From gabriel.devenyi at mcgill.ca  Wed Feb  1 19:10:44 2017
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Wed, 1 Feb 2017 19:10:44 -0500
Subject: [MINC-users] minc tool to extract voxel values within a mask?
Message-ID: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>

Hi all,

I have a user asking about extracting raw intensity values from a MINC
image, from a region defined by a mask (label file, specific bin value).

The closest thing I can find is mincextract but it doesn't have mask
support.

Does anyone know of a script/hack to extract values like this?

Thanks!

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gabriel.devenyi at mcgill.ca

From a.janke at gmail.com  Wed Feb  1 20:33:27 2017
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 2 Feb 2017 11:33:27 +1000
Subject: [MINC-users] minc tool to extract voxel values within a mask?
In-Reply-To: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>
References: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>
Message-ID: <CAG0CB219=hQz3jvPog+deH-5GYuP2FTLYHCmE9sTbiZ_S5zvTw@mail.gmail.com>

Hi Gabriel,

Take a look at mincsample. I wrote it around this purpose.

It also does random sampling of the area via the Mersene Twister algorithm.


a


On 2 February 2017 at 10:10, Gabriel A. Devenyi
<gabriel.devenyi at mcgill.ca> wrote:
> Hi all,
>
> I have a user asking about extracting raw intensity values from a MINC
> image, from a region defined by a mask (label file, specific bin value).
>
> The closest thing I can find is mincextract but it doesn't have mask
> support.
>
> Does anyone know of a script/hack to extract values like this?
>
> Thanks!
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gabriel.devenyi at mcgill.ca
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From pgravel at bic.mni.mcgill.ca  Thu Feb  2 01:00:19 2017
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Thu, 2 Feb 2017 01:00:19 -0500 (EST)
Subject: [MINC-users] Error compiling MINC-Tools on RedHat
In-Reply-To: <CAG0CB219=hQz3jvPog+deH-5GYuP2FTLYHCmE9sTbiZ_S5zvTw@mail.gmail.com>
References: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>
	<CAG0CB219=hQz3jvPog+deH-5GYuP2FTLYHCmE9sTbiZ_S5zvTw@mail.gmail.com>
Message-ID: <alpine.DEB.2.02.1702020052150.4325@login1.bic.mni.mcgill.ca>

Dear All,

I am currently trying to compile the MINC tools on RedHat:
lsb_release -a
LSB Version: 
:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: RedHatEnterpriseAS
Description:    Red Hat Enterprise Linux AS release 6 (Update 5)
Release:        6
Codename:       Update5

I have followed the instructions on:
https://github.com/BIC-MNI/minc-toolkit

git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git 
minc-toolkit
cd minc-toolkit
mkdir build && cd build
ccmake ..

I have installed (I hope!) all the dependencies (BISON, FLEX, GLUT);
Perl, libxi, and libxmu is already on the system.
And the packages (NETCDF, HDF5, PCRE, GSL, FFTW3); zlib is already on the 
system.

That being said, when I run: make

It gets to 94% and then I get this error:
[ 94%] Linking CXX executable mincnlm 
CMakeFiles/mincnlm.dir/mincnlm.cpp.o: In function 
`Exec(minc::simple_volume<float>&, float*, int*, double*, float*)':
mincnlm.cpp:(.text+0xb40): undefined reference to 
`minc::noise_estimate(minc::simple_volume<float> const&, double&, bool, 
bool)'
collect2: ld returned 1 exit status
make[2]: *** [EZminc/mincnlm/mincnlm] Error 1
make[1]: *** [EZminc/mincnlm/CMakeFiles/mincnlm.dir/all] Error 2
make: *** [all] Error 2

Any idea as to why?

As always, any help will be greatly appreciated!

Best Regards,

Paul

From gabriel.devenyi at mcgill.ca  Thu Feb  2 09:49:52 2017
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Thu, 2 Feb 2017 09:49:52 -0500
Subject: [MINC-users] minc tool to extract voxel values within a mask?
In-Reply-To: <3d2886ee5f63478ebcbd6bf19565ce46@BN3PR0301MB1219.namprd03.prod.outlook.com>
References: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>
	<3d2886ee5f63478ebcbd6bf19565ce46@BN3PR0301MB1219.namprd03.prod.outlook.com>
Message-ID: <CAFQOoOqd7WTS3SQbnc6QpdcTf5_dovTwpLPCzQ6oELin3ODE_g@mail.gmail.com>

That's perfect, thanks!

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
McGill University
t: 514.761.6131x4781
e: gabriel.devenyi at mcgill.ca

On Wed, Feb 1, 2017 at 8:33 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Gabriel,
>
> Take a look at mincsample. I wrote it around this purpose.
>
> It also does random sampling of the area via the Mersene Twister algorithm.
>
>
> a
>
>
> On 2 February 2017 at 10:10, Gabriel A. Devenyi
> <gabriel.devenyi at mcgill.ca> wrote:
> > Hi all,
> >
> > I have a user asking about extracting raw intensity values from a MINC
> > image, from a region defined by a mask (label file, specific bin value).
> >
> > The closest thing I can find is mincextract but it doesn't have mask
> > support.
> >
> > Does anyone know of a script/hack to extract values like this?
> >
> > Thanks!
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > McGill University
> > t: 514.761.6131x4781
> > e: gabriel.devenyi at mcgill.ca
> > _______________________________________________
> > 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 redoute at cermep.fr  Fri Feb  3 02:31:19 2017
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Fri, 3 Feb 2017 08:31:19 +0100
Subject: [MINC-users] minc tool to extract voxel values within a mask?
In-Reply-To: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>
References: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>
Message-ID: <3dd3c66c-d24f-612d-239a-0f9972853edb@cermep.fr>

Le 02/02/2017 ? 01:10, Gabriel A. Devenyi a ?crit :
> The closest thing I can find is mincextract but it doesn't have mask
> support.

you can use

mincstats -mean -mask LABELED_IMAG.mnc -mask_binvalue LABEL IMAGE.mnc

-- 
==================================================================
J?r?me Redout?
Ph.D. - Ing?nieur de Recherche - Universit? Claude Bernard - Lyon1
CERMEP - Imagerie du vivant
59 Bd Pinel. 69677 Bron - FRANCE
tel : 33 (0)4 72 68 86 18 (bureau)
tel : 33 (0)4 72 68 86 00 (standard)
fax : 33 (0)4 72 68 86 10
==================================================================



From pgravel at bic.mni.mcgill.ca  Fri Feb  3 10:10:47 2017
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Fri, 3 Feb 2017 10:10:47 -0500 (EST)
Subject: [MINC-users] Error compiling MINC-Tools on RedHat
In-Reply-To: <alpine.DEB.2.02.1702020052150.4325@login1.bic.mni.mcgill.ca>
References: <CAFQOoOqqfZvozaP77rhvp5JNAtpZBan+hTWy0-pS5ypnPRN7DA@mail.gmail.com>
	<CAG0CB219=hQz3jvPog+deH-5GYuP2FTLYHCmE9sTbiZ_S5zvTw@mail.gmail.com>
	<alpine.DEB.2.02.1702020052150.4325@login1.bic.mni.mcgill.ca>
Message-ID: <alpine.DEB.2.02.1702031008390.20153@login1.bic.mni.mcgill.ca>

Dear All,

ok, so I found a workaround which now works!

I set to 'OFF' all fields related to EZMINC (sorry Vlad ;-)!).
However, is there a fix for mincnlm to make it RedHat compatible?

Best,

Paul


On Thu, 2 Feb 2017, Paul GRAVEL wrote:

> Dear All,
>
> I am currently trying to compile the MINC tools on RedHat:
> lsb_release -a
> LSB Version: 
> :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
> Distributor ID: RedHatEnterpriseAS
> Description:    Red Hat Enterprise Linux AS release 6 (Update 5)
> Release:        6
> Codename:       Update5
>
> I have followed the instructions on:
> https://github.com/BIC-MNI/minc-toolkit
>
> git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git minc-toolkit
> cd minc-toolkit
> mkdir build && cd build
> ccmake ..
>
> I have installed (I hope!) all the dependencies (BISON, FLEX, GLUT);
> Perl, libxi, and libxmu is already on the system.
> And the packages (NETCDF, HDF5, PCRE, GSL, FFTW3); zlib is already on the 
> system.
>
> That being said, when I run: make
>
> It gets to 94% and then I get this error:
> [ 94%] Linking CXX executable mincnlm CMakeFiles/mincnlm.dir/mincnlm.cpp.o: 
> In function `Exec(minc::simple_volume<float>&, float*, int*, double*, 
> float*)':
> mincnlm.cpp:(.text+0xb40): undefined reference to 
> `minc::noise_estimate(minc::simple_volume<float> const&, double&, bool, 
> bool)'
> collect2: ld returned 1 exit status
> make[2]: *** [EZminc/mincnlm/mincnlm] Error 1
> make[1]: *** [EZminc/mincnlm/CMakeFiles/mincnlm.dir/all] Error 2
> make: *** [all] Error 2
>
> Any idea as to why?
>
> As always, any help will be greatly appreciated!
>
> Best Regards,
>
> Paul
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From redoute at cermep.fr  Mon Feb  6 04:43:40 2017
From: redoute at cermep.fr (Jerome Redoute)
Date: Mon, 06 Feb 2017 10:43:40 +0100
Subject: [MINC-users] MINC compilation issues
Message-ID: <cb0acfd2614ce85944c2116a9c681cc2@cermep.fr>

Hi, 

I'm trying to update our release of MINC-toolkit-v2 (develop branch),
but I have some issues while compiling. 

many warnings and compilation exits with the following error: 

> CMakeFiles/register.dir/User_interface/event_handling/event_loop.c.o: dans la fonction ? set_quit_program_flag ?:
> event_loop.c:(.text+0xd3): r?f?rence ind?finie vers ? G_exit_loop ?
> collect2: error: ld returned 1 exit status
> Register/CMakeFiles/register.dir/build.make:1594: recipe for target 'Register/register' failed
> make[2]: *** [Register/register] Error 1
> CMakeFiles/Makefile2:16784: recipe for target 'Register/CMakeFiles/register.dir/all' failed
> make[1]: *** [Register/CMakeFiles/register.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2

I'm running Debian x64. 

Any ideas on what's going wrong? 

thank you 

J 

-- 
==================================================
Jerome Redoute
CERMEP - Imagerie du vivant
Centre d'?tude et de recherche multimodal et pluridisciplinaire
59 Bd Pinel
69667 Bron - FRANCE
tel : 33 (0)4 72 68 86 13 (bureau)
tel : 33 (0)4 72 68 86 00 (standard)
fax : 33 (0)4 72 68 86 10
==================================================

From robert.d.vincent at mcgill.ca  Mon Feb  6 10:05:07 2017
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Mon, 6 Feb 2017 10:05:07 -0500
Subject: [MINC-users] MINC compilation issues
In-Reply-To: <cb0acfd2614ce85944c2116a9c681cc2@cermep.fr>
References: <cb0acfd2614ce85944c2116a9c681cc2@cermep.fr>
Message-ID: <CAAd5DeR=soXm4Z49mh8FBVU9jWhFi1sfEhAzOQuPbYH+Yrb2Mw@mail.gmail.com>

Hi Jerome,

Are you checking out the develop branch of all subprojects? If so, you
might need to check out "rdv-new-opengl" from the bicgl project.

    -bert


On Mon, Feb 6, 2017 at 4:43 AM, Jerome Redoute <redoute at cermep.fr> wrote:

> Hi,
>
> I'm trying to update our release of MINC-toolkit-v2 (develop branch),
> but I have some issues while compiling.
>
> many warnings and compilation exits with the following error:
>
> > CMakeFiles/register.dir/User_interface/event_handling/event_loop.c.o:
> dans la fonction ? set_quit_program_flag ?:
> > event_loop.c:(.text+0xd3): r?f?rence ind?finie vers ? G_exit_loop ?
> > collect2: error: ld returned 1 exit status
> > Register/CMakeFiles/register.dir/build.make:1594: recipe for target
> 'Register/register' failed
> > make[2]: *** [Register/register] Error 1
> > CMakeFiles/Makefile2:16784: recipe for target
> 'Register/CMakeFiles/register.dir/all' failed
> > make[1]: *** [Register/CMakeFiles/register.dir/all] Error 2
> > Makefile:160: recipe for target 'all' failed
> > make: *** [all] Error 2
>
> I'm running Debian x64.
>
> Any ideas on what's going wrong?
>
> thank you
>
> J
>
> --
> ==================================================
> Jerome Redoute
> CERMEP - Imagerie du vivant
> Centre d'?tude et de recherche multimodal et pluridisciplinaire
> 59 Bd Pinel
> 69667 Bron - FRANCE
> tel : 33 (0)4 72 68 86 13 (bureau)
> tel : 33 (0)4 72 68 86 00 (standard)
> fax : 33 (0)4 72 68 86 10
> ==================================================
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From redoute at cermep.fr  Tue Feb  7 10:18:10 2017
From: redoute at cermep.fr (Jerome Redoute)
Date: Tue, 07 Feb 2017 16:18:10 +0100
Subject: [MINC-users] MINC compilation issues
In-Reply-To: <CAAd5DeR=soXm4Z49mh8FBVU9jWhFi1sfEhAzOQuPbYH+Yrb2Mw@mail.gmail.com>
References: <cb0acfd2614ce85944c2116a9c681cc2@cermep.fr>
	<CAAd5DeR=soXm4Z49mh8FBVU9jWhFi1sfEhAzOQuPbYH+Yrb2Mw@mail.gmail.com>
Message-ID: <150c1b264b6dfc980c68b475dc25db86@cermep.fr>

Hi Robert, 

I've updated, I think, all subprojects using

> cd minctoolkit-v2
> git pull --all
> cd minctools
> git pull origin develop
> cd ..
> cd libminc 
> 
> etc...

Now, here is what I get when I run again  make:

> CMakeFiles/register.dir/User_interface/event_handling/event_loop.c.o: dans la fonction ? set_quit_program_flag ?:
> event_loop.c:(.text+0xd3): r?f?rence ind?finie vers ? G_exit_loop ?
> collect2: error: ld returned 1 exit status
> Register/CMakeFiles/register.dir/build.make:1594: recipe for target 'Register/register' failed
> make[2]: *** [Register/register] Error 1
> CMakeFiles/Makefile2:16784: recipe for target 'Register/CMakeFiles/register.dir/all' failed
> make[1]: *** [Register/CMakeFiles/register.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2

thanks for your help 

Jerome 

---
==================================================
Jerome Redoute
CERMEP - Imagerie du vivant
Centre d'?tude et de recherche multimodal et pluridisciplinaire
59 Bd Pinel
69667 Bron - FRANCE
tel : 33 (0)4 72 68 86 13 (bureau)
tel : 33 (0)4 72 68 86 00 (standard)
fax : 33 (0)4 72 68 86 10
================================================== 

Le 06/02/2017 16:05, Robert D. Vincent a ?crit :

> Hi Jerome,
> 
> Are you checking out the develop branch of all subprojects? If so, you
> might need to check out "rdv-new-opengl" from the bicgl project.
> 
> -bert
> 
> On Mon, Feb 6, 2017 at 4:43 AM, Jerome Redoute <redoute at cermep.fr> wrote:
> 
> Hi,
> 
> I'm trying to update our release of MINC-toolkit-v2 (develop branch),
> but I have some issues while compiling.
> 
> many warnings and compilation exits with the following error:
> 
> CMakeFiles/register.dir/User_interface/event_handling/event_loop.c.o: dans la fonction ? set_quit_program_flag ?: event_loop.c:(.text+0xd3): r?f?rence ind?finie vers ? G_exit_loop ?
> collect2: error: ld returned 1 exit status
> Register/CMakeFiles/register.dir/build.make:1594: recipe for target 'Register/register' failed make[2]: *** [Register/register] Error 1
> CMakeFiles/Makefile2:16784: recipe for target 'Register/CMakeFiles/register.dir/all' failed make[1]: *** [Register/CMakeFiles/register.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2 
> I'm running Debian x64.
> 
> Any ideas on what's going wrong?
> 
> thank you
> 
> J
> 
> --
> ==================================================
> Jerome Redoute
> CERMEP - Imagerie du vivant
> Centre d'?tude et de recherche multimodal et pluridisciplinaire
> 59 Bd Pinel
> 69667 Bron - FRANCE
> tel : 33 (0)4 72 68 86 13 (bureau)
> tel : 33 (0)4 72 68 86 00 (standard)
> fax : 33 (0)4 72 68 86 10
> ==================================================
> _______________________________________________
> 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 robert.d.vincent at mcgill.ca  Wed Feb  8 10:54:09 2017
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Wed, 8 Feb 2017 10:54:09 -0500
Subject: [MINC-users] MINC compilation issues
In-Reply-To: <150c1b264b6dfc980c68b475dc25db86@cermep.fr>
References: <cb0acfd2614ce85944c2116a9c681cc2@cermep.fr>
	<CAAd5DeR=soXm4Z49mh8FBVU9jWhFi1sfEhAzOQuPbYH+Yrb2Mw@mail.gmail.com>
	<150c1b264b6dfc980c68b475dc25db86@cermep.fr>
Message-ID: <CAAd5DeQPArL7VAOrK8zsqpGqC9Qid_X=knar0RthSuSdB0qjgg@mail.gmail.com>

I think you may need to checkout rdv-new-opengl in the bicgl project,
rather than develop.


On Tue, Feb 7, 2017 at 10:18 AM, Jerome Redoute <redoute at cermep.fr> wrote:

> Hi Robert,
>
> I've updated, I think, all subprojects using
>
> > cd minctoolkit-v2
> > git pull --all
> > cd minctools
> > git pull origin develop
> > cd ..
> > cd libminc
> >
> > etc...
>
> Now, here is what I get when I run again  make:
>
> > CMakeFiles/register.dir/User_interface/event_handling/event_loop.c.o:
> dans la fonction ? set_quit_program_flag ?:
> > event_loop.c:(.text+0xd3): r?f?rence ind?finie vers ? G_exit_loop ?
> > collect2: error: ld returned 1 exit status
> > Register/CMakeFiles/register.dir/build.make:1594: recipe for target
> 'Register/register' failed
> > make[2]: *** [Register/register] Error 1
> > CMakeFiles/Makefile2:16784: recipe for target
> 'Register/CMakeFiles/register.dir/all' failed
> > make[1]: *** [Register/CMakeFiles/register.dir/all] Error 2
> > Makefile:160: recipe for target 'all' failed
> > make: *** [all] Error 2
>
> thanks for your help
>
> Jerome
>
> ---
> ==================================================
> Jerome Redoute
> CERMEP - Imagerie du vivant
> Centre d'?tude et de recherche multimodal et pluridisciplinaire
> 59 Bd Pinel
> 69667 Bron - FRANCE
> tel : 33 (0)4 72 68 86 13 (bureau)
> tel : 33 (0)4 72 68 86 00 (standard)
> fax : 33 (0)4 72 68 86 10
> ==================================================
>
> Le 06/02/2017 16:05, Robert D. Vincent a ?crit :
>
> > Hi Jerome,
> >
> > Are you checking out the develop branch of all subprojects? If so, you
> > might need to check out "rdv-new-opengl" from the bicgl project.
> >
> > -bert
> >
> > On Mon, Feb 6, 2017 at 4:43 AM, Jerome Redoute <redoute at cermep.fr>
> wrote:
> >
> > Hi,
> >
> > I'm trying to update our release of MINC-toolkit-v2 (develop branch),
> > but I have some issues while compiling.
> >
> > many warnings and compilation exits with the following error:
> >
> > CMakeFiles/register.dir/User_interface/event_handling/event_loop.c.o:
> dans la fonction ? set_quit_program_flag ?: event_loop.c:(.text+0xd3):
> r?f?rence ind?finie vers ? G_exit_loop ?
> > collect2: error: ld returned 1 exit status
> > Register/CMakeFiles/register.dir/build.make:1594: recipe for target
> 'Register/register' failed make[2]: *** [Register/register] Error 1
> > CMakeFiles/Makefile2:16784: recipe for target
> 'Register/CMakeFiles/register.dir/all' failed make[1]: ***
> [Register/CMakeFiles/register.dir/all] Error 2
> > Makefile:160: recipe for target 'all' failed
> > make: *** [all] Error 2
> > I'm running Debian x64.
> >
> > Any ideas on what's going wrong?
> >
> > thank you
> >
> > J
> >
> > --
> > ==================================================
> > Jerome Redoute
> > CERMEP - Imagerie du vivant
> > Centre d'?tude et de recherche multimodal et pluridisciplinaire
> > 59 Bd Pinel
> > 69667 Bron - FRANCE
> > tel : 33 (0)4 72 68 86 13 (bureau)
> > tel : 33 (0)4 72 68 86 00 (standard)
> > fax : 33 (0)4 72 68 86 10
> > ==================================================
> > _______________________________________________
> > 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 zijdenbos at gmail.com  Wed Feb 15 10:39:30 2017
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 15 Feb 2017 10:39:30 -0500
Subject: [MINC-users] MINC coordinate system diagram?
Message-ID: <CABEEk17LJTkzN8jHCACx2LV1yxoffE-Z096956NBf2ssnKCppw@mail.gmail.com>

Hi all,

I am looking for a diagram that shows how the MINC coordinate system works
(voxel vs world). It is described in the documentation for instance here:

https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference#Coordinates_and_Dimensions

but that's rather 'dry'. I am sure I have seen some nice MINC coordinate
system diagrams in the past, but I can't find them now. Anybody has these?
And if so, perhaps we can add them to the documentation? Picture speaks
1000 words :)

-- A

From a.janke at gmail.com  Wed Feb 15 16:26:33 2017
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 16 Feb 2017 07:26:33 +1000
Subject: [MINC-users] MINC coordinate system diagram?
In-Reply-To: <CABEEk17LJTkzN8jHCACx2LV1yxoffE-Z096956NBf2ssnKCppw@mail.gmail.com>
References: <CABEEk17LJTkzN8jHCACx2LV1yxoffE-Z096956NBf2ssnKCppw@mail.gmail.com>
Message-ID: <CAG0CB22MRM5ytVUEwMFuCwPu=vzxjnVyqmCqX82aGORa=nYTkw@mail.gmail.com>

Hi Alex,

There are a few images here:

   https://cloudstor.aarnet.edu.au/plus/index.php/s/xlI4a4fmbLxgXzb

Those the ones you are looking for?

a



On 16 February 2017 at 01:39, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Hi all,
>
> I am looking for a diagram that shows how the MINC coordinate system works
> (voxel vs world). It is described in the documentation for instance here:
>
> https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference#Coordinates_and_Dimensions
>
> but that's rather 'dry'. I am sure I have seen some nice MINC coordinate
> system diagrams in the past, but I can't find them now. Anybody has these?
> And if so, perhaps we can add them to the documentation? Picture speaks
> 1000 words :)
>
> -- A
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From zijdenbos at gmail.com  Thu Feb 16 13:30:09 2017
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Thu, 16 Feb 2017 13:30:09 -0500
Subject: [MINC-users] MINC coordinate system diagram?
In-Reply-To: <CAG0CB22MRM5ytVUEwMFuCwPu=vzxjnVyqmCqX82aGORa=nYTkw@mail.gmail.com>
References: <CABEEk17LJTkzN8jHCACx2LV1yxoffE-Z096956NBf2ssnKCppw@mail.gmail.com>
	<CAG0CB22MRM5ytVUEwMFuCwPu=vzxjnVyqmCqX82aGORa=nYTkw@mail.gmail.com>
Message-ID: <CABEEk171271ed_e-6_8Z1FeDPthB3sbnUFXNpC4NyoDkbGVnTg@mail.gmail.com>

Hi Andrew,

Thanks - that gets in the direction, but I seem to recall a more detailed
diagram that was a bit more technical, showing explicitly where the start
values fall, angles of the axes direction, etc. Perhaps I imagined it :)

-- A

On Wed, Feb 15, 2017 at 4:26 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Alex,
>
> There are a few images here:
>
>    https://cloudstor.aarnet.edu.au/plus/index.php/s/xlI4a4fmbLxgXzb
>
> Those the ones you are looking for?
>
> a
>
>
>
> On 16 February 2017 at 01:39, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> > Hi all,
> >
> > I am looking for a diagram that shows how the MINC coordinate system
> works
> > (voxel vs world). It is described in the documentation for instance here:
> >
> > https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/
> MINC2.0_File_Format_Reference#Coordinates_and_Dimensions
> >
> > but that's rather 'dry'. I am sure I have seen some nice MINC coordinate
> > system diagrams in the past, but I can't find them now. Anybody has
> these?
> > And if so, perhaps we can add them to the documentation? Picture speaks
> > 1000 words :)
> >
> > -- A
> > _______________________________________________
> > 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 stebollmann at gmail.com  Fri Feb 17 04:05:08 2017
From: stebollmann at gmail.com (Steffen Bollmann)
Date: Fri, 17 Feb 2017 19:05:08 +1000
Subject: [MINC-users] Could NOT find JPEG (missing: JPEG_LIBRARY
	JPEG_INCLUDE_DIR)
Message-ID: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>

Hi All,

I try to install https://github.com/BIC-MNI/minc-toolkit-v2 by following
the readme on an Ubuntu 16.04, but I get this error:

cmake .. \
> -DCMAKE_BUILD_TYPE:STRING=Release   \
> -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.13   \
> -DMT_BUILD_ABC:BOOL=ON   \
> -DMT_BUILD_ANTS:BOOL=ON   \
> -DMT_BUILD_C3D:BOOL=ON   \
> -DMT_BUILD_ELASTIX:BOOL=ON   \
> -DMT_BUILD_IM:BOOL=OFF   \
> -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
> -DMT_BUILD_LITE:BOOL=OFF   \
> -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
> -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
> -DMT_USE_OPENMP:BOOL=ON   \
> -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
> -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
> -DUSE_SYSTEM_GLUT:BOOL=OFF   \
> -DUSE_SYSTEM_GSL:BOOL=OFF   \
> -DUSE_SYSTEM_HDF5:BOOL=OFF   \
> -DUSE_SYSTEM_ITK:BOOL=OFF   \
> -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
> -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
> -DUSE_SYSTEM_PCRE:BOOL=OFF   \
> -DUSE_SYSTEM_ZLIB:BOOL=OFF
-- Could NOT find JPEG (missing:  JPEG_LIBRARY JPEG_INCLUDE_DIR)
HDF5_DIR=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/share/cmake/hdf5
HDF5_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5.so
HDF5_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5_cpp.so
HDF5_HL_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5_hl.so
HDF5_HL_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5_hl_cpp.so
CMake Error: The following variables are used in this project, but they are
set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake
files:
JPEG_INCLUDE_DIR (ADVANCED)
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/olgx
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
   used as include directory in directory
/home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50

-- Configuring incomplete, errors occurred!
See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeOutput.log".
See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeError.log".

What am I doing wrong here :?

Thanks
Steffen

From vladimir.fonov at gmail.com  Fri Feb 17 10:27:13 2017
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Fri, 17 Feb 2017 10:27:13 -0500
Subject: [MINC-users] Could NOT find JPEG (missing: JPEG_LIBRARY
 JPEG_INCLUDE_DIR)
In-Reply-To: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>
References: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>
Message-ID: <7a84c708-56f7-f9ca-c648-cd3614c865b2@gmail.com>

Latest version of dcm2mnc needs libjpeg and libopenjpeg which need to be 
present.

On 2017-02-17 04:05 AM, Steffen Bollmann wrote:
> Hi All,
>
> I try to install https://github.com/BIC-MNI/minc-toolkit-v2 by following
> the readme on an Ubuntu 16.04, but I get this error:
>
> cmake .. \
>> -DCMAKE_BUILD_TYPE:STRING=Release   \
>> -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.13   \
>> -DMT_BUILD_ABC:BOOL=ON   \
>> -DMT_BUILD_ANTS:BOOL=ON   \
>> -DMT_BUILD_C3D:BOOL=ON   \
>> -DMT_BUILD_ELASTIX:BOOL=ON   \
>> -DMT_BUILD_IM:BOOL=OFF   \
>> -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
>> -DMT_BUILD_LITE:BOOL=OFF   \
>> -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
>> -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
>> -DMT_USE_OPENMP:BOOL=ON   \
>> -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
>> -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
>> -DUSE_SYSTEM_GLUT:BOOL=OFF   \
>> -DUSE_SYSTEM_GSL:BOOL=OFF   \
>> -DUSE_SYSTEM_HDF5:BOOL=OFF   \
>> -DUSE_SYSTEM_ITK:BOOL=OFF   \
>> -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
>> -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
>> -DUSE_SYSTEM_PCRE:BOOL=OFF   \
>> -DUSE_SYSTEM_ZLIB:BOOL=OFF
> -- Could NOT find JPEG (missing:  JPEG_LIBRARY JPEG_INCLUDE_DIR)
> HDF5_DIR=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/share/cmake/hdf5
> HDF5_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5.so
> HDF5_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5_cpp.so
> HDF5_HL_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5_hl.so
> HDF5_HL_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/minc/1.9.13/lib/libhdf5_hl_cpp.so
> CMake Error: The following variables are used in this project, but they are
> set to NOTFOUND.
> Please set them or make sure they are set and tested correctly in the CMake
> files:
> JPEG_INCLUDE_DIR (ADVANCED)
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory /home/minc/minc-toolkit-v2/xdisp
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/olgx
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>    used as include directory in directory
> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>
> -- Configuring incomplete, errors occurred!
> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeOutput.log".
> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeError.log".
>
> What am I doing wrong here :?
>
> Thanks
> Steffen
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From stebollmann at gmail.com  Sat Feb 18 00:50:45 2017
From: stebollmann at gmail.com (Steffen Bollmann)
Date: Sat, 18 Feb 2017 15:50:45 +1000
Subject: [MINC-users] Could NOT find JPEG (missing: JPEG_LIBRARY
	JPEG_INCLUDE_DIR)
In-Reply-To: <7a84c708-56f7-f9ca-c648-cd3614c865b2@gmail.com>
References: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>
	<7a84c708-56f7-f9ca-c648-cd3614c865b2@gmail.com>
Message-ID: <CAEimUjhS1Yk7KCu429tV82YjhhMp4gD8=s3sOwz9zUNbkZRO9w@mail.gmail.com>

Dear Vladimir,

Thankyou for your help. I installed these and it worked. The next error is
the missing zlib version, which was already discussed on the list:

    src='http://zlib.net/zlib-1.2.8.tar.gz'

dst='/home/minc/minc-toolkit-v2/build/ZLIB-prefix/src/zlib-1.2.8.tar.gz'
     timeout='none'
CMake Error at ZLIB-prefix/src/ZLIB-stamp/download-ZLIB.cmake:27 (message):
  error: downloading 'http://zlib.net/zlib-1.2.8.tar.gz' failed

    status_code: 22
    status_string: "HTTP response code said error"
    log:   Trying 69.73.132.10...



Is there a fix for this in the stable branch or should I try to compile the
develop branch where this has been fixed?

Thank you
Seffen

2017-02-18 1:27 GMT+10:00 Vladimir S. Fonov <vladimir.fonov at gmail.com>:

> Latest version of dcm2mnc needs libjpeg and libopenjpeg which need to be
> present.
>
>
> On 2017-02-17 04:05 AM, Steffen Bollmann wrote:
>
>> Hi All,
>>
>> I try to install https://github.com/BIC-MNI/minc-toolkit-v2 by following
>> the readme on an Ubuntu 16.04, but I get this error:
>>
>> cmake .. \
>>
>>> -DCMAKE_BUILD_TYPE:STRING=Release   \
>>> -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.13   \
>>> -DMT_BUILD_ABC:BOOL=ON   \
>>> -DMT_BUILD_ANTS:BOOL=ON   \
>>> -DMT_BUILD_C3D:BOOL=ON   \
>>> -DMT_BUILD_ELASTIX:BOOL=ON   \
>>> -DMT_BUILD_IM:BOOL=OFF   \
>>> -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
>>> -DMT_BUILD_LITE:BOOL=OFF   \
>>> -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
>>> -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
>>> -DMT_USE_OPENMP:BOOL=ON   \
>>> -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
>>> -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
>>> -DUSE_SYSTEM_GLUT:BOOL=OFF   \
>>> -DUSE_SYSTEM_GSL:BOOL=OFF   \
>>> -DUSE_SYSTEM_HDF5:BOOL=OFF   \
>>> -DUSE_SYSTEM_ITK:BOOL=OFF   \
>>> -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
>>> -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
>>> -DUSE_SYSTEM_PCRE:BOOL=OFF   \
>>> -DUSE_SYSTEM_ZLIB:BOOL=OFF
>>>
>> -- Could NOT find JPEG (missing:  JPEG_LIBRARY JPEG_INCLUDE_DIR)
>> HDF5_DIR=/home/minc/minc-toolkit-v2/build/external//opt/
>> minc/1.9.13/share/cmake/hdf5
>> HDF5_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/
>> minc/1.9.13/lib/libhdf5.so
>> HDF5_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//
>> opt/minc/1.9.13/lib/libhdf5_cpp.so
>> HDF5_HL_LIBRARY=/home/minc/minc-toolkit-v2/build/external//
>> opt/minc/1.9.13/lib/libhdf5_hl.so
>> HDF5_HL_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/externa
>> l//opt/minc/1.9.13/lib/libhdf5_hl_cpp.so
>> CMake Error: The following variables are used in this project, but they
>> are
>> set to NOTFOUND.
>> Please set them or make sure they are set and tested correctly in the
>> CMake
>> files:
>> JPEG_INCLUDE_DIR (ADVANCED)
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>> sp
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>    used as include directory in directory
>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>
>> -- Configuring incomplete, errors occurred!
>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeOutput.log".
>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeError.log".
>>
>> What am I doing wrong here :?
>>
>> Thanks
>> Steffen
>> _______________________________________________
>> 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 stebollmann at gmail.com  Mon Feb 20 00:18:46 2017
From: stebollmann at gmail.com (Steffen Bollmann)
Date: Mon, 20 Feb 2017 15:18:46 +1000
Subject: [MINC-users] Could NOT find JPEG (missing: JPEG_LIBRARY
	JPEG_INCLUDE_DIR)
In-Reply-To: <CAEimUjhS1Yk7KCu429tV82YjhhMp4gD8=s3sOwz9zUNbkZRO9w@mail.gmail.com>
References: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>
	<7a84c708-56f7-f9ca-c648-cd3614c865b2@gmail.com>
	<CAEimUjhS1Yk7KCu429tV82YjhhMp4gD8=s3sOwz9zUNbkZRO9w@mail.gmail.com>
Message-ID: <CAEimUjjCtueT+hF5z_dcNDCLXkKTD2_0EZzrVJED=8cpSrhWzQ@mail.gmail.com>

I tried compiling the develop branch and for 'make test' I get one error:

99% tests passed, 1 tests failed out of 104

Total Test time (real) =  44.28 sec

The following tests FAILED:
    104 - minctracc_bfgs_nonlinear (Failed)
Errors while running CTest
Makefile:72: recipe for target 'test' failed
make: *** [test] Error 8



when I try to run 'make install', I get this error:

Install the project...
-- Install configuration: "Release"
-- Installing: /opt/minc-itk4/./bin
CMake Error at cmake_install.cmake:36 (file):
  file INSTALL cannot make directory "/opt/minc-itk4/./bin": No such file or
  directory


Makefile:148: recipe for target 'install' failed
make: *** [install] Error 1


How can I solve this?

Thank you and kind regards
Steffen

2017-02-18 15:50 GMT+10:00 Steffen Bollmann <stebollmann at gmail.com>:

> Dear Vladimir,
>
> Thankyou for your help. I installed these and it worked. The next error is
> the missing zlib version, which was already discussed on the list:
>
>     src='http://zlib.net/zlib-1.2.8.tar.gz'
>      dst='/home/minc/minc-toolkit-v2/build/ZLIB-prefix/src/zlib-
> 1.2.8.tar.gz'
>      timeout='none'
> CMake Error at ZLIB-prefix/src/ZLIB-stamp/download-ZLIB.cmake:27
> (message):
>   error: downloading 'http://zlib.net/zlib-1.2.8.tar.gz' failed
>
>     status_code: 22
>     status_string: "HTTP response code said error"
>     log:   Trying 69.73.132.10...
>
>
>
> Is there a fix for this in the stable branch or should I try to compile
> the develop branch where this has been fixed?
>
> Thank you
> Seffen
>
> 2017-02-18 1:27 GMT+10:00 Vladimir S. Fonov <vladimir.fonov at gmail.com>:
>
>> Latest version of dcm2mnc needs libjpeg and libopenjpeg which need to be
>> present.
>>
>>
>> On 2017-02-17 04:05 AM, Steffen Bollmann wrote:
>>
>>> Hi All,
>>>
>>> I try to install https://github.com/BIC-MNI/minc-toolkit-v2 by following
>>> the readme on an Ubuntu 16.04, but I get this error:
>>>
>>> cmake .. \
>>>
>>>> -DCMAKE_BUILD_TYPE:STRING=Release   \
>>>> -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.13   \
>>>> -DMT_BUILD_ABC:BOOL=ON   \
>>>> -DMT_BUILD_ANTS:BOOL=ON   \
>>>> -DMT_BUILD_C3D:BOOL=ON   \
>>>> -DMT_BUILD_ELASTIX:BOOL=ON   \
>>>> -DMT_BUILD_IM:BOOL=OFF   \
>>>> -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
>>>> -DMT_BUILD_LITE:BOOL=OFF   \
>>>> -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
>>>> -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
>>>> -DMT_USE_OPENMP:BOOL=ON   \
>>>> -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
>>>> -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
>>>> -DUSE_SYSTEM_GLUT:BOOL=OFF   \
>>>> -DUSE_SYSTEM_GSL:BOOL=OFF   \
>>>> -DUSE_SYSTEM_HDF5:BOOL=OFF   \
>>>> -DUSE_SYSTEM_ITK:BOOL=OFF   \
>>>> -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
>>>> -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
>>>> -DUSE_SYSTEM_PCRE:BOOL=OFF   \
>>>> -DUSE_SYSTEM_ZLIB:BOOL=OFF
>>>>
>>> -- Could NOT find JPEG (missing:  JPEG_LIBRARY JPEG_INCLUDE_DIR)
>>> HDF5_DIR=/home/minc/minc-toolkit-v2/build/external//opt/minc
>>> /1.9.13/share/cmake/hdf5
>>> HDF5_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/
>>> minc/1.9.13/lib/libhdf5.so
>>> HDF5_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//
>>> opt/minc/1.9.13/lib/libhdf5_cpp.so
>>> HDF5_HL_LIBRARY=/home/minc/minc-toolkit-v2/build/external//o
>>> pt/minc/1.9.13/lib/libhdf5_hl.so
>>> HDF5_HL_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/externa
>>> l//opt/minc/1.9.13/lib/libhdf5_hl_cpp.so
>>> CMake Error: The following variables are used in this project, but they
>>> are
>>> set to NOTFOUND.
>>> Please set them or make sure they are set and tested correctly in the
>>> CMake
>>> files:
>>> JPEG_INCLUDE_DIR (ADVANCED)
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>> sp
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>    used as include directory in directory
>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>
>>> -- Configuring incomplete, errors occurred!
>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeOutput.log".
>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeError.log".
>>>
>>> What am I doing wrong here :?
>>>
>>> Thanks
>>> Steffen
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>
>>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>

From vladimir.fonov at gmail.com  Mon Feb 20 18:08:46 2017
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 20 Feb 2017 18:08:46 -0500
Subject: [MINC-users] Could NOT find JPEG (missing: JPEG_LIBRARY
 JPEG_INCLUDE_DIR)
In-Reply-To: <CAEimUjjCtueT+hF5z_dcNDCLXkKTD2_0EZzrVJED=8cpSrhWzQ@mail.gmail.com>
References: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>
	<7a84c708-56f7-f9ca-c648-cd3614c865b2@gmail.com>
	<CAEimUjhS1Yk7KCu429tV82YjhhMp4gD8=s3sOwz9zUNbkZRO9w@mail.gmail.com>
	<CAEimUjjCtueT+hF5z_dcNDCLXkKTD2_0EZzrVJED=8cpSrhWzQ@mail.gmail.com>
Message-ID: <7625329e-563e-3392-afb1-bf207fc7df82@gmail.com>

Hello,

On 2017-02-20 12:18 AM, Steffen Bollmann wrote:
> I tried compiling the develop branch and for 'make test' I get one error:
>
> 99% tests passed, 1 tests failed out of 104
>
> Total Test time (real) =  44.28 sec
>
> The following tests FAILED:
>     104 - minctracc_bfgs_nonlinear (Failed)
> Errors while running CTest
> Makefile:72: recipe for target 'test' failed
> make: *** [test] Error 8

You can ignore this one.


>
>
>
> when I try to run 'make install', I get this error:
>
> Install the project...
> -- Install configuration: "Release"
> -- Installing: /opt/minc-itk4/./bin
> CMake Error at cmake_install.cmake:36 (file):
>   file INSTALL cannot make directory "/opt/minc-itk4/./bin": No such file or
>   directory

You don't have permission to create /opt/minc-itk4  (i.e run with sudo)



>
>
> Makefile:148: recipe for target 'install' failed
> make: *** [install] Error 1
>
>
> How can I solve this?
>
> Thank you and kind regards
> Steffen
>
> 2017-02-18 15:50 GMT+10:00 Steffen Bollmann <stebollmann at gmail.com>:
>
>> Dear Vladimir,
>>
>> Thankyou for your help. I installed these and it worked. The next error is
>> the missing zlib version, which was already discussed on the list:
>>
>>     src='http://zlib.net/zlib-1.2.8.tar.gz'
>>      dst='/home/minc/minc-toolkit-v2/build/ZLIB-prefix/src/zlib-
>> 1.2.8.tar.gz'
>>      timeout='none'
>> CMake Error at ZLIB-prefix/src/ZLIB-stamp/download-ZLIB.cmake:27
>> (message):
>>   error: downloading 'http://zlib.net/zlib-1.2.8.tar.gz' failed
>>
>>     status_code: 22
>>     status_string: "HTTP response code said error"
>>     log:   Trying 69.73.132.10...
>>
>>
>>
>> Is there a fix for this in the stable branch or should I try to compile
>> the develop branch where this has been fixed?
>>
>> Thank you
>> Seffen
>>
>> 2017-02-18 1:27 GMT+10:00 Vladimir S. Fonov <vladimir.fonov at gmail.com>:
>>
>>> Latest version of dcm2mnc needs libjpeg and libopenjpeg which need to be
>>> present.
>>>
>>>
>>> On 2017-02-17 04:05 AM, Steffen Bollmann wrote:
>>>
>>>> Hi All,
>>>>
>>>> I try to install https://github.com/BIC-MNI/minc-toolkit-v2 by following
>>>> the readme on an Ubuntu 16.04, but I get this error:
>>>>
>>>> cmake .. \
>>>>
>>>>> -DCMAKE_BUILD_TYPE:STRING=Release   \
>>>>> -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.13   \
>>>>> -DMT_BUILD_ABC:BOOL=ON   \
>>>>> -DMT_BUILD_ANTS:BOOL=ON   \
>>>>> -DMT_BUILD_C3D:BOOL=ON   \
>>>>> -DMT_BUILD_ELASTIX:BOOL=ON   \
>>>>> -DMT_BUILD_IM:BOOL=OFF   \
>>>>> -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
>>>>> -DMT_BUILD_LITE:BOOL=OFF   \
>>>>> -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
>>>>> -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
>>>>> -DMT_USE_OPENMP:BOOL=ON   \
>>>>> -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_GLUT:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_GSL:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_HDF5:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_ITK:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_PCRE:BOOL=OFF   \
>>>>> -DUSE_SYSTEM_ZLIB:BOOL=OFF
>>>>>
>>>> -- Could NOT find JPEG (missing:  JPEG_LIBRARY JPEG_INCLUDE_DIR)
>>>> HDF5_DIR=/home/minc/minc-toolkit-v2/build/external//opt/minc
>>>> /1.9.13/share/cmake/hdf5
>>>> HDF5_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/
>>>> minc/1.9.13/lib/libhdf5.so
>>>> HDF5_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//
>>>> opt/minc/1.9.13/lib/libhdf5_cpp.so
>>>> HDF5_HL_LIBRARY=/home/minc/minc-toolkit-v2/build/external//o
>>>> pt/minc/1.9.13/lib/libhdf5_hl.so
>>>> HDF5_HL_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/externa
>>>> l//opt/minc/1.9.13/lib/libhdf5_hl_cpp.so
>>>> CMake Error: The following variables are used in this project, but they
>>>> are
>>>> set to NOTFOUND.
>>>> Please set them or make sure they are set and tested correctly in the
>>>> CMake
>>>> files:
>>>> JPEG_INCLUDE_DIR (ADVANCED)
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory /home/minc/minc-toolkit-v2/xdi
>>>> sp
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>    used as include directory in directory
>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>
>>>> -- Configuring incomplete, errors occurred!
>>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeOutput.log".
>>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeError.log".
>>>>
>>>> What am I doing wrong here :?
>>>>
>>>> Thanks
>>>> Steffen
>>>> _______________________________________________
>>>> 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
>


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From stebollmann at gmail.com  Mon Feb 20 19:29:35 2017
From: stebollmann at gmail.com (Steffen Bollmann)
Date: Tue, 21 Feb 2017 10:29:35 +1000
Subject: [MINC-users] Could NOT find JPEG (missing: JPEG_LIBRARY
	JPEG_INCLUDE_DIR)
In-Reply-To: <7625329e-563e-3392-afb1-bf207fc7df82@gmail.com>
References: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>
	<7a84c708-56f7-f9ca-c648-cd3614c865b2@gmail.com>
	<CAEimUjhS1Yk7KCu429tV82YjhhMp4gD8=s3sOwz9zUNbkZRO9w@mail.gmail.com>
	<CAEimUjjCtueT+hF5z_dcNDCLXkKTD2_0EZzrVJED=8cpSrhWzQ@mail.gmail.com>
	<7625329e-563e-3392-afb1-bf207fc7df82@gmail.com>
Message-ID: <CAEimUjj2SAaO3NMCz6N7bRiQv7Ynnq+Q7s_zZae7MGbWEw_SrQ@mail.gmail.com>

Dear Vladimir,

Thank you for you help. The sudo should have been obvious, but I did not
realize that I wasn't root anymore when running that :/

Do you think it would be helpful to provide a virtual machine with a
compiled version of MINC for people struggling with compiling minc?

Best
Steffen

2017-02-21 9:08 GMT+10:00 Vladimir S. FONOV <vladimir.fonov at gmail.com>:

> Hello,
>
> On 2017-02-20 12:18 AM, Steffen Bollmann wrote:
>
>> I tried compiling the develop branch and for 'make test' I get one error:
>>
>> 99% tests passed, 1 tests failed out of 104
>>
>> Total Test time (real) =  44.28 sec
>>
>> The following tests FAILED:
>>     104 - minctracc_bfgs_nonlinear (Failed)
>> Errors while running CTest
>> Makefile:72: recipe for target 'test' failed
>> make: *** [test] Error 8
>>
>
> You can ignore this one.
>
>
>
>>
>>
>> when I try to run 'make install', I get this error:
>>
>> Install the project...
>> -- Install configuration: "Release"
>> -- Installing: /opt/minc-itk4/./bin
>> CMake Error at cmake_install.cmake:36 (file):
>>   file INSTALL cannot make directory "/opt/minc-itk4/./bin": No such file
>> or
>>   directory
>>
>
> You don't have permission to create /opt/minc-itk4  (i.e run with sudo)
>
>
>
>
>>
>> Makefile:148: recipe for target 'install' failed
>> make: *** [install] Error 1
>>
>>
>> How can I solve this?
>>
>> Thank you and kind regards
>> Steffen
>>
>> 2017-02-18 15:50 GMT+10:00 Steffen Bollmann <stebollmann at gmail.com>:
>>
>> Dear Vladimir,
>>>
>>> Thankyou for your help. I installed these and it worked. The next error
>>> is
>>> the missing zlib version, which was already discussed on the list:
>>>
>>>     src='http://zlib.net/zlib-1.2.8.tar.gz'
>>>      dst='/home/minc/minc-toolkit-v2/build/ZLIB-prefix/src/zlib-
>>> 1.2.8.tar.gz'
>>>      timeout='none'
>>> CMake Error at ZLIB-prefix/src/ZLIB-stamp/download-ZLIB.cmake:27
>>> (message):
>>>   error: downloading 'http://zlib.net/zlib-1.2.8.tar.gz' failed
>>>
>>>     status_code: 22
>>>     status_string: "HTTP response code said error"
>>>     log:   Trying 69.73.132.10...
>>>
>>>
>>>
>>> Is there a fix for this in the stable branch or should I try to compile
>>> the develop branch where this has been fixed?
>>>
>>> Thank you
>>> Seffen
>>>
>>> 2017-02-18 1:27 GMT+10:00 Vladimir S. Fonov <vladimir.fonov at gmail.com>:
>>>
>>> Latest version of dcm2mnc needs libjpeg and libopenjpeg which need to be
>>>> present.
>>>>
>>>>
>>>> On 2017-02-17 04:05 AM, Steffen Bollmann wrote:
>>>>
>>>> Hi All,
>>>>>
>>>>> I try to install https://github.com/BIC-MNI/minc-toolkit-v2 by
>>>>> following
>>>>> the readme on an Ubuntu 16.04, but I get this error:
>>>>>
>>>>> cmake .. \
>>>>>
>>>>> -DCMAKE_BUILD_TYPE:STRING=Release   \
>>>>>> -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.13   \
>>>>>> -DMT_BUILD_ABC:BOOL=ON   \
>>>>>> -DMT_BUILD_ANTS:BOOL=ON   \
>>>>>> -DMT_BUILD_C3D:BOOL=ON   \
>>>>>> -DMT_BUILD_ELASTIX:BOOL=ON   \
>>>>>> -DMT_BUILD_IM:BOOL=OFF   \
>>>>>> -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
>>>>>> -DMT_BUILD_LITE:BOOL=OFF   \
>>>>>> -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
>>>>>> -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
>>>>>> -DMT_USE_OPENMP:BOOL=ON   \
>>>>>> -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_GLUT:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_GSL:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_HDF5:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_ITK:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_PCRE:BOOL=OFF   \
>>>>>> -DUSE_SYSTEM_ZLIB:BOOL=OFF
>>>>>>
>>>>>> -- Could NOT find JPEG (missing:  JPEG_LIBRARY JPEG_INCLUDE_DIR)
>>>>> HDF5_DIR=/home/minc/minc-toolkit-v2/build/external//opt/minc
>>>>> /1.9.13/share/cmake/hdf5
>>>>> HDF5_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/
>>>>> minc/1.9.13/lib/libhdf5.so
>>>>> HDF5_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//
>>>>> opt/minc/1.9.13/lib/libhdf5_cpp.so
>>>>> HDF5_HL_LIBRARY=/home/minc/minc-toolkit-v2/build/external//o
>>>>> pt/minc/1.9.13/lib/libhdf5_hl.so
>>>>> HDF5_HL_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/externa
>>>>> l//opt/minc/1.9.13/lib/libhdf5_hl_cpp.so
>>>>> CMake Error: The following variables are used in this project, but they
>>>>> are
>>>>> set to NOTFOUND.
>>>>> Please set them or make sure they are set and tested correctly in the
>>>>> CMake
>>>>> files:
>>>>> JPEG_INCLUDE_DIR (ADVANCED)
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>> sp
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>    used as include directory in directory
>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>
>>>>> -- Configuring incomplete, errors occurred!
>>>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeOutput.log
>>>>> ".
>>>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeError.log".
>>>>>
>>>>> What am I doing wrong here :?
>>>>>
>>>>> Thanks
>>>>> Steffen
>>>>> _______________________________________________
>>>>> 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
>>
>>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From stebollmann at gmail.com  Mon Feb 20 20:01:27 2017
From: stebollmann at gmail.com (Steffen Bollmann)
Date: Tue, 21 Feb 2017 11:01:27 +1000
Subject: [MINC-users] Could NOT find JPEG (missing: JPEG_LIBRARY
	JPEG_INCLUDE_DIR)
In-Reply-To: <CAEimUjj2SAaO3NMCz6N7bRiQv7Ynnq+Q7s_zZae7MGbWEw_SrQ@mail.gmail.com>
References: <CAEimUjjj8s_j0PbsC_Xfb8GiArguRc41D3irPb4=XggLzE4XKg@mail.gmail.com>
	<7a84c708-56f7-f9ca-c648-cd3614c865b2@gmail.com>
	<CAEimUjhS1Yk7KCu429tV82YjhhMp4gD8=s3sOwz9zUNbkZRO9w@mail.gmail.com>
	<CAEimUjjCtueT+hF5z_dcNDCLXkKTD2_0EZzrVJED=8cpSrhWzQ@mail.gmail.com>
	<7625329e-563e-3392-afb1-bf207fc7df82@gmail.com>
	<CAEimUjj2SAaO3NMCz6N7bRiQv7Ynnq+Q7s_zZae7MGbWEw_SrQ@mail.gmail.com>
Message-ID: <CAEimUjh0+z9DvXBTaseGFyV=UCjGJ-9c5rDeBgO3XxA_aCqt4g@mail.gmail.com>

Ok, a quick search later: A virtual machine with minc exists already :)
https://github.com/CobraLab/MINC-VM

Thank you
Best
Steffen

2017-02-21 10:29 GMT+10:00 Steffen Bollmann <stebollmann at gmail.com>:

> Dear Vladimir,
>
> Thank you for you help. The sudo should have been obvious, but I did not
> realize that I wasn't root anymore when running that :/
>
> Do you think it would be helpful to provide a virtual machine with a
> compiled version of MINC for people struggling with compiling minc?
>
> Best
> Steffen
>
> 2017-02-21 9:08 GMT+10:00 Vladimir S. FONOV <vladimir.fonov at gmail.com>:
>
>> Hello,
>>
>> On 2017-02-20 12:18 AM, Steffen Bollmann wrote:
>>
>>> I tried compiling the develop branch and for 'make test' I get one error:
>>>
>>> 99% tests passed, 1 tests failed out of 104
>>>
>>> Total Test time (real) =  44.28 sec
>>>
>>> The following tests FAILED:
>>>     104 - minctracc_bfgs_nonlinear (Failed)
>>> Errors while running CTest
>>> Makefile:72: recipe for target 'test' failed
>>> make: *** [test] Error 8
>>>
>>
>> You can ignore this one.
>>
>>
>>
>>>
>>>
>>> when I try to run 'make install', I get this error:
>>>
>>> Install the project...
>>> -- Install configuration: "Release"
>>> -- Installing: /opt/minc-itk4/./bin
>>> CMake Error at cmake_install.cmake:36 (file):
>>>   file INSTALL cannot make directory "/opt/minc-itk4/./bin": No such
>>> file or
>>>   directory
>>>
>>
>> You don't have permission to create /opt/minc-itk4  (i.e run with sudo)
>>
>>
>>
>>
>>>
>>> Makefile:148: recipe for target 'install' failed
>>> make: *** [install] Error 1
>>>
>>>
>>> How can I solve this?
>>>
>>> Thank you and kind regards
>>> Steffen
>>>
>>> 2017-02-18 15:50 GMT+10:00 Steffen Bollmann <stebollmann at gmail.com>:
>>>
>>> Dear Vladimir,
>>>>
>>>> Thankyou for your help. I installed these and it worked. The next error
>>>> is
>>>> the missing zlib version, which was already discussed on the list:
>>>>
>>>>     src='http://zlib.net/zlib-1.2.8.tar.gz'
>>>>      dst='/home/minc/minc-toolkit-v2/build/ZLIB-prefix/src/zlib-
>>>> 1.2.8.tar.gz'
>>>>      timeout='none'
>>>> CMake Error at ZLIB-prefix/src/ZLIB-stamp/download-ZLIB.cmake:27
>>>> (message):
>>>>   error: downloading 'http://zlib.net/zlib-1.2.8.tar.gz' failed
>>>>
>>>>     status_code: 22
>>>>     status_string: "HTTP response code said error"
>>>>     log:   Trying 69.73.132.10...
>>>>
>>>>
>>>>
>>>> Is there a fix for this in the stable branch or should I try to compile
>>>> the develop branch where this has been fixed?
>>>>
>>>> Thank you
>>>> Seffen
>>>>
>>>> 2017-02-18 1:27 GMT+10:00 Vladimir S. Fonov <vladimir.fonov at gmail.com>:
>>>>
>>>> Latest version of dcm2mnc needs libjpeg and libopenjpeg which need to be
>>>>> present.
>>>>>
>>>>>
>>>>> On 2017-02-17 04:05 AM, Steffen Bollmann wrote:
>>>>>
>>>>> Hi All,
>>>>>>
>>>>>> I try to install https://github.com/BIC-MNI/minc-toolkit-v2 by
>>>>>> following
>>>>>> the readme on an Ubuntu 16.04, but I get this error:
>>>>>>
>>>>>> cmake .. \
>>>>>>
>>>>>> -DCMAKE_BUILD_TYPE:STRING=Release   \
>>>>>>> -DCMAKE_INSTALL_PREFIX:PATH=/opt/minc/1.9.13   \
>>>>>>> -DMT_BUILD_ABC:BOOL=ON   \
>>>>>>> -DMT_BUILD_ANTS:BOOL=ON   \
>>>>>>> -DMT_BUILD_C3D:BOOL=ON   \
>>>>>>> -DMT_BUILD_ELASTIX:BOOL=ON   \
>>>>>>> -DMT_BUILD_IM:BOOL=OFF   \
>>>>>>> -DMT_BUILD_ITK_TOOLS:BOOL=ON   \
>>>>>>> -DMT_BUILD_LITE:BOOL=OFF   \
>>>>>>> -DMT_BUILD_SHARED_LIBS:BOOL=ON   \
>>>>>>> -DMT_BUILD_VISUAL_TOOLS:BOOL=ON   \
>>>>>>> -DMT_USE_OPENMP:BOOL=ON   \
>>>>>>> -DUSE_SYSTEM_FFTW3D:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_FFTW3F:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_GLUT:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_GSL:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_HDF5:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_ITK:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_NETCDF:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_NIFTI:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_PCRE:BOOL=OFF   \
>>>>>>> -DUSE_SYSTEM_ZLIB:BOOL=OFF
>>>>>>>
>>>>>>> -- Could NOT find JPEG (missing:  JPEG_LIBRARY JPEG_INCLUDE_DIR)
>>>>>> HDF5_DIR=/home/minc/minc-toolkit-v2/build/external//opt/minc
>>>>>> /1.9.13/share/cmake/hdf5
>>>>>> HDF5_LIBRARY=/home/minc/minc-toolkit-v2/build/external//opt/
>>>>>> minc/1.9.13/lib/libhdf5.so
>>>>>> HDF5_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/external//
>>>>>> opt/minc/1.9.13/lib/libhdf5_cpp.so
>>>>>> HDF5_HL_LIBRARY=/home/minc/minc-toolkit-v2/build/external//o
>>>>>> pt/minc/1.9.13/lib/libhdf5_hl.so
>>>>>> HDF5_HL_CPP_LIBRARY=/home/minc/minc-toolkit-v2/build/externa
>>>>>> l//opt/minc/1.9.13/lib/libhdf5_hl_cpp.so
>>>>>> CMake Error: The following variables are used in this project, but
>>>>>> they
>>>>>> are
>>>>>> set to NOTFOUND.
>>>>>> Please set them or make sure they are set and tested correctly in the
>>>>>> CMake
>>>>>> files:
>>>>>> JPEG_INCLUDE_DIR (ADVANCED)
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdi
>>>>>> sp
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/olgx
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>    used as include directory in directory
>>>>>> /home/minc/minc-toolkit-v2/xdisp/EZWGL-1.50
>>>>>>
>>>>>> -- Configuring incomplete, errors occurred!
>>>>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeOutput.log
>>>>>> ".
>>>>>> See also "/home/minc/minc-toolkit-v2/build/CMakeFiles/CMakeError.log"
>>>>>> .
>>>>>>
>>>>>> What am I doing wrong here :?
>>>>>>
>>>>>> Thanks
>>>>>> Steffen
>>>>>> _______________________________________________
>>>>>> 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
>>>
>>>
>>
>> --
>> Best regards,
>>
>>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>