz
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.\[mnc.rsh\]\[mnc.dns\]\[mnc.nuc\].Br.70_p2.mnc

[nu_correct] [ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:56]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/nu_estimate_np_and_em -parzen
-log -sharpen 0.1 0.01 -iterations 100 -stop 0.001 -shrink 3 -auto_mask
-nonotify -b_spline 1.0e-7 -distance 100 -verbose -execute -clobber
-nokeeptmp -tmpdir /var/tmp/nu_correct_39946/
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2.imp

Uncorrected volume (input):
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
Intensity mapping (output):
/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2.imp

# Start of NU estimation algorithm
[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:56]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincresample -clobber -verbose
-nearest_neighbour -nelements 61 86 86 -step 3 3 3
'/Network/MEDICS/B/images/13671/bl/MR.T1.MP-RAGE/1034/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz'
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'
Transforming
slices:......................................................................................Done

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58] /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincmath
-clobber -verbose -clamp -const2 1 1.7e+308
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc.temp'
Processing:......................................................................................Done

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincmath -clobber -verbose
-zero -log
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc.temp'
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc'
Processing:......................................................................................Done

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58] /bin/rm
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns][mnc.nuc].Br.70_p2_log.mnc.temp'

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58] /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/mincinfo
-attvalue xspace:spacetype -attvalue yspace:spacetype -attvalue
zspace:spacetype
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'

[nu_estimate_np_and_em]
[ex at neon.crulrg.local:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin]
[2010-05-17 10:12:58]
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/bin/volume_stats -quiet -biModalT
'/var/tmp/nu_correct_39946/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc'
Assertion failed at line 32 in file templates/Pool.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination
status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)

That last part attemps to run volume_stats so I gave it a try all by itself:

neon:Darwin:# volume_stats
Assertion failed at line 32 in file templates/Pool.cc

I believe that Pool.cc file belongs to EBTKS, I'm using version 1.6.2. I
checked the output generated during its build, no apparent problem there. I
built it again, just to make sure, and did the same for N3. Everything went
well but the failed assertion error persists.

The relevant section of Pool.cc is:

    26    template <class Type>
    27    Pool<Type>::Pool(unsigned nElements)
    28    : _elementSize(sizeof(Type)),
    29      _expansionSize(nElements),
    30      _blocks(_POOL_N_BLOCKS)
    31    {
    32      assert(_elementSize >= sizeof(_Link *));
    33      assert(nElements);
    34      _head = 0;
    35    }
    36

Any ideas?

Thanks again,

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 a.janke at gmail.com  Mon May 17 11:56:25 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 18 May 2010 01:56:25 +1000
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com>
Message-ID: <AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com>

> Can't wait to get this OS X 64-bit build going... Man this is tough...
> (sigh)

Welcome to the EBTKS ornery beast! :)  Well actually that probably
isn't fair on Alex, it's at least half C++'s fault for continually
changing the spec!.  (but I digress...)

> neon:Darwin:# volume_stats
> Assertion failed at line 32 in file templates/Pool.cc
>
> I believe that Pool.cc file belongs to EBTKS, I'm using version 1.6.2. I
> checked the output generated during its build, no apparent problem there. I
> built it again, just to make sure, and did the same for N3. Everything went
> well but the failed assertion error persists.

> Any ideas?

And this is just running volume_stats by itself?  ie: it was trying to
produce the -help output?


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

From burt.crepeault at crulrg.ulaval.ca  Mon May 17 12:12:02 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Mon, 17 May 2010 12:12:02 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com> 
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com>
Message-ID: <AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com>

I've put the original file here:
https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz

Andrew: yes, running a dry volume_stats command still fails.

Burt.




On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com> wrote:

> > Can't wait to get this OS X 64-bit build going... Man this is tough...
> > (sigh)
>
> Welcome to the EBTKS ornery beast! :)  Well actually that probably
> isn't fair on Alex, it's at least half C++'s fault for continually
> changing the spec!.  (but I digress...)
>
> > neon:Darwin:# volume_stats
> > Assertion failed at line 32 in file templates/Pool.cc
> >
> > I believe that Pool.cc file belongs to EBTKS, I'm using version 1.6.2. I
> > checked the output generated during its build, no apparent problem there.
> I
> > built it again, just to make sure, and did the same for N3. Everything
> went
> > well but the failed assertion error persists.
>
> > Any ideas?
>
> And this is just running volume_stats by itself?  ie: it was trying to
> produce the -help output?
>
>
> --
> 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  Mon May 17 12:19:54 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 18 May 2010 02:19:54 +1000
Subject: [MINC-users] mincblur and single slices
In-Reply-To: <AANLkTinDZ2QHvI1w-p8mA5qlFhm6gzHSJgPjEr9LaXvl@mail.gmail.com>
References: <AANLkTinDZ2QHvI1w-p8mA5qlFhm6gzHSJgPjEr9LaXvl@mail.gmail.com>
Message-ID: <AANLkTinv4N0SohLvny2axWpLlQ23IZ9EvcG0r-FfSKk2@mail.gmail.com>

Hi Alex,

> I have also seen such wraparound effects appear as a function of image
> dimensions (regardless of data type). So from what I can tell mincblur
> is broken when it comes to dealing with single-slice data; but broken
> in a somewhat unpredictable way because in certain circumstances it
> will actually do the right thing (as in the 'byte' example I gave).
> Padding the image with a slice above and below will make the problem
> from this example go away; but again, I am not sure how the failures
> depend on the number of slices added.

Louis wrote mincblur and used an FFT to do the blurring, thus there is
a fair bit of dimension re-ordering going on before and after the
blur. From my looking in the code of mincblur regarding this I suspect
there is a hardcoded dimension name going wrong somewhere in
pathological cases. Especially if these are MINC 2 files and apparent
dimension ordering is being used...

Would this match your experience or is this happening with older
netcdf based MINC files also?


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

From acveilleux at mrs.mni.mcgill.ca  Mon May 17 12:31:29 2010
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Mon, 17 May 2010 12:31:29 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com>
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com>
	<AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com>
Message-ID: <20100517163129.GC29312@mrs.mni.mcgill.ca>

I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
environment (Mac OS X 10.5.8, most of the libs as per the package I made
last year, minc 2.0.15). 

1.10.1 with 1.6.1 works for me
1.11.0 with 1.6.1 works for me
1.11.0 with 1.6.2 works for me

Where works for me means: (a) -help works and (b) it prints out the
stats of a random minc file I had on hand.

I used this to build both tools:

./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch x86_64 -m64" \
--prefix=//localscratch/compile/newtemp \
--with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
--with-minc2

/locascratch/compile/newtemp is where I built the new EBTKS.


This is very annoying,

Alex

On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> Date: Mon, 17 May 2010 12:12:02 -0400
> From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> 
> I've put the original file here:
> https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> 
> Andrew: yes, running a dry volume_stats command still fails.
> 
> Burt.
> 
> 
> 
> 
> On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com> wrote:
> 
> > > Can't wait to get this OS X 64-bit build going... Man this is tough...
> > > (sigh)
> >
> > Welcome to the EBTKS ornery beast! :)  Well actually that probably
> > isn't fair on Alex, it's at least half C++'s fault for continually
> > changing the spec!.  (but I digress...)
> >
> > > neon:Darwin:# volume_stats
> > > Assertion failed at line 32 in file templates/Pool.cc
> > >
> > > I believe that Pool.cc file belongs to EBTKS, I'm using version 1.6.2. I
> > > checked the output generated during its build, no apparent problem there.
> > I
> > > built it again, just to make sure, and did the same for N3. Everything
> > went
> > > well but the failed assertion error persists.
> >
> > > Any ideas?
> >
> > And this is just running volume_stats by itself?  ie: it was trying to
> > produce the -help output?
> >
> >
> > --
> > 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
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From alex at bic.mni.mcgill.ca  Mon May 17 12:56:37 2010
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Mon, 17 May 2010 12:56:37 -0400
Subject: [MINC-users] mincblur and single slices
In-Reply-To: <AANLkTinv4N0SohLvny2axWpLlQ23IZ9EvcG0r-FfSKk2@mail.gmail.com>
References: <AANLkTinDZ2QHvI1w-p8mA5qlFhm6gzHSJgPjEr9LaXvl@mail.gmail.com>
	<AANLkTinv4N0SohLvny2axWpLlQ23IZ9EvcG0r-FfSKk2@mail.gmail.com>
Message-ID: <AANLkTikm8Al2GNdFE0HouqclOE0pWD7K7Kvn97MSuDEI@mail.gmail.com>

On Mon, May 17, 2010 at 12:19 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Alex,
>
>> I have also seen such wraparound effects appear as a function of image
>> dimensions (regardless of data type). So from what I can tell mincblur
>> is broken when it comes to dealing with single-slice data; but broken
>> in a somewhat unpredictable way because in certain circumstances it
>> will actually do the right thing (as in the 'byte' example I gave).
>> Padding the image with a slice above and below will make the problem
>> from this example go away; but again, I am not sure how the failures
>> depend on the number of slices added.
>
> Louis wrote mincblur and used an FFT to do the blurring, thus there is
> a fair bit of dimension re-ordering going on before and after the
> blur. From my looking in the code of mincblur regarding this I suspect
> there is a hardcoded dimension name going wrong somewhere in
> pathological cases. Especially if these are MINC 2 files and apparent
> dimension ordering is being used...
>
> Would this match your experience or is this happening with older
> netcdf based MINC files also?

Not sure - I never tried with older netcdf volumes :) But I just
converted my test images to minc1/netcdf and ran the same mincblur
commands - same result. That may not be the test you were looking for
- if you think it useful I suppose I could dig out an old netcdf
volume and simulate the same scenario?

Also, Claude suggested it might be an issue of version; but I get the
same results both with 0.99.3 and 0.99.6.

-- A

From burt.crepeault at crulrg.ulaval.ca  Mon May 17 13:47:24 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Mon, 17 May 2010 13:47:24 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <20100517163129.GC29312@mrs.mni.mcgill.ca>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com> 
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com> 
	<AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com> 
	<20100517163129.GC29312@mrs.mni.mcgill.ca>
Message-ID: <AANLkTilo5aOsA7eyK9qHQJcZ5slNQTZWDXRD43aXkPsz@mail.gmail.com>

Ah, new builds, old libs... I used the exact same compiler flags, as per
your recommendations, so everything should work. Perhaps I should try
another build using 2.0.15 as a basis. Still, it'd be nice to know what the
problem is with 2.0.18.

Burt.




On Mon, May 17, 2010 at 12:31, Alexandre CARMEL-VEILLEUX <
acveilleux at mrs.mni.mcgill.ca> wrote:

> I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
> environment (Mac OS X 10.5.8, most of the libs as per the package I made
> last year, minc 2.0.15).
>
> 1.10.1 with 1.6.1 works for me
> 1.11.0 with 1.6.1 works for me
> 1.11.0 with 1.6.2 works for me
>
> Where works for me means: (a) -help works and (b) it prints out the
> stats of a random minc file I had on hand.
>
> I used this to build both tools:
>
> ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch x86_64 -m64"
> \
> --prefix=//localscratch/compile/newtemp \
> --with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
> --with-minc2
>
> /locascratch/compile/newtemp is where I built the new EBTKS.
>
>
> This is very annoying,
>
> Alex
>
> On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> > Date: Mon, 17 May 2010 12:12:02 -0400
> > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >
> > I've put the original file here:
> >
> https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> >
> > Andrew: yes, running a dry volume_stats command still fails.
> >
> > Burt.
> >
> >
> >
> >
> > On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com> wrote:
> >
> > > > Can't wait to get this OS X 64-bit build going... Man this is
> tough...
> > > > (sigh)
> > >
> > > Welcome to the EBTKS ornery beast! :)  Well actually that probably
> > > isn't fair on Alex, it's at least half C++'s fault for continually
> > > changing the spec!.  (but I digress...)
> > >
> > > > neon:Darwin:# volume_stats
> > > > Assertion failed at line 32 in file templates/Pool.cc
> > > >
> > > > I believe that Pool.cc file belongs to EBTKS, I'm using version
> 1.6.2. I
> > > > checked the output generated during its build, no apparent problem
> there.
> > > I
> > > > built it again, just to make sure, and did the same for N3.
> Everything
> > > went
> > > > well but the failed assertion error persists.
> > >
> > > > Any ideas?
> > >
> > > And this is just running volume_stats by itself?  ie: it was trying to
> > > produce the -help output?
> > >
> > >
> > > --
> > > 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
> > >
> > _______________________________________________
> > 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 acveilleux at mrs.mni.mcgill.ca  Mon May 17 14:11:42 2010
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Mon, 17 May 2010 14:11:42 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <AANLkTilo5aOsA7eyK9qHQJcZ5slNQTZWDXRD43aXkPsz@mail.gmail.com>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com>
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com>
	<AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com>
	<20100517163129.GC29312@mrs.mni.mcgill.ca>
	<AANLkTilo5aOsA7eyK9qHQJcZ5slNQTZWDXRD43aXkPsz@mail.gmail.com>
Message-ID: <20100517181142.GD29312@mrs.mni.mcgill.ca>

What's the exact platform you're building on?

I'm using:

uname -a:
Darwin mrspc.bic.mni.mcgill.ca 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

gcc:
mrspc [/localscratch/compile/newtemp/bin] gcc --version
i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)

I've just built this tool line from scratch and it works:

minc 2.0.18
ebtks 1.6.2
N3 1.11.0


It's all very weird.

Alex

Extraneous output:



mrspc [/localscratch/compile/newtemp/bin] strings
/localscratch/compile/newtemp/lib/libminc2.1.dylib | grep '2\.0\.'
2.0.18
mrspc [/localscratch/compile/newtemp/bin] otool -L volume_stats
volume_stats:
        /localscratch/compile/newtemp/lib/libvolume_io2.1.dylib (compatibility version 3.0.0, current version 3.2.0)
        /localscratch/compile/newtemp/lib/libminc2.1.dylib (compatibility version 3.0.0, current version 3.2.0)
        /usr/local/lib/libhdf5.0.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)
        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.4.0)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
mrspc [/localscratch/compile/newtemp/bin] volume_stats -version
The program <volume_stats> was built from:
Package MNI N3, version 1.11.0, compiled by acveilleux at mrspc.bic.mni.mcgill.ca (i686-apple-darwin9.8.0) on 2010-05-17 at 14:03:52



On Mon, May 17, 2010 at 01:47:24PM -0400, Burt Cr?peault wrote:
> Date: Mon, 17 May 2010 13:47:24 -0400
> From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> 
> Ah, new builds, old libs... I used the exact same compiler flags, as per
> your recommendations, so everything should work. Perhaps I should try
> another build using 2.0.15 as a basis. Still, it'd be nice to know what the
> problem is with 2.0.18.
> 
> Burt.
> 
> 
> 
> 
> On Mon, May 17, 2010 at 12:31, Alexandre CARMEL-VEILLEUX <
> acveilleux at mrs.mni.mcgill.ca> wrote:
> 
> > I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
> > environment (Mac OS X 10.5.8, most of the libs as per the package I made
> > last year, minc 2.0.15).
> >
> > 1.10.1 with 1.6.1 works for me
> > 1.11.0 with 1.6.1 works for me
> > 1.11.0 with 1.6.2 works for me
> >
> > Where works for me means: (a) -help works and (b) it prints out the
> > stats of a random minc file I had on hand.
> >
> > I used this to build both tools:
> >
> > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch x86_64 -m64"
> > \
> > --prefix=//localscratch/compile/newtemp \
> > --with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
> > --with-minc2
> >
> > /locascratch/compile/newtemp is where I built the new EBTKS.
> >
> >
> > This is very annoying,
> >
> > Alex
> >
> > On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> > > Date: Mon, 17 May 2010 12:12:02 -0400
> > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > >
> > > I've put the original file here:
> > >
> > https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> > >
> > > Andrew: yes, running a dry volume_stats command still fails.
> > >
> > > Burt.
> > >
> > >
> > >
> > >
> > > On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com> wrote:
> > >
> > > > > Can't wait to get this OS X 64-bit build going... Man this is
> > tough...
> > > > > (sigh)
> > > >
> > > > Welcome to the EBTKS ornery beast! :)  Well actually that probably
> > > > isn't fair on Alex, it's at least half C++'s fault for continually
> > > > changing the spec!.  (but I digress...)
> > > >
> > > > > neon:Darwin:# volume_stats
> > > > > Assertion failed at line 32 in file templates/Pool.cc
> > > > >
> > > > > I believe that Pool.cc file belongs to EBTKS, I'm using version
> > 1.6.2. I
> > > > > checked the output generated during its build, no apparent problem
> > there.
> > > > I
> > > > > built it again, just to make sure, and did the same for N3.
> > Everything
> > > > went
> > > > > well but the failed assertion error persists.
> > > >
> > > > > Any ideas?
> > > >
> > > > And this is just running volume_stats by itself?  ie: it was trying to
> > > > produce the -help output?
> > > >
> > > >
> > > > --
> > > > 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
> > > >
> > > _______________________________________________
> > > 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 burt.crepeault at crulrg.ulaval.ca  Mon May 17 14:36:05 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Mon, 17 May 2010 14:36:05 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <20100517181142.GD29312@mrs.mni.mcgill.ca>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com> 
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com> 
	<AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com> 
	<20100517163129.GC29312@mrs.mni.mcgill.ca>
	<AANLkTilo5aOsA7eyK9qHQJcZ5slNQTZWDXRD43aXkPsz@mail.gmail.com> 
	<20100517181142.GD29312@mrs.mni.mcgill.ca>
Message-ID: <AANLkTiloVG2x3yyylHDlC6Q3nWuALML2Xrq87zzHWHO-@mail.gmail.com>

Must be a case of bad fingers then because everything below appears very
similar.

One difference I can see is that yours doesn't list EBTKS as a library of
volume_stats. Also, I built all the dependencies (libz, netcdf, hdf5)
directly in the build path with the same prefix directive. To allow
everything to work, I must set DYLD_LIBRARY_PATH and PERL5LIB as such:

# echo $DYLD_LIBRARY_PATH
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib

# echo $PERL5LIB
/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/Library/Perl/Updates/5.8.8:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/perl5/site_perl/5.8.8/darwin-thread-multi-2level

# uname -a
Darwin beryllium.crulrg.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386

# gcc --version
i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)

# strings /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib |
grep '2\.0\.'
2.0.18

# otool -L volume_stats
volume_stats:
    /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libvolume_io2.1.dylib
(compatibility version 3.0.0, current version 3.2.0)
    /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
(compatibility version 3.0.0, current version 3.2.0)
    /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libhdf5.0.dylib
(compatibility version 1.0.0, current version 1.0.0)
    /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libz.1.dylib
(compatibility version 1.0.0, current version 1.2.5)
    /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libnetcdf.4.dylib
(compatibility version 5.0.0, current version 5.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
111.0.0)
    /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libEBTKS.0.dylib
(compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
7.4.0)
    /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
1.0.0)

# volume_stats -version
Assertion failed at line 32 in file templates/Pool.cc

Burt.




On Mon, May 17, 2010 at 14:11, Alexandre CARMEL-VEILLEUX <
acveilleux at mrs.mni.mcgill.ca> wrote:

> What's the exact platform you're building on?
>
> I'm using:
>
> uname -a:
> Darwin mrspc.bic.mni.mcgill.ca 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul
> 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
>
> gcc:
> mrspc [/localscratch/compile/newtemp/bin] gcc --version
> i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
>
> I've just built this tool line from scratch and it works:
>
> minc 2.0.18
> ebtks 1.6.2
> N3 1.11.0
>
>
> It's all very weird.
>
> Alex
>
> Extraneous output:
>
>
>
> mrspc [/localscratch/compile/newtemp/bin] strings
> /localscratch/compile/newtemp/lib/libminc2.1.dylib | grep '2\.0\.'
> 2.0.18
> mrspc [/localscratch/compile/newtemp/bin] otool -L volume_stats
> volume_stats:
>        /localscratch/compile/newtemp/lib/libvolume_io2.1.dylib
> (compatibility version 3.0.0, current version 3.2.0)
>        /localscratch/compile/newtemp/lib/libminc2.1.dylib (compatibility
> version 3.0.0, current version 3.2.0)
>        /usr/local/lib/libhdf5.0.dylib (compatibility version 1.0.0, current
> version 1.0.0)
>        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
> 1.2.3)
>        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version 111.1.4)
>        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> version 7.4.0)
>        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> version 1.0.0)
> mrspc [/localscratch/compile/newtemp/bin] volume_stats -version
> The program <volume_stats> was built from:
> Package MNI N3, version 1.11.0, compiled by
> acveilleux at mrspc.bic.mni.mcgill.ca (i686-apple-darwin9.8.0) on 2010-05-17
> at 14:03:52
>
>
>
> On Mon, May 17, 2010 at 01:47:24PM -0400, Burt Cr?peault wrote:
> > Date: Mon, 17 May 2010 13:47:24 -0400
> > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >
> > Ah, new builds, old libs... I used the exact same compiler flags, as per
> > your recommendations, so everything should work. Perhaps I should try
> > another build using 2.0.15 as a basis. Still, it'd be nice to know what
> the
> > problem is with 2.0.18.
> >
> > Burt.
> >
> >
> >
> >
> > On Mon, May 17, 2010 at 12:31, Alexandre CARMEL-VEILLEUX <
> > acveilleux at mrs.mni.mcgill.ca> wrote:
> >
> > > I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
> > > environment (Mac OS X 10.5.8, most of the libs as per the package I
> made
> > > last year, minc 2.0.15).
> > >
> > > 1.10.1 with 1.6.1 works for me
> > > 1.11.0 with 1.6.1 works for me
> > > 1.11.0 with 1.6.2 works for me
> > >
> > > Where works for me means: (a) -help works and (b) it prints out the
> > > stats of a random minc file I had on hand.
> > >
> > > I used this to build both tools:
> > >
> > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch x86_64
> -m64"
> > > \
> > > --prefix=//localscratch/compile/newtemp \
> > > --with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
> > > --with-minc2
> > >
> > > /locascratch/compile/newtemp is where I built the new EBTKS.
> > >
> > >
> > > This is very annoying,
> > >
> > > Alex
> > >
> > > On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> > > > Date: Mon, 17 May 2010 12:12:02 -0400
> > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > >
> > > > I've put the original file here:
> > > >
> > >
> https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> > > >
> > > > Andrew: yes, running a dry volume_stats command still fails.
> > > >
> > > > Burt.
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com>
> wrote:
> > > >
> > > > > > Can't wait to get this OS X 64-bit build going... Man this is
> > > tough...
> > > > > > (sigh)
> > > > >
> > > > > Welcome to the EBTKS ornery beast! :)  Well actually that probably
> > > > > isn't fair on Alex, it's at least half C++'s fault for continually
> > > > > changing the spec!.  (but I digress...)
> > > > >
> > > > > > neon:Darwin:# volume_stats
> > > > > > Assertion failed at line 32 in file templates/Pool.cc
> > > > > >
> > > > > > I believe that Pool.cc file belongs to EBTKS, I'm using version
> > > 1.6.2. I
> > > > > > checked the output generated during its build, no apparent
> problem
> > > there.
> > > > > I
> > > > > > built it again, just to make sure, and did the same for N3.
> > > Everything
> > > > > went
> > > > > > well but the failed assertion error persists.
> > > > >
> > > > > > Any ideas?
> > > > >
> > > > > And this is just running volume_stats by itself?  ie: it was trying
> to
> > > > > produce the -help output?
> > > > >
> > > > >
> > > > > --
> > > > > 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
> > > > >
> > > > _______________________________________________
> > > > 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 acveilleux at mrs.mni.mcgill.ca  Mon May 17 14:42:33 2010
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Mon, 17 May 2010 14:42:33 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <AANLkTiloVG2x3yyylHDlC6Q3nWuALML2Xrq87zzHWHO-@mail.gmail.com>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com>
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com>
	<AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com>
	<20100517163129.GC29312@mrs.mni.mcgill.ca>
	<AANLkTilo5aOsA7eyK9qHQJcZ5slNQTZWDXRD43aXkPsz@mail.gmail.com>
	<20100517181142.GD29312@mrs.mni.mcgill.ca>
	<AANLkTiloVG2x3yyylHDlC6Q3nWuALML2Xrq87zzHWHO-@mail.gmail.com>
Message-ID: <20100517184233.GE29312@mrs.mni.mcgill.ca>

EBTKS is not built as a static library, I link directly to it. Maybe
that's the problem? Because otherwise your environment looks like
mine... I might have skipped a land mine by not dynamically linking
EBTKS.

Alex

On Mon, May 17, 2010 at 02:36:05PM -0400, Burt Cr?peault wrote:
> Date: Mon, 17 May 2010 14:36:05 -0400
> From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> 
> Must be a case of bad fingers then because everything below appears very
> similar.
> 
> One difference I can see is that yours doesn't list EBTKS as a library of
> volume_stats. Also, I built all the dependencies (libz, netcdf, hdf5)
> directly in the build path with the same prefix directive. To allow
> everything to work, I must set DYLD_LIBRARY_PATH and PERL5LIB as such:
> 
> # echo $DYLD_LIBRARY_PATH
> /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib
> 
> # echo $PERL5LIB
> /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/Library/Perl/Updates/5.8.8:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/perl5/site_perl/5.8.8/darwin-thread-multi-2level
> 
> # uname -a
> Darwin beryllium.crulrg.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15
> 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> 
> # gcc --version
> i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> 
> # strings /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib |
> grep '2\.0\.'
> 2.0.18
> 
> # otool -L volume_stats
> volume_stats:
>     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libvolume_io2.1.dylib
> (compatibility version 3.0.0, current version 3.2.0)
>     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
> (compatibility version 3.0.0, current version 3.2.0)
>     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libhdf5.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
>     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libz.1.dylib
> (compatibility version 1.0.0, current version 1.2.5)
>     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libnetcdf.4.dylib
> (compatibility version 5.0.0, current version 5.0.0)
>     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 111.0.0)
>     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libEBTKS.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
>     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
> 7.4.0)
>     /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
> 1.0.0)
> 
> # volume_stats -version
> Assertion failed at line 32 in file templates/Pool.cc
> 
> Burt.
> 
> 
> 
> 
> On Mon, May 17, 2010 at 14:11, Alexandre CARMEL-VEILLEUX <
> acveilleux at mrs.mni.mcgill.ca> wrote:
> 
> > What's the exact platform you're building on?
> >
> > I'm using:
> >
> > uname -a:
> > Darwin mrspc.bic.mni.mcgill.ca 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul
> > 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> >
> > gcc:
> > mrspc [/localscratch/compile/newtemp/bin] gcc --version
> > i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> >
> > I've just built this tool line from scratch and it works:
> >
> > minc 2.0.18
> > ebtks 1.6.2
> > N3 1.11.0
> >
> >
> > It's all very weird.
> >
> > Alex
> >
> > Extraneous output:
> >
> >
> >
> > mrspc [/localscratch/compile/newtemp/bin] strings
> > /localscratch/compile/newtemp/lib/libminc2.1.dylib | grep '2\.0\.'
> > 2.0.18
> > mrspc [/localscratch/compile/newtemp/bin] otool -L volume_stats
> > volume_stats:
> >        /localscratch/compile/newtemp/lib/libvolume_io2.1.dylib
> > (compatibility version 3.0.0, current version 3.2.0)
> >        /localscratch/compile/newtemp/lib/libminc2.1.dylib (compatibility
> > version 3.0.0, current version 3.2.0)
> >        /usr/local/lib/libhdf5.0.dylib (compatibility version 1.0.0, current
> > version 1.0.0)
> >        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version
> > 1.2.3)
> >        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> > version 111.1.4)
> >        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> > version 7.4.0)
> >        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> > version 1.0.0)
> > mrspc [/localscratch/compile/newtemp/bin] volume_stats -version
> > The program <volume_stats> was built from:
> > Package MNI N3, version 1.11.0, compiled by
> > acveilleux at mrspc.bic.mni.mcgill.ca (i686-apple-darwin9.8.0) on 2010-05-17
> > at 14:03:52
> >
> >
> >
> > On Mon, May 17, 2010 at 01:47:24PM -0400, Burt Cr?peault wrote:
> > > Date: Mon, 17 May 2010 13:47:24 -0400
> > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > >
> > > Ah, new builds, old libs... I used the exact same compiler flags, as per
> > > your recommendations, so everything should work. Perhaps I should try
> > > another build using 2.0.15 as a basis. Still, it'd be nice to know what
> > the
> > > problem is with 2.0.18.
> > >
> > > Burt.
> > >
> > >
> > >
> > >
> > > On Mon, May 17, 2010 at 12:31, Alexandre CARMEL-VEILLEUX <
> > > acveilleux at mrs.mni.mcgill.ca> wrote:
> > >
> > > > I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
> > > > environment (Mac OS X 10.5.8, most of the libs as per the package I
> > made
> > > > last year, minc 2.0.15).
> > > >
> > > > 1.10.1 with 1.6.1 works for me
> > > > 1.11.0 with 1.6.1 works for me
> > > > 1.11.0 with 1.6.2 works for me
> > > >
> > > > Where works for me means: (a) -help works and (b) it prints out the
> > > > stats of a random minc file I had on hand.
> > > >
> > > > I used this to build both tools:
> > > >
> > > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch x86_64
> > -m64"
> > > > \
> > > > --prefix=//localscratch/compile/newtemp \
> > > > --with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
> > > > --with-minc2
> > > >
> > > > /locascratch/compile/newtemp is where I built the new EBTKS.
> > > >
> > > >
> > > > This is very annoying,
> > > >
> > > > Alex
> > > >
> > > > On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> > > > > Date: Mon, 17 May 2010 12:12:02 -0400
> > > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > > >
> > > > > I've put the original file here:
> > > > >
> > > >
> > https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> > > > >
> > > > > Andrew: yes, running a dry volume_stats command still fails.
> > > > >
> > > > > Burt.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com>
> > wrote:
> > > > >
> > > > > > > Can't wait to get this OS X 64-bit build going... Man this is
> > > > tough...
> > > > > > > (sigh)
> > > > > >
> > > > > > Welcome to the EBTKS ornery beast! :)  Well actually that probably
> > > > > > isn't fair on Alex, it's at least half C++'s fault for continually
> > > > > > changing the spec!.  (but I digress...)
> > > > > >
> > > > > > > neon:Darwin:# volume_stats
> > > > > > > Assertion failed at line 32 in file templates/Pool.cc
> > > > > > >
> > > > > > > I believe that Pool.cc file belongs to EBTKS, I'm using version
> > > > 1.6.2. I
> > > > > > > checked the output generated during its build, no apparent
> > problem
> > > > there.
> > > > > > I
> > > > > > > built it again, just to make sure, and did the same for N3.
> > > > Everything
> > > > > > went
> > > > > > > well but the failed assertion error persists.
> > > > > >
> > > > > > > Any ideas?
> > > > > >
> > > > > > And this is just running volume_stats by itself?  ie: it was trying
> > to
> > > > > > produce the -help output?
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > _______________________________________________
> > > > > 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 burt.crepeault at crulrg.ulaval.ca  Mon May 17 15:37:15 2010
From: burt.crepeault at crulrg.ulaval.ca (=?ISO-8859-1?Q?Burt_Cr=E9peault?=)
Date: Mon, 17 May 2010 15:37:15 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <20100517184233.GE29312@mrs.mni.mcgill.ca>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com> 
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com> 
	<AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com> 
	<20100517163129.GC29312@mrs.mni.mcgill.ca>
	<AANLkTilo5aOsA7eyK9qHQJcZ5slNQTZWDXRD43aXkPsz@mail.gmail.com> 
	<20100517181142.GD29312@mrs.mni.mcgill.ca>
	<AANLkTiloVG2x3yyylHDlC6Q3nWuALML2Xrq87zzHWHO-@mail.gmail.com> 
	<20100517184233.GE29312@mrs.mni.mcgill.ca>
Message-ID: <AANLkTikxDDqimVcsihyBHVnOxAKZqgZVlApjIggZ1GO-@mail.gmail.com>

Well whaddaya know, that was it!

Rebuilt EBTKS static only, rebuilt N3 against it and voil?!

Once again, thank you all for this quick and (almost) painless fix.

By the way, just so that I don't have to build everything again, what other
minc packages use ebtks?

Burt.




On Mon, May 17, 2010 at 14:42, Alexandre CARMEL-VEILLEUX <
acveilleux at mrs.mni.mcgill.ca> wrote:

> EBTKS is not built as a static library, I link directly to it. Maybe
> that's the problem? Because otherwise your environment looks like
> mine... I might have skipped a land mine by not dynamically linking
> EBTKS.
>
> Alex
>
> On Mon, May 17, 2010 at 02:36:05PM -0400, Burt Cr?peault wrote:
> > Date: Mon, 17 May 2010 14:36:05 -0400
> > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >
> > Must be a case of bad fingers then because everything below appears very
> > similar.
> >
> > One difference I can see is that yours doesn't list EBTKS as a library of
> > volume_stats. Also, I built all the dependencies (libz, netcdf, hdf5)
> > directly in the build path with the same prefix directive. To allow
> > everything to work, I must set DYLD_LIBRARY_PATH and PERL5LIB as such:
> >
> > # echo $DYLD_LIBRARY_PATH
> > /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib
> >
> > # echo $PERL5LIB
> >
> /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/Library/Perl/Updates/5.8.8:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/perl5/site_perl/5.8.8/darwin-thread-multi-2level
> >
> > # uname -a
> > Darwin beryllium.crulrg.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul
> 15
> > 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> >
> > # gcc --version
> > i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> >
> > # strings /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
> |
> > grep '2\.0\.'
> > 2.0.18
> >
> > # otool -L volume_stats
> > volume_stats:
> >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libvolume_io2.1.dylib
> > (compatibility version 3.0.0, current version 3.2.0)
> >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
> > (compatibility version 3.0.0, current version 3.2.0)
> >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libhdf5.0.dylib
> > (compatibility version 1.0.0, current version 1.0.0)
> >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libz.1.dylib
> > (compatibility version 1.0.0, current version 1.2.5)
> >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libnetcdf.4.dylib
> > (compatibility version 5.0.0, current version 5.0.0)
> >     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> version
> > 111.0.0)
> >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libEBTKS.0.dylib
> > (compatibility version 1.0.0, current version 1.0.0)
> >     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> version
> > 7.4.0)
> >     /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> version
> > 1.0.0)
> >
> > # volume_stats -version
> > Assertion failed at line 32 in file templates/Pool.cc
> >
> > Burt.
> >
> >
> >
> >
> > On Mon, May 17, 2010 at 14:11, Alexandre CARMEL-VEILLEUX <
> > acveilleux at mrs.mni.mcgill.ca> wrote:
> >
> > > What's the exact platform you're building on?
> > >
> > > I'm using:
> > >
> > > uname -a:
> > > Darwin mrspc.bic.mni.mcgill.ca 9.8.0 Darwin Kernel Version 9.8.0: Wed
> Jul
> > > 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> > >
> > > gcc:
> > > mrspc [/localscratch/compile/newtemp/bin] gcc --version
> > > i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> > >
> > > I've just built this tool line from scratch and it works:
> > >
> > > minc 2.0.18
> > > ebtks 1.6.2
> > > N3 1.11.0
> > >
> > >
> > > It's all very weird.
> > >
> > > Alex
> > >
> > > Extraneous output:
> > >
> > >
> > >
> > > mrspc [/localscratch/compile/newtemp/bin] strings
> > > /localscratch/compile/newtemp/lib/libminc2.1.dylib | grep '2\.0\.'
> > > 2.0.18
> > > mrspc [/localscratch/compile/newtemp/bin] otool -L volume_stats
> > > volume_stats:
> > >        /localscratch/compile/newtemp/lib/libvolume_io2.1.dylib
> > > (compatibility version 3.0.0, current version 3.2.0)
> > >        /localscratch/compile/newtemp/lib/libminc2.1.dylib
> (compatibility
> > > version 3.0.0, current version 3.2.0)
> > >        /usr/local/lib/libhdf5.0.dylib (compatibility version 1.0.0,
> current
> > > version 1.0.0)
> > >        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current
> version
> > > 1.2.3)
> > >        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> > > version 111.1.4)
> > >        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> > > version 7.4.0)
> > >        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> > > version 1.0.0)
> > > mrspc [/localscratch/compile/newtemp/bin] volume_stats -version
> > > The program <volume_stats> was built from:
> > > Package MNI N3, version 1.11.0, compiled by
> > > acveilleux at mrspc.bic.mni.mcgill.ca (i686-apple-darwin9.8.0) on
> 2010-05-17
> > > at 14:03:52
> > >
> > >
> > >
> > > On Mon, May 17, 2010 at 01:47:24PM -0400, Burt Cr?peault wrote:
> > > > Date: Mon, 17 May 2010 13:47:24 -0400
> > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > >
> > > > Ah, new builds, old libs... I used the exact same compiler flags, as
> per
> > > > your recommendations, so everything should work. Perhaps I should try
> > > > another build using 2.0.15 as a basis. Still, it'd be nice to know
> what
> > > the
> > > > problem is with 2.0.18.
> > > >
> > > > Burt.
> > > >
> > > >
> > > >
> > > >
> > > > On Mon, May 17, 2010 at 12:31, Alexandre CARMEL-VEILLEUX <
> > > > acveilleux at mrs.mni.mcgill.ca> wrote:
> > > >
> > > > > I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
> > > > > environment (Mac OS X 10.5.8, most of the libs as per the package I
> > > made
> > > > > last year, minc 2.0.15).
> > > > >
> > > > > 1.10.1 with 1.6.1 works for me
> > > > > 1.11.0 with 1.6.1 works for me
> > > > > 1.11.0 with 1.6.2 works for me
> > > > >
> > > > > Where works for me means: (a) -help works and (b) it prints out the
> > > > > stats of a random minc file I had on hand.
> > > > >
> > > > > I used this to build both tools:
> > > > >
> > > > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch
> x86_64
> > > -m64"
> > > > > \
> > > > > --prefix=//localscratch/compile/newtemp \
> > > > > --with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
> > > > > --with-minc2
> > > > >
> > > > > /locascratch/compile/newtemp is where I built the new EBTKS.
> > > > >
> > > > >
> > > > > This is very annoying,
> > > > >
> > > > > Alex
> > > > >
> > > > > On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> > > > > > Date: Mon, 17 May 2010 12:12:02 -0400
> > > > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion
> failed
> > > > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > > > >
> > > > > > I've put the original file here:
> > > > > >
> > > > >
> > >
> https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> > > > > >
> > > > > > Andrew: yes, running a dry volume_stats command still fails.
> > > > > >
> > > > > > Burt.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com>
> > > wrote:
> > > > > >
> > > > > > > > Can't wait to get this OS X 64-bit build going... Man this is
> > > > > tough...
> > > > > > > > (sigh)
> > > > > > >
> > > > > > > Welcome to the EBTKS ornery beast! :)  Well actually that
> probably
> > > > > > > isn't fair on Alex, it's at least half C++'s fault for
> continually
> > > > > > > changing the spec!.  (but I digress...)
> > > > > > >
> > > > > > > > neon:Darwin:# volume_stats
> > > > > > > > Assertion failed at line 32 in file templates/Pool.cc
> > > > > > > >
> > > > > > > > I believe that Pool.cc file belongs to EBTKS, I'm using
> version
> > > > > 1.6.2. I
> > > > > > > > checked the output generated during its build, no apparent
> > > problem
> > > > > there.
> > > > > > > I
> > > > > > > > built it again, just to make sure, and did the same for N3.
> > > > > Everything
> > > > > > > went
> > > > > > > > well but the failed assertion error persists.
> > > > > > >
> > > > > > > > Any ideas?
> > > > > > >
> > > > > > > And this is just running volume_stats by itself?  ie: it was
> trying
> > > to
> > > > > > > produce the -help output?
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > 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
> > > > > > >
> > > > > > _______________________________________________
> > > > > > 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 acveilleux at mrs.mni.mcgill.ca  Mon May 17 17:02:34 2010
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Mon, 17 May 2010 17:02:34 -0400
Subject: [MINC-users] nu_correct (volume_stats) assertion failed
In-Reply-To: <AANLkTikxDDqimVcsihyBHVnOxAKZqgZVlApjIggZ1GO-@mail.gmail.com>
References: <AANLkTikobjzKkifjiKwz7LE3tQb_7F8khKjHfwMr1glr@mail.gmail.com>
	<AANLkTinYWMpyBPlDi-qi_ZHiHbLi2E8JHnKeMrCUZvuT@mail.gmail.com>
	<AANLkTikQHyNx9YxTbz5Mzp8Sg-e2zaalUU_3NrCor0em@mail.gmail.com>
	<20100517163129.GC29312@mrs.mni.mcgill.ca>
	<AANLkTilo5aOsA7eyK9qHQJcZ5slNQTZWDXRD43aXkPsz@mail.gmail.com>
	<20100517181142.GD29312@mrs.mni.mcgill.ca>
	<AANLkTiloVG2x3yyylHDlC6Q3nWuALML2Xrq87zzHWHO-@mail.gmail.com>
	<20100517184233.GE29312@mrs.mni.mcgill.ca>
	<AANLkTikxDDqimVcsihyBHVnOxAKZqgZVlApjIggZ1GO-@mail.gmail.com>
Message-ID: <20100517210233.GG29312@mrs.mni.mcgill.ca>

Off the top of my head (well, grep really):

N3
classify
inormalize

They're the 3 that have checks for EBTKS in configure.

Alex

On Mon, May 17, 2010 at 03:37:15PM -0400, Burt Cr?peault wrote:
> Date: Mon, 17 May 2010 15:37:15 -0400
> From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> 
> Well whaddaya know, that was it!
> 
> Rebuilt EBTKS static only, rebuilt N3 against it and voil?!
> 
> Once again, thank you all for this quick and (almost) painless fix.
> 
> By the way, just so that I don't have to build everything again, what other
> minc packages use ebtks?
> 
> Burt.
> 
> 
> 
> 
> On Mon, May 17, 2010 at 14:42, Alexandre CARMEL-VEILLEUX <
> acveilleux at mrs.mni.mcgill.ca> wrote:
> 
> > EBTKS is not built as a static library, I link directly to it. Maybe
> > that's the problem? Because otherwise your environment looks like
> > mine... I might have skipped a land mine by not dynamically linking
> > EBTKS.
> >
> > Alex
> >
> > On Mon, May 17, 2010 at 02:36:05PM -0400, Burt Cr?peault wrote:
> > > Date: Mon, 17 May 2010 14:36:05 -0400
> > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > >
> > > Must be a case of bad fingers then because everything below appears very
> > > similar.
> > >
> > > One difference I can see is that yours doesn't list EBTKS as a library of
> > > volume_stats. Also, I built all the dependencies (libz, netcdf, hdf5)
> > > directly in the build path with the same prefix directive. To allow
> > > everything to work, I must set DYLD_LIBRARY_PATH and PERL5LIB as such:
> > >
> > > # echo $DYLD_LIBRARY_PATH
> > > /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib
> > >
> > > # echo $PERL5LIB
> > >
> > /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/Library/Perl/Updates/5.8.8:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/perl5/site_perl/5.8.8/darwin-thread-multi-2level
> > >
> > > # uname -a
> > > Darwin beryllium.crulrg.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul
> > 15
> > > 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> > >
> > > # gcc --version
> > > i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> > >
> > > # strings /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
> > |
> > > grep '2\.0\.'
> > > 2.0.18
> > >
> > > # otool -L volume_stats
> > > volume_stats:
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libvolume_io2.1.dylib
> > > (compatibility version 3.0.0, current version 3.2.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
> > > (compatibility version 3.0.0, current version 3.2.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libhdf5.0.dylib
> > > (compatibility version 1.0.0, current version 1.0.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libz.1.dylib
> > > (compatibility version 1.0.0, current version 1.2.5)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libnetcdf.4.dylib
> > > (compatibility version 5.0.0, current version 5.0.0)
> > >     /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> > version
> > > 111.0.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libEBTKS.0.dylib
> > > (compatibility version 1.0.0, current version 1.0.0)
> > >     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> > version
> > > 7.4.0)
> > >     /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> > version
> > > 1.0.0)
> > >
> > > # volume_stats -version
> > > Assertion failed at line 32 in file templates/Pool.cc
> > >
> > > Burt.
> > >
> > >
> > >
> > >
> > > On Mon, May 17, 2010 at 14:11, Alexandre CARMEL-VEILLEUX <
> > > acveilleux at mrs.mni.mcgill.ca> wrote:
> > >
> > > > What's the exact platform you're building on?
> > > >
> > > > I'm using:
> > > >
> > > > uname -a:
> > > > Darwin mrspc.bic.mni.mcgill.ca 9.8.0 Darwin Kernel Version 9.8.0: Wed
> > Jul
> > > > 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> > > >
> > > > gcc:
> > > > mrspc [/localscratch/compile/newtemp/bin] gcc --version
> > > > i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> > > >
> > > > I've just built this tool line from scratch and it works:
> > > >
> > > > minc 2.0.18
> > > > ebtks 1.6.2
> > > > N3 1.11.0
> > > >
> > > >
> > > > It's all very weird.
> > > >
> > > > Alex
> > > >
> > > > Extraneous output:
> > > >
> > > >
> > > >
> > > > mrspc [/localscratch/compile/newtemp/bin] strings
> > > > /localscratch/compile/newtemp/lib/libminc2.1.dylib | grep '2\.0\.'
> > > > 2.0.18
> > > > mrspc [/localscratch/compile/newtemp/bin] otool -L volume_stats
> > > > volume_stats:
> > > >        /localscratch/compile/newtemp/lib/libvolume_io2.1.dylib
> > > > (compatibility version 3.0.0, current version 3.2.0)
> > > >        /localscratch/compile/newtemp/lib/libminc2.1.dylib
> > (compatibility
> > > > version 3.0.0, current version 3.2.0)
> > > >        /usr/local/lib/libhdf5.0.dylib (compatibility version 1.0.0,
> > current
> > > > version 1.0.0)
> > > >        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current
> > version
> > > > 1.2.3)
> > > >        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> > > > version 111.1.4)
> > > >        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> > > > version 7.4.0)
> > > >        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> > > > version 1.0.0)
> > > > mrspc [/localscratch/compile/newtemp/bin] volume_stats -version
> > > > The program <volume_stats> was built from:
> > > > Package MNI N3, version 1.11.0, compiled by
> > > > acveilleux at mrspc.bic.mni.mcgill.ca (i686-apple-darwin9.8.0) on
> > 2010-05-17
> > > > at 14:03:52
> > > >
> > > >
> > > >
> > > > On Mon, May 17, 2010 at 01:47:24PM -0400, Burt Cr?peault wrote:
> > > > > Date: Mon, 17 May 2010 13:47:24 -0400
> > > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > > >
> > > > > Ah, new builds, old libs... I used the exact same compiler flags, as
> > per
> > > > > your recommendations, so everything should work. Perhaps I should try
> > > > > another build using 2.0.15 as a basis. Still, it'd be nice to know
> > what
> > > > the
> > > > > problem is with 2.0.18.
> > > > >
> > > > > Burt.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Mon, May 17, 2010 at 12:31, Alexandre CARMEL-VEILLEUX <
> > > > > acveilleux at mrs.mni.mcgill.ca> wrote:
> > > > >
> > > > > > I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
> > > > > > environment (Mac OS X 10.5.8, most of the libs as per the package I
> > > > made
> > > > > > last year, minc 2.0.15).
> > > > > >
> > > > > > 1.10.1 with 1.6.1 works for me
> > > > > > 1.11.0 with 1.6.1 works for me
> > > > > > 1.11.0 with 1.6.2 works for me
> > > > > >
> > > > > > Where works for me means: (a) -help works and (b) it prints out the
> > > > > > stats of a random minc file I had on hand.
> > > > > >
> > > > > > I used this to build both tools:
> > > > > >
> > > > > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch
> > x86_64
> > > > -m64"
> > > > > > \
> > > > > > --prefix=//localscratch/compile/newtemp \
> > > > > > --with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
> > > > > > --with-minc2
> > > > > >
> > > > > > /locascratch/compile/newtemp is where I built the new EBTKS.
> > > > > >
> > > > > >
> > > > > > This is very annoying,
> > > > > >
> > > > > > Alex
> > > > > >
> > > > > > On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> > > > > > > Date: Mon, 17 May 2010 12:12:02 -0400
> > > > > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion
> > failed
> > > > > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > > > > >
> > > > > > > I've put the original file here:
> > > > > > >
> > > > > >
> > > >
> > https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> > > > > > >
> > > > > > > Andrew: yes, running a dry volume_stats command still fails.
> > > > > > >
> > > > > > > Burt.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com>
> > > > wrote:
> > > > > > >
> > > > > > > > > Can't wait to get this OS X 64-bit build going... Man this is
> > > > > > tough...
> > > > > > > > > (sigh)
> > > > > > > >
> > > > > > > > Welcome to the EBTKS ornery beast! :)  Well actually that
> > probably
> > > > > > > > isn't fair on Alex, it's at least half C++'s fault for
> > continually
> > > > > > > > changing the spec!.  (but I digress...)
> > > > > > > >
> > > > > > > > > neon:Darwin:# volume_stats
> > > > > > > > > Assertion failed at line 32 in file templates/Pool.cc
> > > > > > > > >
> > > > > > > > > I believe that Pool.cc file belongs to EBTKS, I'm using
> > version
> > > > > > 1.6.2. I
> > > > > > > > > checked the output generated during its build, no apparent
> > > > problem
> > > > > > there.
> > > > > > > > I
> > > > > > > > > built it again, just to make sure, and did the same for N3.
> > > > > > Everything
> > > > > > > > went
> > > > > > > > > well but the failed assertion error persists.
> > > > > > > >
> > > > > > > > > Any ideas?
> > > > > > > >
> > > > > > > > And this is just running volume_stats by itself?  ie: it was
> > trying
> > > > to
> > > > > > > > produce the -help output?
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > 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
> > > > > > > >
> > > > > > > _______________________________________________
> > > > > > > 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
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From claude at bic.mni.mcgill.ca  Mon May 17 17:06:11 2010
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Mon, 17 May 2010 17:06:11 -0400
Subject: [MINC-users] mincblur and single slices
In-Reply-To: <AANLkTinDZ2QHvI1w-p8mA5qlFhm6gzHSJgPjEr9LaXvl@mail.gmail.com>
Message-ID: <201005172106.o4HL6BwE030141@grumio.bic.mni.mcgill.ca>

Hi Alex,

After some investigation, this bug has been fixed. Somewhere deep in
initialize_minc_input_from_minc_id() (file minc/volume_io/Volumes/input_mnc.c),
the new code looks like:

    file->n_slab_dims = 0;
    slab_size = 1;
    int unit_size = get_type_size( get_volume_data_type(volume) );
    int full_dim = 1;

    for( d = file->n_file_dimensions-1; d >= 0; d-- ) {
      if( file->to_volume_index[d] != INVALID_AXIS ) {
        if( MI_MAX_VAR_BUFFER_SIZE > file->sizes_in_file[d] * slab_size * unit_size && full_dim ) {
          slab_size *= file->sizes_in_file[d];
          file->n_slab_dims++;  /* integral number of complete dimensions */
        } else {
          slab_size *= MIN( file->sizes_in_file[d],
                            (hsize_t)( MI_MAX_VAR_BUFFER_SIZE / ( slab_size * unit_size ) ) );
          full_dim = 0;
        }
      }
    }

In comparison, the old code from minc-2.0.18 does not have the full_dim check. 
There is an analogous piece of code in output_mnc.c. Do I really need to explain 
what this cryptic piece of code is doing or can your trust me? The changes are
in CVS:

2009-11-06 Claude Lepage <claude@@bic.mni.mcgill.ca>
   * volume_io/Volumes/output_mnc.c: fix output buffers for a slice
          as only first buffer would be written out

So either checkout minc from cvs or wait till Andrew releases the next version 
(which should be two months ago). :-)

Claude


> I ran into a number of mincblur oddities when dealing with
> single-slice minc volumes. For example, I have a single-slice image
> that, when blurred with:
>
>    mincblur -no_apodize -dim 2 -fwhm 1 <in.mnc> <out>
>
> generates the expected result; However, when I happened to convert the
> datatype of that same slice from byte to short ran the same mincblur
> call, the result suffered from a wraparound effect. See the image at
>
>    http://dl.dropbox.com/u/5709165/mincblur/test_blur.jpg
>
> with the underlying data in
>
>    http://dl.dropbox.com/u/5709165/mincblur/test_blur.tar.gz
>
> I have also seen such wraparound effects appear as a function of image
> dimensions (regardless of data type). So from what I can tell mincblur
> is broken when it comes to dealing with single-slice data; but broken
> in a somewhat unpredictable way because in certain circumstances it
> will actually do the right thing (as in the 'byte' example I gave).
> Padding the image with a slice above and below will make the problem
> from this example go away; but again, I am not sure how the failures
> depend on the number of slices added.
>
> Is anybody familiar enough with the innards of mincblur to address
> this issue? Ideally it would be fixed such as to allow proper 2D
> blurring on single-slice volumes; but barring that, it would be good
> if at least it generated an error as opposed to silently and
> unpredictably doing the right or wrong thing.
>
> Thanks,
>
> -- Alex
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue May 18 19:24:05 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 19 May 2010 09:24:05 +1000
Subject: [MINC-users] Ubuntu Lynx Packages
Message-ID: <AANLkTimDyCJXA-bU6wzLptcR66skAQ-71BZ69TyPOSik@mail.gmail.com>

Hi all,

I am currently uploading packages for ubuntu lynx here:

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

This has required some changes to EBTKS for a build against gcc 4.3
and a few other things. It is currently missing brain-view as there is
some qt3/4 build config issue that I am yet to hunt down. Let me know
if something breaks with them for you.


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

From Paul.Rasser at newcastle.edu.au  Tue May 18 22:57:13 2010
From: Paul.Rasser at newcastle.edu.au (Paul Rasser)
Date: Wed, 19 May 2010 12:57:13 +1000
Subject: [MINC-users] dilate_volume
Message-ID: <4BF3E02C0200001F0002D221@WINDOMPRD00.newcastle.edu.au>

Dear minc-users,

I'm unable to find the package dilate_volume. Is it still available? 

Thanks,
Paul


From a.janke at gmail.com  Tue May 18 23:17:48 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 19 May 2010 13:17:48 +1000
Subject: [MINC-users] dilate_volume
In-Reply-To: <4BF3E02C0200001F0002D221@WINDOMPRD00.newcastle.edu.au>
References: <4BF3E02C0200001F0002D221@WINDOMPRD00.newcastle.edu.au>
Message-ID: <AANLkTimmNWbG5vr0YFvIV6ipxryuwxr1C8bIm_Ca0Tm3@mail.gmail.com>

Hi paul,

at one stage it was part of conglomerate.  You can get the same
functionality in mincmorph too.

A

On 2010-05-19, Paul Rasser <Paul.Rasser at newcastle.edu.au> wrote:
> Dear minc-users,
>
> I'm unable to find the package dilate_volume. Is it still available?
>
> Thanks,
> Paul
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From francois.hebert007 at gmail.com  Wed May 19 09:49:57 2010
From: francois.hebert007 at gmail.com (francois hebert)
Date: Wed, 19 May 2010 09:49:57 -0400
Subject: [MINC-users] link problem
Message-ID: <AANLkTim1RhNQhpugV9VBNS3gheQuH6wkddZjysjj5asH@mail.gmail.com>

Hi All there,

New in the MINC world, I'm trying to implement C stuffs into MINC. For a
simple test, I implemented a basic C program (Test.c  attached) and tried to
compiled it using a command line found in minc_wikibook as below:

arsene at balvenie:~$ gcc -g -o Test1 -I/usr/local/bic/include
-L/usr/local/bic/lib -lminc2 -lhdf5 ~/Desktop/Test.c


And I've got the following error message:

/tmp/ccyMXdho.o: In function `main':
/home/arsene/Desktop/Cluster.
c:20: undefined reference to `miopen_volume'
/home/arsene/Desktop/Cluster.c:29: undefined reference to
`miconvert_world_to_voxel'
/home/arsene/Desktop/Cluster.c:40: undefined reference to `miget_real_value'
collect2: ld returned 1 exit status


It seems like the program is compiled but links are not performed...
!?!?!?!?


What wrong?



Thanks in advance,

From acveilleux at mrs.mni.mcgill.ca  Wed May 19 11:41:34 2010
From: acveilleux at mrs.mni.mcgill.ca (Alexandre CARMEL-VEILLEUX)
Date: Wed, 19 May 2010 11:41:34 -0400
Subject: [MINC-users] link problem
In-Reply-To: <AANLkTim1RhNQhpugV9VBNS3gheQuH6wkddZjysjj5asH@mail.gmail.com>
References: <AANLkTim1RhNQhpugV9VBNS3gheQuH6wkddZjysjj5asH@mail.gmail.com>
Message-ID: <20100519154133.GI29312@mrs.mni.mcgill.ca>

Maybe try to link in netcdf as well.

gcc -g -o Test1 -I/usr/local/bic/include -L/usr/local/bic/lib -lminc2 -lhdf5 -lnetcdf ~/Desktop/Test.c

Alex


On Wed, May 19, 2010 at 09:49:57AM -0400, francois hebert wrote:
> Date: Wed, 19 May 2010 09:49:57 -0400
> From: francois hebert <francois.hebert007 at gmail.com>
> Subject: [MINC-users] link problem
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> 
> Hi All there,
> 
> New in the MINC world, I'm trying to implement C stuffs into MINC. For a
> simple test, I implemented a basic C program (Test.c  attached) and tried to
> compiled it using a command line found in minc_wikibook as below:
> 
> arsene at balvenie:~$ gcc -g -o Test1 -I/usr/local/bic/include
> -L/usr/local/bic/lib -lminc2 -lhdf5 ~/Desktop/Test.c
> 
> 
> And I've got the following error message:
> 
> /tmp/ccyMXdho.o: In function `main':
> /home/arsene/Desktop/Cluster.
> c:20: undefined reference to `miopen_volume'
> /home/arsene/Desktop/Cluster.c:29: undefined reference to
> `miconvert_world_to_voxel'
> /home/arsene/Desktop/Cluster.c:40: undefined reference to `miget_real_value'
> collect2: ld returned 1 exit status
> 
> 
> It seems like the program is compiled but links are not performed...
> !?!?!?!?
> 
> 
> What wrong?
> 
> 
> 
> Thanks in advance,
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From stephencohen at jgh.mcgill.ca  Wed May 19 11:43:27 2010
From: stephencohen at jgh.mcgill.ca (Stephen Cohen)
Date: Wed, 19 May 2010 11:43:27 -0400
Subject: [MINC-users] freeglut fatal error in remote X sessions
Message-ID: <02d201caf76a$060a68e0$121f3aa0$@mcgill.ca>

Hello all,

 

I have installed the BIC software via the Ubuntu Lucid Lynx packages that
were released yesterday.  I have been testing the Display program, which
appears to run properly while working on the system locally, however if
connected to the system via a remote X session, using NX or VNC, the program
fails with the following error:

 

freeglut (no_program_name):  ERROR:  Internal error <FBConfig with necessary
capabilities not found> in function fgOpenWindow

X Error of failed request:  BadWindow (invalid Window parameter)

  Major opcode of failed request:  4 (X_DestroyWindow)

  Resource id in failed request:  0x0

  Serial number of failed request:  27

  Current serial number in output stream:  30

 

I have done some Googling on this and it appears that this might be related
to a bug in Freeglut:

http://bugs.freedesktop.org/show_bug.cgi?id=24226

 

If I connect to the system using SSH with X11Forwarding the programs runs
properly.  However I would preferring working with the system in a remote
desktop scenario.  

 

Is anyone running these programs remotely in this way?  I haven't tested any
other program besides Display.

 

Installed packages

Freeglut3 2.6.0-ubuntu2

Freeglut3-dev 2.6.0-ubuntu2

Libglut3 3.7-25

Libglut3-dev 3.7-25

Glutg3 3.7-25

Glutg3-dev 3.7-25

 

 

Thank you for your time,

Stephen Cohen 

Computer Analyst 

Lady Davis Institute 

514 340-8222 ext 3795

 


From a.janke at gmail.com  Wed May 19 23:59:47 2010
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 20 May 2010 13:59:47 +1000
Subject: [MINC-users] freeglut fatal error in remote X sessions
In-Reply-To: <02d201caf76a$060a68e0$121f3aa0$@mcgill.ca>
References: <02d201caf76a$060a68e0$121f3aa0$@mcgill.ca>
Message-ID: <AANLkTinkmutuK1sN2sCK4XWW5dawKOLGm5FICVNek5T8@mail.gmail.com>

Hi Stephen,

> I have installed the BIC software via the Ubuntu Lucid Lynx packages that
> were released yesterday. ?I have been testing the Display program, which
> appears to run properly while working on the system locally, however if
> connected to the system via a remote X session, using NX or VNC, the program
> fails with the following error:

I'm afraid you might be on your own with this one. :(  Register and
Display make use of a few undocumented features of GLUT from back in
the day it was written. I have already patched a few bugs related to
this in any case. The problem is that I can't reproduce the issue you
are having here with two Ubuntu Karmic/Lynx machines so I can't offer
any help.

No doubt it is related to glut/freeglut but just where I can't say.


good luck.


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

From alex at bic.mni.mcgill.ca  Thu May 20 00:15:00 2010
From: alex at bic.mni.mcgill.ca (Alex Zijdenbos)
Date: Thu, 20 May 2010 00:15:00 -0400
Subject: [MINC-users] freeglut fatal error in remote X sessions
In-Reply-To: <AANLkTinkmutuK1sN2sCK4XWW5dawKOLGm5FICVNek5T8@mail.gmail.com>
References: <02d201caf76a$060a68e0$121f3aa0$@mcgill.ca>
	<AANLkTinkmutuK1sN2sCK4XWW5dawKOLGm5FICVNek5T8@mail.gmail.com>
Message-ID: <AANLkTilolJkzoVdzrpSFvjUz00lnsS-bfL48LeBa9dxz@mail.gmail.com>

Hi Stephen,

I may have one tip: I had the same issue, and managed to fix it (somewhat) by

   apt-get install nvidia-glx-185
   (reboot)

(obviously that only makes sense on a machine with an nvidia card).
After this I am able to run register and Display through NX - with one
caveat: they will still segfault when quitting them 'nicely'. So I've
just gotten used to use Ctrl-C when done running register and Display
in an NX session :)

It might work for you too.

-- Alex

On Wed, May 19, 2010 at 11:59 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Stephen,
>
>> I have installed the BIC software via the Ubuntu Lucid Lynx packages that
>> were released yesterday. ?I have been testing the Display program, which
>> appears to run properly while working on the system locally, however if
>> connected to the system via a remote X session, using NX or VNC, the program
>> fails with the following error:
>
> I'm afraid you might be on your own with this one. :( ?Register and
> Display make use of a few undocumented features of GLUT from back in
> the day it was written. I have already patched a few bugs related to
> this in any case. The problem is that I can't reproduce the issue you
> are having here with two Ubuntu Karmic/Lynx machines so I can't offer
> any help.
>
> No doubt it is related to glut/freeglut but just where I can't say.
>
>
> good luck.
>
>
> --
> 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 stephencohen at jgh.mcgill.ca  Thu May 20 08:47:59 2010
From: stephencohen at jgh.mcgill.ca (Stephen Cohen)
Date: Thu, 20 May 2010 08:47:59 -0400
Subject: [MINC-users] freeglut fatal error in remote X sessions
In-Reply-To: <AANLkTilolJkzoVdzrpSFvjUz00lnsS-bfL48LeBa9dxz@mail.gmail.com>
References: <02d201caf76a$060a68e0$121f3aa0$@mcgill.ca>
	<AANLkTinkmutuK1sN2sCK4XWW5dawKOLGm5FICVNek5T8@mail.gmail.com>
	<AANLkTilolJkzoVdzrpSFvjUz00lnsS-bfL48LeBa9dxz@mail.gmail.com>
Message-ID: <008c01caf81a$ad5557d0$08000770$@mcgill.ca>

Thanks all for the replies.  Shouldn't be much of a problem getting an
nVidia card into the server.  I think I can handle that caveat.

Thanks again,
Stephen Cohen 
Computer Analyst 
Lady Davis Institute 
514 340-8222 ext 3795


-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca
[mailto:minc-users-bounces at bic.mni.mcgill.ca] On Behalf Of Alex Zijdenbos
Sent: May-20-10 12:15 AM
To: MINC users mailing list
Subject: Re: [MINC-users] freeglut fatal error in remote X sessions

Hi Stephen,

I may have one tip: I had the same issue, and managed to fix it (somewhat)
by

   apt-get install nvidia-glx-185
   (reboot)

(obviously that only makes sense on a machine with an nvidia card).
After this I am able to run register and Display through NX - with one
caveat: they will still segfault when quitting them 'nicely'. So I've
just gotten used to use Ctrl-C when done running register and Display
in an NX session :)

It might work for you too.

-- Alex

On Wed, May 19, 2010 at 11:59 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Stephen,
>
>> I have installed the BIC software via the Ubuntu Lucid Lynx packages that
>> were released yesterday. ?I have been testing the Display program, which
>> appears to run properly while working on the system locally, however if
>> connected to the system via a remote X session, using NX or VNC, the
program
>> fails with the following error:
>
> I'm afraid you might be on your own with this one. :( ?Register and
> Display make use of a few undocumented features of GLUT from back in
> the day it was written. I have already patched a few bugs related to
> this in any case. The problem is that I can't reproduce the issue you
> are having here with two Ubuntu Karmic/Lynx machines so I can't offer
> any help.
>
> No doubt it is related to glut/freeglut but just where I can't say.
>
>
> good luck.
>
>
> --
> 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
>
>
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users


From francois.hebert007 at gmail.com  Thu May 20 09:57:20 2010
From: francois.hebert007 at gmail.com (francois hebert)
Date: Thu, 20 May 2010 09:57:20 -0400
Subject: [MINC-users] link problem
In-Reply-To: <20100519154133.GI29312@mrs.mni.mcgill.ca>
References: <AANLkTim1RhNQhpugV9VBNS3gheQuH6wkddZjysjj5asH@mail.gmail.com>
	<20100519154133.GI29312@mrs.mni.mcgill.ca>
Message-ID: <AANLkTikGyng8vdC_pQtWX-Fy-ytYUMdjUYTcQe_9lRdw@mail.gmail.com>

Thank you for the help but it seems that the problem comes from the link
against shared library.
I'm not sure but I have to dig in.

Francois

2010/5/19 Alexandre CARMEL-VEILLEUX <acveilleux at mrs.mni.mcgill.ca>

> Maybe try to link in netcdf as well.
>
> gcc -g -o Test1 -I/usr/local/bic/include -L/usr/local/bic/lib -lminc2
> -lhdf5 -lnetcdf ~/Desktop/Test.c
>
> Alex
>
>
> On Wed, May 19, 2010 at 09:49:57AM -0400, francois hebert wrote:
> > Date: Wed, 19 May 2010 09:49:57 -0400
> > From: francois hebert <francois.hebert007 at gmail.com>
> > Subject: [MINC-users] link problem
> > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> >
> > Hi All there,
> >
> > New in the MINC world, I'm trying to implement C stuffs into MINC. For a
> > simple test, I implemented a basic C program (Test.c  attached) and tried
> to
> > compiled it using a command line found in minc_wikibook as below:
> >
> > arsene at balvenie:~$ gcc -g -o Test1 -I/usr/local/bic/include
> > -L/usr/local/bic/lib -lminc2 -lhdf5 ~/Desktop/Test.c
> >
> >
> > And I've got the following error message:
> >
> > /tmp/ccyMXdho.o: In function `main':
> > /home/arsene/Desktop/Cluster.
> > c:20: undefined reference to `miopen_volume'
> > /home/arsene/Desktop/Cluster.c:29: undefined reference to
> > `miconvert_world_to_voxel'
> > /home/arsene/Desktop/Cluster.c:40: undefined reference to
> `miget_real_value'
> > collect2: ld returned 1 exit status
> >
> >
> > It seems like the program is compiled but links are not performed...
> > !?!?!?!?
> >
> >
> > What wrong?
> >
> >
> >
> > Thanks in advance,
> > _______________________________________________
> > 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  Thu May 20 11:40:15 2010
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Thu, 20 May 2010 11:40:15 -0400
Subject: [MINC-users] link problem
In-Reply-To: <AANLkTikGyng8vdC_pQtWX-Fy-ytYUMdjUYTcQe_9lRdw@mail.gmail.com>
Message-ID: <201005201540.o4KFeFvN000447@grumio.bic.mni.mcgill.ca>

Hi,

This sounds too simple to be true, but can you verify that you are
compiling/linking all in 32 bits or all in 64 bits?

Claude

> Thank you for the help but it seems that the problem comes from the link
> against shared library.
> I'm not sure but I have to dig in.
>
> Francois
>
> 2010/5/19 Alexandre CARMEL-VEILLEUX <acveilleux at mrs.mni.mcgill.ca>
>
> > Maybe try to link in netcdf as well.
> >
> > gcc -g -o Test1 -I/usr/local/bic/include -L/usr/local/bic/lib -lminc2
> > -lhdf5 -lnetcdf ~/Desktop/Test.c
> >
> > Alex
> >
> >
> > On Wed, May 19, 2010 at 09:49:57AM -0400, francois hebert wrote:
> > > Date: Wed, 19 May 2010 09:49:57 -0400
> > > From: francois hebert <francois.hebert007 at gmail.com>
> > > Subject: [MINC-users] link problem
> > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > >
> > > Hi All there,
> > >
> > > New in the MINC world, I'm trying to implement C stuffs into MINC. For a
> > > simple test, I implemented a basic C program (Test.c  attached) and tried
> > to
> > > compiled it using a command line found in minc_wikibook as below:
> > >
> > > arsene at balvenie:~$ gcc -g -o Test1 -I/usr/local/bic/include
> > > -L/usr/local/bic/lib -lminc2 -lhdf5 ~/Desktop/Test.c
> > >
> > >
> > > And I've got the following error message:
> > >
> > > /tmp/ccyMXdho.o: In function `main':
> > > /home/arsene/Desktop/Cluster.
> > > c:20: undefined reference to `miopen_volume'
> > > /home/arsene/Desktop/Cluster.c:29: undefined reference to
> > > `miconvert_world_to_voxel'
> > > /home/arsene/Desktop/Cluster.c:40: undefined reference to
> > `miget_real_value'
> > > collect2: ld returned 1 exit status
> > >
> > >
> > > It seems like the program is compiled but links are not performed...
> > > !?!?!?!?
> > >
> > >
> > > What wrong?
> > >
> > >
> > >
> > > Thanks in advance,
> > > _______________________________________________
> > > 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 lconcha at gmail.com  Thu May 20 13:10:20 2010
From: lconcha at gmail.com (Luis Concha)
Date: Thu, 20 May 2010 12:10:20 -0500
Subject: [MINC-users] Ubuntu Lynx Packages
Message-ID: <AANLkTikw5V3pvpBHYRNZ3NOTRyUQuaej4UaQqwYDdyG8@mail.gmail.com>

Hello Andrew.

Thanks for posting the ubuntu-lucid packages. Is there any chance there will
be the equivalent 32-bit versions?

Thanks

Luis Concha



From: Andrew Janke <a.janke at gmail.com>

> Subject: [MINC-users] Ubuntu Lynx Packages
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
>        <AANLkTimDyCJXA-bU6wzLptcR66skAQ-71BZ69TyPOSik at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi all,
>
> I am currently uploading packages for ubuntu lynx here:
>
>   http://packages.bic.mni.mcgill.ca/ubuntu-lucid/
>
> This has required some changes to EBTKS for a build against gcc 4.3
> and a few other things. It is currently missing brain-view as there is
> some qt3/4 build config issue that I am yet to hunt down. Let me know
> if something breaks with them for you.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>

From fling at pet.rh.dk  Mon May 31 04:51:16 2010
From: fling at pet.rh.dk (Flemming Littrup Andersen)
Date: Mon, 31 May 2010 10:51:16 +0200
Subject: [MINC-users] Ubuntu Lynx Packages
In-Reply-To: <AANLkTimDyCJXA-bU6wzLptcR66skAQ-71BZ69TyPOSik@mail.gmail.com>
References: <AANLkTimDyCJXA-bU6wzLptcR66skAQ-71BZ69TyPOSik@mail.gmail.com>
Message-ID: <AANLkTikRp3s8_KKZ5ZMzu8l9z_GxTzbJm0bCLVaPVSaz@mail.gmail.com>

Hi Andrew,

I have a few display related errors:

postf will crash with an X error as soon as I try to adjust the color scale:

X Error of failed request:  BadValue (integer parameter out of range
for operation)
  Major opcode of failed request:  88 (X_FreeColors)
  Value in failed request:  0xeddfec81
  Serial number of failed request:  777
  Current serial number in output stream:  778

Also - Display is segfaulting on startup - even with no input data.

Thus is on a fresh 64-bit install of Lynx on a Lenovo Thinkcentre
(82Q35 graphics using i915 as far as I know).

Any ideas?

Best regards,
Flemming


On Wed, May 19, 2010 at 1:24 AM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi all,
>
> I am currently uploading packages for ubuntu lynx here:
>
> ? http://packages.bic.mni.mcgill.ca/ubuntu-lucid/
>
> This has required some changes to EBTKS for a build against gcc 4.3
> and a few other things. It is currently missing brain-view as there is
> some qt3/4 build config issue that I am yet to hunt down. Let me know
> if something breaks with them for you.
>
>
> --
> 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
>
>



-- 
Flemming Littrup Andersen, Ph.D
Rigshospitalet Copenhagen, Dep. PET-3982
Phone: +45 3545-8143
Mobile: +45 2615-7368