From ptcougopinto at gmail.com  Mon May  2 11:08:28 2016
From: ptcougopinto at gmail.com (Pedro)
Date: Mon, 2 May 2016 12:08:28 -0300
Subject: [MINC-users] Extract coord and voxel data
In-Reply-To: <CAHfsrRard0aGpZQpdnLSYwuwtUWrCjywFJ6E-DPMU90Hc0nY9A@mail.gmail.com>
References: <D555EA71-3EB9-4767-90F6-A54B5B1A9D88@gmail.com>
	<CAAd5DeSskGqueY4HagrGOu5Z1OqdHkjR_7n4i+9bLAuCf3S_3w@mail.gmail.com>
	<CAHfsrRard0aGpZQpdnLSYwuwtUWrCjywFJ6E-DPMU90Hc0nY9A@mail.gmail.com>
Message-ID: <76590F2C-135B-4D77-AB78-B15FC83FD472@gmail.com>

Thanks, all. Exactly what I was looking for. However, voxel values are rounded to integer. I saw there is an old email thread from 2004 about this.
> Em 30 de abr de 2016, ?(s) 14:30, Soren Christensen <sorench at gmail.com> escreveu:
> 
> Hi,
> Alternatively I guess the output is implicitly ordered by voxel coordinate
> (fastest to slowest varying dim I assume). So the actual output index is
> the linear index of the voxel location and you then simply have to
> translate the line number to the voxel coordinate with the appropriate
> calculation.
> 
> Soren
> 
> 
> On Fri, Apr 29, 2016 at 7:44 PM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
> 
>> Hi,
>> 
>> There is a tool called minctotag, which does exactly that:
>> 
>> minctotag file.mnc file.tag
>> 
>> extracts all values and  into an MNI .tag format file, which is a fairly
>> simple ASCII file. I think it outputs world coordinates rather than voxel
>> coordinates, however.
>> 
>>    -bert
>> 
>> 
>> 
>> On Fri, Apr 29, 2016 at 9:28 PM, Pedro Telles Cougo Pinto <
>> ptcougopinto at gmail.com> wrote:
>> 
>>> Hi, everyone ?
>>> 
>>> Mincextract exports voxel value, but is it possible to also extract the
>>> corresponding voxel coordinate data together with the scalar value?
>>> 
>>> Thanks
>>> Pedro
>>> _______________________________________________
>>> 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 robert.d.vincent at mcgill.ca  Mon May  2 11:11:56 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Mon, 2 May 2016 11:11:56 -0400
Subject: [MINC-users] Extract coord and voxel data
In-Reply-To: <76590F2C-135B-4D77-AB78-B15FC83FD472@gmail.com>
References: <D555EA71-3EB9-4767-90F6-A54B5B1A9D88@gmail.com>
	<CAAd5DeSskGqueY4HagrGOu5Z1OqdHkjR_7n4i+9bLAuCf3S_3w@mail.gmail.com>
	<CAHfsrRard0aGpZQpdnLSYwuwtUWrCjywFJ6E-DPMU90Hc0nY9A@mail.gmail.com>
	<76590F2C-135B-4D77-AB78-B15FC83FD472@gmail.com>
Message-ID: <CAAd5DeT6_tEX4ktQjVFN93KZoiqFQAfrmEhe1ue-BXCWNkdJKw@mail.gmail.com>

Easy enough to fix. I'll add this to my "todo" list and either add a
"coordinates" option to mincextract or other output options for minctotag.

    -bert

On Mon, May 2, 2016 at 11:08 AM, Pedro <ptcougopinto at gmail.com> wrote:

> Thanks, all. Exactly what I was looking for. However, voxel values are
> rounded to integer. I saw there is an old email thread from 2004 about this.
> > Em 30 de abr de 2016, ?(s) 14:30, Soren Christensen <sorench at gmail.com>
> escreveu:
> >
> > Hi,
> > Alternatively I guess the output is implicitly ordered by voxel
> coordinate
> > (fastest to slowest varying dim I assume). So the actual output index is
> > the linear index of the voxel location and you then simply have to
> > translate the line number to the voxel coordinate with the appropriate
> > calculation.
> >
> > Soren
> >
> >
> > On Fri, Apr 29, 2016 at 7:44 PM, Robert D. Vincent <
> > robert.d.vincent at mcgill.ca> wrote:
> >
> >> Hi,
> >>
> >> There is a tool called minctotag, which does exactly that:
> >>
> >> minctotag file.mnc file.tag
> >>
> >> extracts all values and  into an MNI .tag format file, which is a fairly
> >> simple ASCII file. I think it outputs world coordinates rather than
> voxel
> >> coordinates, however.
> >>
> >>    -bert
> >>
> >>
> >>
> >> On Fri, Apr 29, 2016 at 9:28 PM, Pedro Telles Cougo Pinto <
> >> ptcougopinto at gmail.com> wrote:
> >>
> >>> Hi, everyone ?
> >>>
> >>> Mincextract exports voxel value, but is it possible to also extract the
> >>> corresponding voxel coordinate data together with the scalar value?
> >>>
> >>> Thanks
> >>> Pedro
> >>> _______________________________________________
> >>> 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 ptcougopinto at gmail.com  Mon May  2 11:33:59 2016
From: ptcougopinto at gmail.com (Pedro)
Date: Mon, 2 May 2016 12:33:59 -0300
Subject: [MINC-users] Extract coord and voxel data
In-Reply-To: <CAAd5DeT6_tEX4ktQjVFN93KZoiqFQAfrmEhe1ue-BXCWNkdJKw@mail.gmail.com>
References: <D555EA71-3EB9-4767-90F6-A54B5B1A9D88@gmail.com>
	<CAAd5DeSskGqueY4HagrGOu5Z1OqdHkjR_7n4i+9bLAuCf3S_3w@mail.gmail.com>
	<CAHfsrRard0aGpZQpdnLSYwuwtUWrCjywFJ6E-DPMU90Hc0nY9A@mail.gmail.com>
	<76590F2C-135B-4D77-AB78-B15FC83FD472@gmail.com>
	<CAAd5DeT6_tEX4ktQjVFN93KZoiqFQAfrmEhe1ue-BXCWNkdJKw@mail.gmail.com>
Message-ID: <81E63E89-6865-4124-A18D-357F34CE845A@gmail.com>

Thanks, Robert. (Wish I knew C)

> Em 2 de mai de 2016, ?(s) 12:11, Robert D. Vincent <robert.d.vincent at mcgill.ca> escreveu:
> 
> Easy enough to fix. I'll add this to my "todo" list and either add a
> "coordinates" option to mincextract or other output options for minctotag.
> 
>    -bert
> 
> On Mon, May 2, 2016 at 11:08 AM, Pedro <ptcougopinto at gmail.com> wrote:
> 
>> Thanks, all. Exactly what I was looking for. However, voxel values are
>> rounded to integer. I saw there is an old email thread from 2004 about this.
>>> Em 30 de abr de 2016, ?(s) 14:30, Soren Christensen <sorench at gmail.com>
>> escreveu:
>>> 
>>> Hi,
>>> Alternatively I guess the output is implicitly ordered by voxel
>> coordinate
>>> (fastest to slowest varying dim I assume). So the actual output index is
>>> the linear index of the voxel location and you then simply have to
>>> translate the line number to the voxel coordinate with the appropriate
>>> calculation.
>>> 
>>> Soren
>>> 
>>> 
>>> On Fri, Apr 29, 2016 at 7:44 PM, Robert D. Vincent <
>>> robert.d.vincent at mcgill.ca> wrote:
>>> 
>>>> Hi,
>>>> 
>>>> There is a tool called minctotag, which does exactly that:
>>>> 
>>>> minctotag file.mnc file.tag
>>>> 
>>>> extracts all values and  into an MNI .tag format file, which is a fairly
>>>> simple ASCII file. I think it outputs world coordinates rather than
>> voxel
>>>> coordinates, however.
>>>> 
>>>>   -bert
>>>> 
>>>> 
>>>> 
>>>> On Fri, Apr 29, 2016 at 9:28 PM, Pedro Telles Cougo Pinto <
>>>> ptcougopinto at gmail.com> wrote:
>>>> 
>>>>> Hi, everyone ?
>>>>> 
>>>>> Mincextract exports voxel value, but is it possible to also extract the
>>>>> corresponding voxel coordinate data together with the scalar value?
>>>>> 
>>>>> Thanks
>>>>> Pedro
>>>>> _______________________________________________
>>>>> 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 ptcougopinto at gmail.com  Tue May  3 09:36:51 2016
From: ptcougopinto at gmail.com (Pedro)
Date: Tue, 3 May 2016 10:36:51 -0300
Subject: [MINC-users] classify: how to use
Message-ID: <F796399C-64DF-4418-B6A8-6594116BA750@gmail.com>


Hi, everyone ?

What should be the minimum command line for classify? What are the inputs and output? I could?t figure out from -help. (Just found out that I?m not happy with registration based segmentation of my data).

Thanks!
Pedro

From redoute at cermep.fr  Tue May  3 10:46:48 2016
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Tue, 3 May 2016 16:46:48 +0200
Subject: [MINC-users] minc-toolkit-v2 compilation
Message-ID: <5728B9D8.6090605@cermep.fr>

Hi,
Could someone help me to set up my debian environment for compiling 
minc-toolkit-v2 using git repository?

> |git clone --recursive https://github.com/BIC-MNI/minc-toolkit-v2.git 
> minc-toolkit-v2 |
allows me to copy all the repository.. but how can I compile the develop 
branch only?

is there specific instructions for ccmake et make?

Thanks for your help
Jerome


-- 
==================================================================
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 robert.d.vincent at mcgill.ca  Tue May  3 11:55:37 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Tue, 3 May 2016 11:55:37 -0400
Subject: [MINC-users] minc-toolkit-v2 compilation
In-Reply-To: <5728B9D8.6090605@cermep.fr>
References: <5728B9D8.6090605@cermep.fr>
Message-ID: <CAAd5DeSH24eZC7H2UdWmOi0TMPL8VsK5LsKCNn8ebM2-DE0vWg@mail.gmail.com>

Hi Jerome,

Here is how I check out 'develop' and build for everything on Ubuntu
(although this is for minc-toolkit, not minc-toolkit-v2, the same idea
should work).

 sudo apt-get install -y \
 build-essential \
 g++ \
 cmake \
 cmake-curses-gui \
 bison \
 flex \
 freeglut3 \
 freeglut3-dev \
 libxi6 \
 libxi-dev \
 libxmu6 \
 libxmu-dev \
 libxmu-headers \
 zlib1g-dev \
 libexpat1-dev \
 bc \
 git

git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git
cd minc-toolkit
git checkout develop
git submodule foreach --recursive 'git checkout develop || :'

mkdir ../minc-build
cd ../minc-build
cmake ../minc-toolkit -DCMAKE_BUILD_TYPE=Release -DMT_BUILD_VISUAL_TOOLS=ON
make




On Tue, May 3, 2016 at 10:46 AM, J?r?me Redout? <redoute at cermep.fr> wrote:

> Hi,
> Could someone help me to set up my debian environment for compiling
> minc-toolkit-v2 using git repository?
>
> |git clone --recursive https://github.com/BIC-MNI/minc-toolkit-v2.git
>> minc-toolkit-v2 |
>>
> allows me to copy all the repository.. but how can I compile the develop
> branch only?
>
> is there specific instructions for ccmake et make?
>
> Thanks for your help
> Jerome
>
>
> --
> ==================================================================
> 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
> ==================================================================
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From trisanna.sprung-much at mail.mcgill.ca  Tue May  3 18:50:06 2016
From: trisanna.sprung-much at mail.mcgill.ca (Trisanna Sprung-Much)
Date: Tue, 3 May 2016 18:50:06 -0400
Subject: [MINC-users] computing SNR
Message-ID: <CAG+ToRv2E1_7W5vQrb_RzpZhF91LXjm7654GsF=u49sn-Mkb0w@mail.gmail.com>

Hi All

Is there an automated way of computing SNR for T1 images using minc tools?

thanks!

Trisanna Sprung-Much
Petrides Lab
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology

From a.janke at gmail.com  Tue May  3 19:17:29 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 4 May 2016 09:17:29 +1000
Subject: [MINC-users] computing SNR
In-Reply-To: <CAG+ToRv2E1_7W5vQrb_RzpZhF91LXjm7654GsF=u49sn-Mkb0w@mail.gmail.com>
References: <CAG+ToRv2E1_7W5vQrb_RzpZhF91LXjm7654GsF=u49sn-Mkb0w@mail.gmail.com>
Message-ID: <CAG0CB22X2WmTMCszJMxPMk51Mbzne3Qcg+OK1PaXWwiHXZCfyQ@mail.gmail.com>

Hi Trisanna,

I'm not aware of a specific tool but the usual approach would be to
register to the ICBM and then use the head mask against the background
using mincmath -mask if this makes sense?


a

On 4 May 2016 at 08:50, Trisanna Sprung-Much
<trisanna.sprung-much at mail.mcgill.ca> wrote:
> Hi All
>
> Is there an automated way of computing SNR for T1 images using minc tools?
>
> thanks!
>
> Trisanna Sprung-Much
> Petrides Lab
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
> _______________________________________________
> 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  3 19:21:48 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 4 May 2016 09:21:48 +1000
Subject: [MINC-users] classify: how to use
In-Reply-To: <F796399C-64DF-4418-B6A8-6594116BA750@gmail.com>
References: <F796399C-64DF-4418-B6A8-6594116BA750@gmail.com>
Message-ID: <CAG0CB20enpaZAkdW7DHRA=DP0Lo-WXTEQBXQdE0MCzj6jWhisg@mail.gmail.com>

Hi Pedro,

This is my approach:

   classify_clean \
         -tagdir <tags> \
         -tag_transform <image-to-tags.xfm> \
         input.mnc output.mnc

<tags> is a directory with the classify tags in it eg:

ls tags/
ntags_1000_bg.tag  ntags_1000_prob_90_nobg.tag


<image-to-tags.xfm> is a tranform from your native data space
(input.mnc) to the space of the tags. If you are using the ones in the
standard package this will be a transform from native space to the
icbm152 model.


a



On 3 May 2016 at 23:36, Pedro <ptcougopinto at gmail.com> wrote:
>
> Hi, everyone ?
>
> What should be the minimum command line for classify? What are the inputs and output? I could?t figure out from -help. (Just found out that I?m not happy with registration based segmentation of my data).
>
> Thanks!
> Pedro
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From vladimir.fonov at gmail.com  Tue May  3 23:47:29 2016
From: vladimir.fonov at gmail.com (Vladimir S. Fonov)
Date: Tue, 3 May 2016 23:47:29 -0400
Subject: [MINC-users] computing SNR
In-Reply-To: <CAG+ToRv2E1_7W5vQrb_RzpZhF91LXjm7654GsF=u49sn-Mkb0w@mail.gmail.com>
References: <CAG+ToRv2E1_7W5vQrb_RzpZhF91LXjm7654GsF=u49sn-Mkb0w@mail.gmail.com>
Message-ID: <572970D1.3040407@gmail.com>

Hello,

yes, there is

noise_estimate --snr  <input.mnc>

- will estimate SNR using method from this paper: 
http://www.ncbi.nlm.nih.gov/pubmed/20426161

On 16-05-03 06:50 PM, Trisanna Sprung-Much wrote:
> Hi All
>
> Is there an automated way of computing SNR for T1 images using minc tools?
>
> thanks!
>
> Trisanna Sprung-Much
> Petrides Lab
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


From redoute at cermep.fr  Wed May  4 05:42:37 2016
From: redoute at cermep.fr (Jerome Redoute)
Date: Wed, 04 May 2016 11:42:37 +0200
Subject: [MINC-users] minc-toolkit-v2 compilation
In-Reply-To: <CAAd5DeSH24eZC7H2UdWmOi0TMPL8VsK5LsKCNn8ebM2-DE0vWg@mail.gmail.com>
References: <5728B9D8.6090605@cermep.fr>
	<CAAd5DeSH24eZC7H2UdWmOi0TMPL8VsK5LsKCNn8ebM2-DE0vWg@mail.gmail.com>
Message-ID: <940e72858d5b2428d31419a6cd2c5d61@cermep.fr>

Thank you for these tips... compilation went further, but still have
some issues: 

- Warnings about modification time in the future: 

I've checked my time/date: they are OK 

- compilation ends with this error:

> [ 71%] Building C object mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/Extra_progs/xfm2param.c.o
> [ 71%] Linking C executable xfm2param
> lib_minctracc.a(init_params.c.o): dans la fonction ? vol_to_cov ?:
> init_params.c:(.text+0xcd0): d?finitions multiples de ? vol_to_cov ?
> CMakeFiles/xfm2param.dir/Extra_progs/xfm2param.c.o:xfm2param.c:(.text+0x0): d?fini pour la premi?re fois ici
> collect2: error: ld returned 1 exit status
> mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/build.make:109: recipe for target 'mni_autoreg/minctracc/xfm2param' failed
> make[2]: *** [mni_autoreg/minctracc/xfm2param] Error 1
> CMakeFiles/Makefile2:15671: recipe for target 'mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/all' failed
> make[1]: *** [mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2

and same for make install 

so the built binaries are not installed... 

any ideas on how to fix that? 

Thank you again 

---
==================================================
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 03/05/2016 17:55, Robert D. Vincent a ?crit :

> Hi Jerome,
> 
> Here is how I check out 'develop' and build for everything on Ubuntu
> (although this is for minc-toolkit, not minc-toolkit-v2, the same idea
> should work).
> 
> sudo apt-get install -y \
> build-essential \
> g++ \
> cmake \
> cmake-curses-gui \
> bison \
> flex \
> freeglut3 \
> freeglut3-dev \
> libxi6 \
> libxi-dev \
> libxmu6 \
> libxmu-dev \
> libxmu-headers \
> zlib1g-dev \
> libexpat1-dev \
> bc \
> git
> 
> git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git
> cd minc-toolkit
> git checkout develop
> git submodule foreach --recursive 'git checkout develop || :'
> 
> mkdir ../minc-build
> cd ../minc-build
> cmake ../minc-toolkit -DCMAKE_BUILD_TYPE=Release -DMT_BUILD_VISUAL_TOOLS=ON
> make
> 
> On Tue, May 3, 2016 at 10:46 AM, J?r?me Redout? <redoute at cermep.fr> wrote:
> 
> Hi,
> Could someone help me to set up my debian environment for compiling
> minc-toolkit-v2 using git repository?
> 
> |git clone --recursive https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2 |
> allows me to copy all the repository.. but how can I compile the develop
> branch only?
> 
> is there specific instructions for ccmake et make?
> 
> Thanks for your help
> Jerome
> 
> --
> ==================================================================
> 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
> ==================================================================
> 
> _______________________________________________
> 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 jason at mouseimaging.ca  Wed May  4 07:14:52 2016
From: jason at mouseimaging.ca (Jason Lerch)
Date: Wed, 4 May 2016 07:14:52 -0400
Subject: [MINC-users] classify: how to use
In-Reply-To: <CAG0CB20enpaZAkdW7DHRA=DP0Lo-WXTEQBXQdE0MCzj6jWhisg@mail.gmail.com>
References: <F796399C-64DF-4418-B6A8-6594116BA750@gmail.com>
	<CAG0CB20enpaZAkdW7DHRA=DP0Lo-WXTEQBXQdE0MCzj6jWhisg@mail.gmail.com>
Message-ID: <4FCCF28A-94CA-4051-AE55-27C21C4CE0CA@mouseimaging.ca>

Hi all, 

for those interested, we created a sort of replacement for classify:

https://github.com/Mouse-Imaging-Centre/classify-sklearn <https://github.com/Mouse-Imaging-Centre/classify-sklearn>

It?s based on python?s scikit-learn, and currently comes with a mix of classifiers (random forests, bayes, etc.). An example or two of how to use it is on the wiki part of that github page (though obviously more documentation is needed).

Biggest advantage over classify - doesn?t crash when outputting posterior probabilities with multispectral input - and doesn?t require the creation of a frankenbrain when training a classifier based on multiple subjects. Otherwise should be quite similar to the venerable old classify.

Doesn?t have a variant of classify_clean yet though.

Jason

> On May 3, 2016, at 7:21 PM, Andrew Janke <a.janke at gmail.com> wrote:
> 
> Hi Pedro,
> 
> This is my approach:
> 
>   classify_clean \
>         -tagdir <tags> \
>         -tag_transform <image-to-tags.xfm> \
>         input.mnc output.mnc
> 
> <tags> is a directory with the classify tags in it eg:
> 
> ls tags/
> ntags_1000_bg.tag  ntags_1000_prob_90_nobg.tag
> 
> 
> <image-to-tags.xfm> is a tranform from your native data space
> (input.mnc) to the space of the tags. If you are using the ones in the
> standard package this will be a transform from native space to the
> icbm152 model.
> 
> 
> a
> 
> 
> 
> On 3 May 2016 at 23:36, Pedro <ptcougopinto at gmail.com> wrote:
>> 
>> Hi, everyone ?
>> 
>> What should be the minimum command line for classify? What are the inputs and output? I could?t figure out from -help. (Just found out that I?m not happy with registration based segmentation of my data).
>> 
>> Thanks!
>> Pedro
>> _______________________________________________
>> 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  Wed May  4 07:47:13 2016
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Wed, 4 May 2016 13:47:13 +0200
Subject: [MINC-users] minc-toolkit-v2 compilation
In-Reply-To: <940e72858d5b2428d31419a6cd2c5d61@cermep.fr>
References: <5728B9D8.6090605@cermep.fr>
	<CAAd5DeSH24eZC7H2UdWmOi0TMPL8VsK5LsKCNn8ebM2-DE0vWg@mail.gmail.com>
	<940e72858d5b2428d31419a6cd2c5d61@cermep.fr>
Message-ID: <5729E141.3070100@cermep.fr>

I think I've found:
it was because my source files were located on a NFS share....
Have a nice day !
JR


Le 04/05/2016 11:42, Jerome Redoute a ?crit :
> Thank you for these tips... compilation went further, but still have
> some issues:
>
> - Warnings about modification time in the future:
>
> I've checked my time/date: they are OK
>
> - compilation ends with this error:
>
>> [ 71%] Building C object mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/Extra_progs/xfm2param.c.o
>> [ 71%] Linking C executable xfm2param
>> lib_minctracc.a(init_params.c.o): dans la fonction ? vol_to_cov ?:
>> init_params.c:(.text+0xcd0): d?finitions multiples de ? vol_to_cov ?
>> CMakeFiles/xfm2param.dir/Extra_progs/xfm2param.c.o:xfm2param.c:(.text+0x0): d?fini pour la premi?re fois ici
>> collect2: error: ld returned 1 exit status
>> mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/build.make:109: recipe for target 'mni_autoreg/minctracc/xfm2param' failed
>> make[2]: *** [mni_autoreg/minctracc/xfm2param] Error 1
>> CMakeFiles/Makefile2:15671: recipe for target 'mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/all' failed
>> make[1]: *** [mni_autoreg/minctracc/CMakeFiles/xfm2param.dir/all] Error 2
>> Makefile:160: recipe for target 'all' failed
>> make: *** [all] Error 2
> and same for make install
>
> so the built binaries are not installed...
>
> any ideas on how to fix that?
>
> Thank you again
>
> ---
> ==================================================
> 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 03/05/2016 17:55, Robert D. Vincent a ?crit :
>
>> Hi Jerome,
>>
>> Here is how I check out 'develop' and build for everything on Ubuntu
>> (although this is for minc-toolkit, not minc-toolkit-v2, the same idea
>> should work).
>>
>> sudo apt-get install -y \
>> build-essential \
>> g++ \
>> cmake \
>> cmake-curses-gui \
>> bison \
>> flex \
>> freeglut3 \
>> freeglut3-dev \
>> libxi6 \
>> libxi-dev \
>> libxmu6 \
>> libxmu-dev \
>> libxmu-headers \
>> zlib1g-dev \
>> libexpat1-dev \
>> bc \
>> git
>>
>> git clone --recursive git://github.com/BIC-MNI/minc-toolkit.git
>> cd minc-toolkit
>> git checkout develop
>> git submodule foreach --recursive 'git checkout develop || :'
>>
>> mkdir ../minc-build
>> cd ../minc-build
>> cmake ../minc-toolkit -DCMAKE_BUILD_TYPE=Release -DMT_BUILD_VISUAL_TOOLS=ON
>> make
>>
>> On Tue, May 3, 2016 at 10:46 AM, J?r?me Redout? <redoute at cermep.fr> wrote:
>>
>> Hi,
>> Could someone help me to set up my debian environment for compiling
>> minc-toolkit-v2 using git repository?
>>
>> |git clone --recursive https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2 |
>> allows me to copy all the repository.. but how can I compile the develop
>> branch only?
>>
>> is there specific instructions for ccmake et make?
>>
>> Thanks for your help
>> Jerome
>>
>> --
>> ==================================================================
>> 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
>> ==================================================================
>>
>> _______________________________________________
>> 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
>


-- 
==================================================================
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 zijdenbos at gmail.com  Wed May  4 08:43:47 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 4 May 2016 08:43:47 -0400
Subject: [MINC-users] classify: how to use
In-Reply-To: <4FCCF28A-94CA-4051-AE55-27C21C4CE0CA@mouseimaging.ca>
References: <F796399C-64DF-4418-B6A8-6594116BA750@gmail.com>
	<CAG0CB20enpaZAkdW7DHRA=DP0Lo-WXTEQBXQdE0MCzj6jWhisg@mail.gmail.com>
	<4FCCF28A-94CA-4051-AE55-27C21C4CE0CA@mouseimaging.ca>
Message-ID: <CABEEk15KC2w2f650YW6gA5zrDSshv10ymZJgOXJxBiq0SR6wYg@mail.gmail.com>

Nice, Jason! Next time I see Vasco I'll let him know ;-) I thought that
crashing bit was fixed somewhere along the way, but perhaps not - haven't
tried in a while.

To answer Pedro's initial question though - the most common way to invoke
good old classify directly would look something like this:

   classify [options] -<classifier> -tagfile <tags.tag> <in.mnc> [<in.mnc>
...] <classified.mnc>

where you should only need to provide a tag file with training samples for
the supervised classifiers. classify_clean, as Andrew suggested, runs two
of these calls (minimum distance followed by ANN) so its logfile will also
help you.

-- A




On Wed, May 4, 2016 at 7:14 AM, Jason Lerch <jason at mouseimaging.ca> wrote:

> Hi all,
>
> for those interested, we created a sort of replacement for classify:
>
> https://github.com/Mouse-Imaging-Centre/classify-sklearn <
> https://github.com/Mouse-Imaging-Centre/classify-sklearn>
>
> It?s based on python?s scikit-learn, and currently comes with a mix of
> classifiers (random forests, bayes, etc.). An example or two of how to use
> it is on the wiki part of that github page (though obviously more
> documentation is needed).
>
> Biggest advantage over classify - doesn?t crash when outputting posterior
> probabilities with multispectral input - and doesn?t require the creation
> of a frankenbrain when training a classifier based on multiple subjects.
> Otherwise should be quite similar to the venerable old classify.
>
> Doesn?t have a variant of classify_clean yet though.
>
> Jason
>
> > On May 3, 2016, at 7:21 PM, Andrew Janke <a.janke at gmail.com> wrote:
> >
> > Hi Pedro,
> >
> > This is my approach:
> >
> >   classify_clean \
> >         -tagdir <tags> \
> >         -tag_transform <image-to-tags.xfm> \
> >         input.mnc output.mnc
> >
> > <tags> is a directory with the classify tags in it eg:
> >
> > ls tags/
> > ntags_1000_bg.tag  ntags_1000_prob_90_nobg.tag
> >
> >
> > <image-to-tags.xfm> is a tranform from your native data space
> > (input.mnc) to the space of the tags. If you are using the ones in the
> > standard package this will be a transform from native space to the
> > icbm152 model.
> >
> >
> > a
> >
> >
> >
> > On 3 May 2016 at 23:36, Pedro <ptcougopinto at gmail.com> wrote:
> >>
> >> Hi, everyone ?
> >>
> >> What should be the minimum command line for classify? What are the
> inputs and output? I could?t figure out from -help. (Just found out that
> I?m not happy with registration based segmentation of my data).
> >>
> >> Thanks!
> >> Pedro
> >> _______________________________________________
> >> 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 redoute at cermep.fr  Wed May  4 10:30:21 2016
From: redoute at cermep.fr (=?UTF-8?B?SsOpcsO0bWUgUmVkb3V0w6k=?=)
Date: Wed, 4 May 2016 16:30:21 +0200
Subject: [MINC-users] ecattominc - minctoecat
Message-ID: <572A077D.2020003@cermep.fr>

Dear all,
I'm now using the dev branch of Minc toolkit.

I've got an issue converting between MINC & ECAT formats

I can convert dynamic PET file from mnc to ecat
but I can't convert ecat back to minc ==> segmentation fault

Same issue with stable release
Any ideas?
Thank you
Jerome

-- 
==================================================================
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 robert.d.vincent at mcgill.ca  Wed May  4 10:37:23 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Wed, 4 May 2016 10:37:23 -0400
Subject: [MINC-users] ecattominc - minctoecat
In-Reply-To: <572A077D.2020003@cermep.fr>
References: <572A077D.2020003@cermep.fr>
Message-ID: <CAAd5DeTz0LyPo1tO5=pYTESKAh8VYzYWLQw2MMhvKtUYE-EoOA@mail.gmail.com>

Hi J?r?me,

Can you provide an example file that exhibits the problem? I just tried the
latest develop branch for minctoecat/ecattominc for a 160-frame PET file
and it seems to work.

    -bert

On Wed, May 4, 2016 at 10:30 AM, J?r?me Redout? <redoute at cermep.fr> wrote:

> Dear all,
> I'm now using the dev branch of Minc toolkit.
>
> I've got an issue converting between MINC & ECAT formats
>
> I can convert dynamic PET file from mnc to ecat
> but I can't convert ecat back to minc ==> segmentation fault
>
> Same issue with stable release
> Any ideas?
> Thank you
> Jerome
>
> --
> ==================================================================
> 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
> ==================================================================
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From gdevenyi at gmail.com  Wed May  4 13:22:17 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 4 May 2016 13:22:17 -0400
Subject: [MINC-users] Computing a "orthogonalizing" rotation transform?
Message-ID: <CAFQOoOp2B8GBitd3d6PZLQaK5OMOa1M6hdamwnHZkDmE=W2aAw@mail.gmail.com>

Hi minc-users,

Many nifti tools are "helpful" in that they orthogonalize your view
relative to the principal axes they compute from a native scan on
load. This makes it hard to compare to Display.

Obviously, Display doesn't do this, but is there a tool or method to
compute such a transform so I can apply it to a MINC file?

Thanks!

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From vladimir.fonov at gmail.com  Wed May  4 13:36:35 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 4 May 2016 13:36:35 -0400
Subject: [MINC-users] Computing a "orthogonalizing" rotation transform?
In-Reply-To: <CAFQOoOp2B8GBitd3d6PZLQaK5OMOa1M6hdamwnHZkDmE=W2aAw@mail.gmail.com>
References: <CAFQOoOp2B8GBitd3d6PZLQaK5OMOa1M6hdamwnHZkDmE=W2aAw@mail.gmail.com>
Message-ID: <572A3323.2040205@gmail.com>

What is the definition of orthogonalized view?

perhaps itk_resample --uniformize 1 will do it for you?


On 16-05-04 01:22 PM, Gabriel A. Devenyi wrote:
> Hi minc-users,
>
> Many nifti tools are "helpful" in that they orthogonalize your view
> relative to the principal axes they compute from a native scan on
> load. This makes it hard to compare to Display.
>
> Obviously, Display doesn't do this, but is there a tool or method to
> compute such a transform so I can apply it to a MINC file?
>
> Thanks!
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> _______________________________________________
> 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 andrew at biospective.com  Wed May  4 13:44:10 2016
From: andrew at biospective.com (Andrew Wood)
Date: Wed, 4 May 2016 13:44:10 -0400
Subject: [MINC-users] Computing a "orthogonalizing" rotation transform?
In-Reply-To: <572A3323.2040205@gmail.com>
References: <CAFQOoOp2B8GBitd3d6PZLQaK5OMOa1M6hdamwnHZkDmE=W2aAw@mail.gmail.com>
	<572A3323.2040205@gmail.com>
Message-ID: <CABApf9HK8Mw-L9uDHHD6vsHwTmFKg_y2isey77rTzFwc4a8UAQ@mail.gmail.com>

Hi Gabriel,

I think you need to resample the image such that the voxel lattice lines up
with the world dimensions. Would this do it?

$ mincresample in.mnc -dircos 1 0 0  0 1 0  0 0 1 out.mnc

- Andrew


On Wed, May 4, 2016 at 1:36 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com>
wrote:

> What is the definition of orthogonalized view?
>
> perhaps itk_resample --uniformize 1 will do it for you?
>
>
>
> On 16-05-04 01:22 PM, Gabriel A. Devenyi wrote:
>
>> Hi minc-users,
>>
>> Many nifti tools are "helpful" in that they orthogonalize your view
>> relative to the principal axes they compute from a native scan on
>> load. This makes it hard to compare to Display.
>>
>> Obviously, Display doesn't do this, but is there a tool or method to
>> compute such a transform so I can apply it to a MINC file?
>>
>> Thanks!
>>
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> Affiliate, Department of Psychiatry
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
>> _______________________________________________
>> 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 gdevenyi at gmail.com  Wed May  4 14:13:48 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 4 May 2016 14:13:48 -0400
Subject: [MINC-users] Computing a "orthogonalizing" rotation transform?
In-Reply-To: <CABApf9HK8Mw-L9uDHHD6vsHwTmFKg_y2isey77rTzFwc4a8UAQ@mail.gmail.com>
References: <CAFQOoOp2B8GBitd3d6PZLQaK5OMOa1M6hdamwnHZkDmE=W2aAw@mail.gmail.com>
	<572A3323.2040205@gmail.com>
	<CABApf9HK8Mw-L9uDHHD6vsHwTmFKg_y2isey77rTzFwc4a8UAQ@mail.gmail.com>
Message-ID: <CAFQOoOqtnPOvg0qt92ysytSx5r1Xwc2mkZDJLJ1P61rZ80-rrA@mail.gmail.com>

Thanks Andrew/Vlad,

Vlad: that's a good question, I think what the apps are doing is
computing the principal axes of the volume distribution, and aligning
those with the slice directions

Andrew: thanks, that's helpful if I ever run into that case.
--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com


On Wed, May 4, 2016 at 1:44 PM, Andrew Wood <andrew at biospective.com> wrote:
> Hi Gabriel,
>
> I think you need to resample the image such that the voxel lattice lines up
> with the world dimensions. Would this do it?
>
> $ mincresample in.mnc -dircos 1 0 0  0 1 0  0 0 1 out.mnc
>
> - Andrew
>
>
> On Wed, May 4, 2016 at 1:36 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com>
> wrote:
>
>> What is the definition of orthogonalized view?
>>
>> perhaps itk_resample --uniformize 1 will do it for you?
>>
>>
>>
>> On 16-05-04 01:22 PM, Gabriel A. Devenyi wrote:
>>
>>> Hi minc-users,
>>>
>>> Many nifti tools are "helpful" in that they orthogonalize your view
>>> relative to the principal axes they compute from a native scan on
>>> load. This makes it hard to compare to Display.
>>>
>>> Obviously, Display doesn't do this, but is there a tool or method to
>>> compute such a transform so I can apply it to a MINC file?
>>>
>>> Thanks!
>>>
>>> --
>>> Gabriel A. Devenyi B.Eng. Ph.D.
>>> Research Computing Associate
>>> Computational Brain Anatomy Laboratory
>>> Cerebral Imaging Center
>>> Douglas Mental Health University Institute
>>> Affiliate, Department of Psychiatry
>>> McGill University
>>> t: 514.761.6131x4781
>>> e: gdevenyi at gmail.com
>>> _______________________________________________
>>> 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
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From andrew at biospective.com  Wed May  4 14:32:58 2016
From: andrew at biospective.com (Andrew Wood)
Date: Wed, 4 May 2016 14:32:58 -0400
Subject: [MINC-users] Computing a "orthogonalizing" rotation transform?
In-Reply-To: <CAFQOoOqtnPOvg0qt92ysytSx5r1Xwc2mkZDJLJ1P61rZ80-rrA@mail.gmail.com>
References: <CAFQOoOp2B8GBitd3d6PZLQaK5OMOa1M6hdamwnHZkDmE=W2aAw@mail.gmail.com>
	<572A3323.2040205@gmail.com>
	<CABApf9HK8Mw-L9uDHHD6vsHwTmFKg_y2isey77rTzFwc4a8UAQ@mail.gmail.com>
	<CAFQOoOqtnPOvg0qt92ysytSx5r1Xwc2mkZDJLJ1P61rZ80-rrA@mail.gmail.com>
Message-ID: <CABApf9FrkiutvffUm4DJTmxkjnea=cehWqYTx+mt9Pyx=m-0eQ@mail.gmail.com>

Hi Gabriel,

You might already be aware of this, but Nifti files can simultaneously
encode two different world spaces (see qform and sform).  It's my
understanding that the Nifti standard stately clearly how they're to be
used, but many toolsets choose to not conform; one must be very careful
when using tools coming from different nifti toolkits.

Here's an example where the qform/sform issue could lead to confusion: a
viewer could use the sform to position the image in the viewer, but then a
nifti-minc converter could pick up the qform to generate the world axes;
the sform orientation information would then be lost.

Not sure if that helps, but it could be related.

Cheers,
Andrew

On Wed, May 4, 2016 at 2:13 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> Thanks Andrew/Vlad,
>
> Vlad: that's a good question, I think what the apps are doing is
> computing the principal axes of the volume distribution, and aligning
> those with the slice directions
>
> Andrew: thanks, that's helpful if I ever run into that case.
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
>
> On Wed, May 4, 2016 at 1:44 PM, Andrew Wood <andrew at biospective.com>
> wrote:
> > Hi Gabriel,
> >
> > I think you need to resample the image such that the voxel lattice lines
> up
> > with the world dimensions. Would this do it?
> >
> > $ mincresample in.mnc -dircos 1 0 0  0 1 0  0 0 1 out.mnc
> >
> > - Andrew
> >
> >
> > On Wed, May 4, 2016 at 1:36 PM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com>
> > wrote:
> >
> >> What is the definition of orthogonalized view?
> >>
> >> perhaps itk_resample --uniformize 1 will do it for you?
> >>
> >>
> >>
> >> On 16-05-04 01:22 PM, Gabriel A. Devenyi wrote:
> >>
> >>> Hi minc-users,
> >>>
> >>> Many nifti tools are "helpful" in that they orthogonalize your view
> >>> relative to the principal axes they compute from a native scan on
> >>> load. This makes it hard to compare to Display.
> >>>
> >>> Obviously, Display doesn't do this, but is there a tool or method to
> >>> compute such a transform so I can apply it to a MINC file?
> >>>
> >>> Thanks!
> >>>
> >>> --
> >>> Gabriel A. Devenyi B.Eng. Ph.D.
> >>> Research Computing Associate
> >>> Computational Brain Anatomy Laboratory
> >>> Cerebral Imaging Center
> >>> Douglas Mental Health University Institute
> >>> Affiliate, Department of Psychiatry
> >>> McGill University
> >>> t: 514.761.6131x4781
> >>> e: gdevenyi at gmail.com
> >>> _______________________________________________
> >>> 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
> >>
> > _______________________________________________
> > 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 gdevenyi at gmail.com  Wed May  4 14:35:43 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 4 May 2016 14:35:43 -0400
Subject: [MINC-users] Computing a "orthogonalizing" rotation transform?
In-Reply-To: <CABApf9FrkiutvffUm4DJTmxkjnea=cehWqYTx+mt9Pyx=m-0eQ@mail.gmail.com>
References: <CAFQOoOp2B8GBitd3d6PZLQaK5OMOa1M6hdamwnHZkDmE=W2aAw@mail.gmail.com>
	<572A3323.2040205@gmail.com>
	<CABApf9HK8Mw-L9uDHHD6vsHwTmFKg_y2isey77rTzFwc4a8UAQ@mail.gmail.com>
	<CAFQOoOqtnPOvg0qt92ysytSx5r1Xwc2mkZDJLJ1P61rZ80-rrA@mail.gmail.com>
	<CABApf9FrkiutvffUm4DJTmxkjnea=cehWqYTx+mt9Pyx=m-0eQ@mail.gmail.com>
Message-ID: <CAFQOoOoJxqRVnF5=wMxA5Mav5V2z=2rpzYX3sXUUtrAxOd4_mg@mail.gmail.com>

Thanks Andrew, I was aware of this, this is messyness above and beyond
the sform/qform.

MRICron does this, for example.
--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com


On Wed, May 4, 2016 at 2:32 PM, Andrew Wood <andrew at biospective.com> wrote:
> Hi Gabriel,
>
> You might already be aware of this, but Nifti files can simultaneously
> encode two different world spaces (see qform and sform).  It's my
> understanding that the Nifti standard stately clearly how they're to be
> used, but many toolsets choose to not conform; one must be very careful
> when using tools coming from different nifti toolkits.
>
> Here's an example where the qform/sform issue could lead to confusion: a
> viewer could use the sform to position the image in the viewer, but then a
> nifti-minc converter could pick up the qform to generate the world axes;
> the sform orientation information would then be lost.
>
> Not sure if that helps, but it could be related.
>
> Cheers,
> Andrew
>
> On Wed, May 4, 2016 at 2:13 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
> wrote:
>
>> Thanks Andrew/Vlad,
>>
>> Vlad: that's a good question, I think what the apps are doing is
>> computing the principal axes of the volume distribution, and aligning
>> those with the slice directions
>>
>> Andrew: thanks, that's helpful if I ever run into that case.
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> Affiliate, Department of Psychiatry
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
>>
>>
>> On Wed, May 4, 2016 at 1:44 PM, Andrew Wood <andrew at biospective.com>
>> wrote:
>> > Hi Gabriel,
>> >
>> > I think you need to resample the image such that the voxel lattice lines
>> up
>> > with the world dimensions. Would this do it?
>> >
>> > $ mincresample in.mnc -dircos 1 0 0  0 1 0  0 0 1 out.mnc
>> >
>> > - Andrew
>> >
>> >
>> > On Wed, May 4, 2016 at 1:36 PM, Vladimir S. FONOV <
>> vladimir.fonov at gmail.com>
>> > wrote:
>> >
>> >> What is the definition of orthogonalized view?
>> >>
>> >> perhaps itk_resample --uniformize 1 will do it for you?
>> >>
>> >>
>> >>
>> >> On 16-05-04 01:22 PM, Gabriel A. Devenyi wrote:
>> >>
>> >>> Hi minc-users,
>> >>>
>> >>> Many nifti tools are "helpful" in that they orthogonalize your view
>> >>> relative to the principal axes they compute from a native scan on
>> >>> load. This makes it hard to compare to Display.
>> >>>
>> >>> Obviously, Display doesn't do this, but is there a tool or method to
>> >>> compute such a transform so I can apply it to a MINC file?
>> >>>
>> >>> Thanks!
>> >>>
>> >>> --
>> >>> Gabriel A. Devenyi B.Eng. Ph.D.
>> >>> Research Computing Associate
>> >>> Computational Brain Anatomy Laboratory
>> >>> Cerebral Imaging Center
>> >>> Douglas Mental Health University Institute
>> >>> Affiliate, Department of Psychiatry
>> >>> McGill University
>> >>> t: 514.761.6131x4781
>> >>> e: gdevenyi at gmail.com
>> >>> _______________________________________________
>> >>> 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
>> >>
>> > _______________________________________________
>> > 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 trisanna.sprung-much at mail.mcgill.ca  Wed May  4 14:40:24 2016
From: trisanna.sprung-much at mail.mcgill.ca (Trisanna Sprung-Much)
Date: Wed, 4 May 2016 14:40:24 -0400
Subject: [MINC-users] computing SNR
In-Reply-To: <572970D1.3040407@gmail.com>
References: <CAG+ToRv2E1_7W5vQrb_RzpZhF91LXjm7654GsF=u49sn-Mkb0w@mail.gmail.com>
	<572970D1.3040407@gmail.com>
Message-ID: <CAG+ToRvL=4dSkN-M1cyfAqHwHVqP5c3reGNJKJ7fZeigY5O-4g@mail.gmail.com>

thank you!

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, May 3, 2016 at 11:47 PM, Vladimir S. Fonov <vladimir.fonov at gmail.com
> wrote:

> Hello,
>
> yes, there is
>
> noise_estimate --snr  <input.mnc>
>
> - will estimate SNR using method from this paper:
> http://www.ncbi.nlm.nih.gov/pubmed/20426161
>
>
> On 16-05-03 06:50 PM, Trisanna Sprung-Much wrote:
>
>> Hi All
>>
>> Is there an automated way of computing SNR for T1 images using minc tools?
>>
>> thanks!
>>
>> Trisanna Sprung-Much
>> Petrides Lab
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>> _______________________________________________
>> 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 gdevenyi at gmail.com  Mon May  9 15:38:23 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Mon, 9 May 2016 15:38:23 -0400
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command lines in
 parallel (serial farm) on SGE/PBS clusters
Message-ID: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>

We (Gabriel A. Devenyi and Jon Pipitone) would like to announce the 1.0
release <https://github.com/pipitone/qbatch/releases> of qbatch, a
command-line tool for easily running a list of commands in parallel (serial
farming) on a compute cluster. This tool takes the list of commands,
divides them up into batches of arbitrary size, and then submits each batch
as a separate job or as part of an array job. qbatch also gives you a
consistent interface to use to submit commands on PBS and SGE clusters or
locally, (support for others are planned/in testing, PRs welcome) while
setting requirements for processors, walltime, memory and job dependencies.
This tool can be used as a quick interface to spread work out on a cluster,
or as the glue for for connecting a simple pipeline to a cluster (see
https://github.com/CobraLab/antsRegistration-MAGeT for a sample
implementation)

The target audience of qbatch is two-fold: it is immediately available for
users of PBS or SGE clusters to simplify their job construction, in
addition, through the use of environment variables, cluster administrations
can craft a default qbatch deployment which allows new cluster users to
quickly submit jobs which honours the cluster?s policies.

For more information, check out our github webpage here:
http://github.com/pipitone/qbatch
qbatch is also available in pypi via pip install qbatch

?
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com
?

From eskild at gmail.com  Tue May 10 09:07:21 2016
From: eskild at gmail.com (Simon Eskildsen)
Date: Tue, 10 May 2016 15:07:21 +0200
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
Message-ID: <CAD3v437DxV0dTMzYBudEczF=2f=aYhwJGMS0Ja2UaPnx221ooA@mail.gmail.com>

Sounds great. Is this related in any way (other than the name) to Andrew's
qbatch script? https://github.com/andrewjanke/qbatch


On Mon, May 9, 2016 at 9:38 PM, Gabriel A. Devenyi <gdevenyi at gmail.com>
wrote:

> We (Gabriel A. Devenyi and Jon Pipitone) would like to announce the 1.0
> release <https://github.com/pipitone/qbatch/releases> of qbatch, a
> command-line tool for easily running a list of commands in parallel (serial
> farming) on a compute cluster. This tool takes the list of commands,
> divides them up into batches of arbitrary size, and then submits each batch
> as a separate job or as part of an array job. qbatch also gives you a
> consistent interface to use to submit commands on PBS and SGE clusters or
> locally, (support for others are planned/in testing, PRs welcome) while
> setting requirements for processors, walltime, memory and job dependencies.
> This tool can be used as a quick interface to spread work out on a cluster,
> or as the glue for for connecting a simple pipeline to a cluster (see
> https://github.com/CobraLab/antsRegistration-MAGeT for a sample
> implementation)
>
> The target audience of qbatch is two-fold: it is immediately available for
> users of PBS or SGE clusters to simplify their job construction, in
> addition, through the use of environment variables, cluster administrations
> can craft a default qbatch deployment which allows new cluster users to
> quickly submit jobs which honours the cluster?s policies.
>
> For more information, check out our github webpage here:
> http://github.com/pipitone/qbatch
> qbatch is also available in pypi via pip install qbatch
>
> ?
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> ?
> _______________________________________________
> 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 10 09:07:41 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Tue, 10 May 2016 21:07:41 +0800
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
Message-ID: <CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>

Very tasty.

Was it designed as a drop in replacement for qbatch?

   https://github.com/andrewjanke/qbatch/blob/master/qbatch

I note a number of similarities in the C/L arguments. Any plans for
handling dependencies? I see code in there but no arguments to make
use of it? In particular to get around the hoops of tracking
dependencies via job numbers (that my qbatch returns) in PBS and/or
via names in gridengine? ie:

   $ for i in *.mnc; do qbatch --name STEP1-$i -- <blah>; done
   $ qbatch --name STEP2 --depends 'STEP1-*' -- <blah>

I ask as I use qbatch internally in things like volgenmodel in order
to abstract away from the various qsub's. Currently I handle this via
some pretty horrendous perl code here:

   https://github.com/andrewjanke/volgenmodel/blob/master/volgenmodel#L751

It'd be nice to be able to do away with it via your version!

I also find the notion of being able to define a queue via an ENV var
useful when you have a number of levels of scripts/perl/etc that don't
always pass arguments through.  ie:

   https://github.com/andrewjanke/qbatch/blob/master/qbatch#L69


a

On 10 May 2016 at 03:38, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> We (Gabriel A. Devenyi and Jon Pipitone) would like to announce the 1.0
> release <https://github.com/pipitone/qbatch/releases> of qbatch, a
> command-line tool for easily running a list of commands in parallel (serial
> farming) on a compute cluster. This tool takes the list of commands,
> divides them up into batches of arbitrary size, and then submits each batch
> as a separate job or as part of an array job. qbatch also gives you a
> consistent interface to use to submit commands on PBS and SGE clusters or
> locally, (support for others are planned/in testing, PRs welcome) while
> setting requirements for processors, walltime, memory and job dependencies.
> This tool can be used as a quick interface to spread work out on a cluster,
> or as the glue for for connecting a simple pipeline to a cluster (see
> https://github.com/CobraLab/antsRegistration-MAGeT for a sample
> implementation)
>
> The target audience of qbatch is two-fold: it is immediately available for
> users of PBS or SGE clusters to simplify their job construction, in
> addition, through the use of environment variables, cluster administrations
> can craft a default qbatch deployment which allows new cluster users to
> quickly submit jobs which honours the cluster?s policies.
>
> For more information, check out our github webpage here:
> http://github.com/pipitone/qbatch
> qbatch is also available in pypi via pip install qbatch
>
> ?
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From gdevenyi at gmail.com  Tue May 10 09:23:17 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 10 May 2016 09:23:17 -0400
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
	<CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>
Message-ID: <CAFQOoOrgE5Xz4yULyhg4r7T-fnfmGMfRqnsQiTEDsKWz00FDtg@mail.gmail.com>

Simon/Andrew, indeed this was written as an intended replacement for
sge_batch and/or the original qbatch (we at CoBrALab also had an earlier
internal qbatch which was not Andrew's version).
Having said that, we didn't ensure that it was a one-to-one drop in
replacement, so use may require some modification.

Andrew:
Yes, dependencies in PBS/SGE (and LSF, but I haven't tested LSF at all yet)
are already implemented, just missing from the README, will add :) My
antsRegistration-MaGeT pipeline makes extensive use of them already.

For PBS we parse the XML joblist and do pattern matching on names:
https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L138-L171
And for SGE we use jobname pattern matching built into SGE:
https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L381-L382

As for the queue, I have an in progress branch to specify "other" batch
options, handled by environment variable, see
https://github.com/pipitone/qbatch/pull/80
I just need to solve the append vs. replace issue I'm having with argparse.
Thoughts here welcome :)

For bugs/feature requests/modifications, please feel free to request! Our
goal is to provide a maintained tool to support existing workflows and
enable new ones.

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Tue, May 10, 2016 at 9:07 AM, Andrew Janke <a.janke at gmail.com> wrote:

> Very tasty.
>
> Was it designed as a drop in replacement for qbatch?
>
>    https://github.com/andrewjanke/qbatch/blob/master/qbatch
>
> I note a number of similarities in the C/L arguments. Any plans for
> handling dependencies? I see code in there but no arguments to make
> use of it? In particular to get around the hoops of tracking
> dependencies via job numbers (that my qbatch returns) in PBS and/or
> via names in gridengine? ie:
>
>    $ for i in *.mnc; do qbatch --name STEP1-$i -- <blah>; done
>    $ qbatch --name STEP2 --depends 'STEP1-*' -- <blah>
>
> I ask as I use qbatch internally in things like volgenmodel in order
> to abstract away from the various qsub's. Currently I handle this via
> some pretty horrendous perl code here:
>
>    https://github.com/andrewjanke/volgenmodel/blob/master/volgenmodel#L751
>
> It'd be nice to be able to do away with it via your version!
>
> I also find the notion of being able to define a queue via an ENV var
> useful when you have a number of levels of scripts/perl/etc that don't
> always pass arguments through.  ie:
>
>    https://github.com/andrewjanke/qbatch/blob/master/qbatch#L69
>
>
> a
>
> On 10 May 2016 at 03:38, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> > We (Gabriel A. Devenyi and Jon Pipitone) would like to announce the 1.0
> > release <https://github.com/pipitone/qbatch/releases> of qbatch, a
> > command-line tool for easily running a list of commands in parallel
> (serial
> > farming) on a compute cluster. This tool takes the list of commands,
> > divides them up into batches of arbitrary size, and then submits each
> batch
> > as a separate job or as part of an array job. qbatch also gives you a
> > consistent interface to use to submit commands on PBS and SGE clusters or
> > locally, (support for others are planned/in testing, PRs welcome) while
> > setting requirements for processors, walltime, memory and job
> dependencies.
> > This tool can be used as a quick interface to spread work out on a
> cluster,
> > or as the glue for for connecting a simple pipeline to a cluster (see
> > https://github.com/CobraLab/antsRegistration-MAGeT for a sample
> > implementation)
> >
> > The target audience of qbatch is two-fold: it is immediately available
> for
> > users of PBS or SGE clusters to simplify their job construction, in
> > addition, through the use of environment variables, cluster
> administrations
> > can craft a default qbatch deployment which allows new cluster users to
> > quickly submit jobs which honours the cluster?s policies.
> >
> > For more information, check out our github webpage here:
> > http://github.com/pipitone/qbatch
> > qbatch is also available in pypi via pip install qbatch
> >
> > ?
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > Affiliate, Department of Psychiatry
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Wed May 11 20:30:57 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 12 May 2016 08:30:57 +0800
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAFQOoOrgE5Xz4yULyhg4r7T-fnfmGMfRqnsQiTEDsKWz00FDtg@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
	<CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>
	<CAFQOoOrgE5Xz4yULyhg4r7T-fnfmGMfRqnsQiTEDsKWz00FDtg@mail.gmail.com>
Message-ID: <CAG0CB20g-JtWcXGDAdnXZj4Ys=+N3ihABJZk0TEDZKB5cj7f4g@mail.gmail.com>

I've taken a proper look at this now. It currently is in no way a drop
in replacement but from what I can see it shouldn't be too hard. I'm
more than happy to do away with my old perl version. For one your
handling of dependencies is much nicer and self contained. There big
differences are:

1. qbatch(mine), was designed equivalent to nohup. ie: write a
command, test it, add qbatch.

   $ for i in *.mnc; do process_something.sh -args *.mnc; done

When happy you'd do this:

   $ for i in *.mnc; do qbatch --queue my.q --name $i --
process-something.sh -args *.mnc;
done

Whereas qbatch(python) expects commands to be in a file, this makes it
difficult to use things like globs with qbatch:

   $ qbatch --logfile blah.log -- do_something_args.pl *.mnc

I see a PR which is along these lines:

   https://github.com/pipitone/qbatch/issues/90

How hard would it be to support a single command after "--"? I note
that you can pipe things to qbatch via echo but this is a real pain to
use in things like perl and python scripts. OK in shell though.


2. I find debugging output in the logfiles to be invaluable when
debugging things. Stuff like the hostname and time of execution.

https://github.com/andrewjanke/qbatch/blob/master/qbatch#L151

and

https://github.com/andrewjanke/qbatch/blob/master/qbatch#L172

This means that I can quickly grep for "exit status" on a directory of logfiles.


3. I note slight differences in how we handle cwd, is there are a
reason for you cd?

   https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L67

I found this problematic for NFS mounts if using relative paths, and
let gridengine sort out things itself.:

   https://github.com/andrewjanke/qbatch/blob/master/qbatch#L108

There are a number of smaller things (job name larger than 15
characters == FAIL in PBS). This causes issues when tracking
dependencies as your unique job name may be longer than this. You can
either bomb and error out to the user (choose a shorter job name!) or
you have to track an internal database of jobnumbers (capture the
return value of qsub) and match these to input job names.  Currently
in your implementation I think this will fail.

There are also issues around re-running jobs:

   https://github.com/andrewjanke/qbatch/blob/master/qbatch#L103

As this can also screw up checking dependencies. In your case I think
this is handled better as you query based upon name. I didn't see from
the code but can you specify a dependency as a job number?

ta


a

On 10 May 2016 at 21:23, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> Simon/Andrew, indeed this was written as an intended replacement for
> sge_batch and/or the original qbatch (we at CoBrALab also had an earlier
> internal qbatch which was not Andrew's version).
> Having said that, we didn't ensure that it was a one-to-one drop in
> replacement, so use may require some modification.
>
> Andrew:
> Yes, dependencies in PBS/SGE (and LSF, but I haven't tested LSF at all yet)
> are already implemented, just missing from the README, will add :) My
> antsRegistration-MaGeT pipeline makes extensive use of them already.
>
> For PBS we parse the XML joblist and do pattern matching on names:
> https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L138-L171
> And for SGE we use jobname pattern matching built into SGE:
> https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L381-L382
>
> As for the queue, I have an in progress branch to specify "other" batch
> options, handled by environment variable, see
> https://github.com/pipitone/qbatch/pull/80
> I just need to solve the append vs. replace issue I'm having with argparse.
> Thoughts here welcome :)
>
> For bugs/feature requests/modifications, please feel free to request! Our
> goal is to provide a maintained tool to support existing workflows and
> enable new ones.
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Tue, May 10, 2016 at 9:07 AM, Andrew Janke <a.janke at gmail.com> wrote:
>>
>> Very tasty.
>>
>> Was it designed as a drop in replacement for qbatch?
>>
>>    https://github.com/andrewjanke/qbatch/blob/master/qbatch
>>
>> I note a number of similarities in the C/L arguments. Any plans for
>> handling dependencies? I see code in there but no arguments to make
>> use of it? In particular to get around the hoops of tracking
>> dependencies via job numbers (that my qbatch returns) in PBS and/or
>> via names in gridengine? ie:
>>
>>    $ for i in *.mnc; do qbatch --name STEP1-$i -- <blah>; done
>>    $ qbatch --name STEP2 --depends 'STEP1-*' -- <blah>
>>
>> I ask as I use qbatch internally in things like volgenmodel in order
>> to abstract away from the various qsub's. Currently I handle this via
>> some pretty horrendous perl code here:
>>
>>    https://github.com/andrewjanke/volgenmodel/blob/master/volgenmodel#L751
>>
>> It'd be nice to be able to do away with it via your version!
>>
>> I also find the notion of being able to define a queue via an ENV var
>> useful when you have a number of levels of scripts/perl/etc that don't
>> always pass arguments through.  ie:
>>
>>    https://github.com/andrewjanke/qbatch/blob/master/qbatch#L69
>>
>>
>> a
>>
>> On 10 May 2016 at 03:38, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
>> > We (Gabriel A. Devenyi and Jon Pipitone) would like to announce the 1.0
>> > release <https://github.com/pipitone/qbatch/releases> of qbatch, a
>> > command-line tool for easily running a list of commands in parallel
>> > (serial
>> > farming) on a compute cluster. This tool takes the list of commands,
>> > divides them up into batches of arbitrary size, and then submits each
>> > batch
>> > as a separate job or as part of an array job. qbatch also gives you a
>> > consistent interface to use to submit commands on PBS and SGE clusters
>> > or
>> > locally, (support for others are planned/in testing, PRs welcome) while
>> > setting requirements for processors, walltime, memory and job
>> > dependencies.
>> > This tool can be used as a quick interface to spread work out on a
>> > cluster,
>> > or as the glue for for connecting a simple pipeline to a cluster (see
>> > https://github.com/CobraLab/antsRegistration-MAGeT for a sample
>> > implementation)
>> >
>> > The target audience of qbatch is two-fold: it is immediately available
>> > for
>> > users of PBS or SGE clusters to simplify their job construction, in
>> > addition, through the use of environment variables, cluster
>> > administrations
>> > can craft a default qbatch deployment which allows new cluster users to
>> > quickly submit jobs which honours the cluster?s policies.
>> >
>> > For more information, check out our github webpage here:
>> > http://github.com/pipitone/qbatch
>> > qbatch is also available in pypi via pip install qbatch
>> >
>> > ?
>> > Gabriel A. Devenyi B.Eng. Ph.D.
>> > Research Computing Associate
>> > Computational Brain Anatomy Laboratory
>> > Cerebral Imaging Center
>> > Douglas Mental Health University Institute
>> > Affiliate, Department of Psychiatry
>> > McGill University
>> > t: 514.761.6131x4781
>> > e: gdevenyi at gmail.com
>> >
>> > _______________________________________________
>> > 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 gdevenyi at gmail.com  Wed May 11 21:42:37 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 11 May 2016 21:42:37 -0400
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAG0CB20g-JtWcXGDAdnXZj4Ys=+N3ihABJZk0TEDZKB5cj7f4g@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
	<CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>
	<CAFQOoOrgE5Xz4yULyhg4r7T-fnfmGMfRqnsQiTEDsKWz00FDtg@mail.gmail.com>
	<CAG0CB20g-JtWcXGDAdnXZj4Ys=+N3ihABJZk0TEDZKB5cj7f4g@mail.gmail.com>
Message-ID: <CAFQOoOqS3OvPpACU1Qhi4r4-L0XqG5=Hhf68ymHjbsvRgbQG8g@mail.gmail.com>

Thanks for your feedback! See responses inline.

On Wed, May 11, 2016 at 8:30 PM, Andrew Janke a.janke at gmail.com wrote:

I?ve taken a proper look at this now. It currently is in no way a drop
in replacement but from what I can see it shouldn?t be too hard. I?m
more than happy to do away with my old perl version. For one your
handling of dependencies is much nicer and self contained. There big
differences are:

qbatch(mine), was designed equivalent to nohup. ie: write a
command, test it, add qbatch.

$ for i in .mnc; do process_something.sh -args .mnc; done

When happy you?d do this:

$ for i in .mnc; do qbatch ?queue my.q ?name $i ?
process-something.sh -args .mnc;
done

Whereas qbatch(python) expects commands to be in a file, this makes it
difficult to use things like globs with qbatch:

$ qbatch ?logfile blah.log ? do_something_args.pl *.mnc

I see a PR which is along these lines:

https://github.com/pipitone/qbatch/issues/90

How hard would it be to support a single command after ???? I note
that you can pipe things to qbatch via echo but this is a real pain to
use in things like perl and python scripts. OK in shell though.

We do support job lists input via STDIN

#From this:
$ for i in *.mnc; do process_something.sh -args *.mnc; done
#To this
$ for i in *.mnc; do echo process_something.sh -args *.mnc; done | qbatch -

Would this work for you?

We?ve thought a bit about single command as you?ve seen, we may end up
providing a simple wrapper to handle your use case.

The version with ??? is also interesting, hadn?t thought of that,
will note it in the issue. Cleaner without needing a warpper

I find debugging output in the logfiles to be invaluable when
debugging things. Stuff like the hostname and time of execution.

https://github.com/andrewjanke/qbatch/blob/master/qbatch#L151

and

https://github.com/andrewjanke/qbatch/blob/master/qbatch#L172

This means that I can quickly grep for ?exit status? on a directory of logfiles.

On our main PBS cluster the prolog and epilog scripts provide this for
us, I?ve actually been scraping the net for prolog and epilog examples
for SGE and yet to find them.

Would you be amenable to allowing ?header-file and ?footer-file
inserts into the joblist? I?m not sure about hard coding that kind of
status lines into the tool.

I?ll open an issue to discuss further
https://github.com/pipitone/qbatch/issues/93

I note slight differences in how we handle cwd, is there are a
reason for you cd?

https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L67

I found this problematic for NFS mounts if using relative paths, and
let gridengine sort out things itself.:

https://github.com/andrewjanke/qbatch/blob/master/qbatch#L108

You?re pointing to the ?local? template which is for qbatch to
parallelize work on a local machine, for the SGE and PBS templates we
use the cluster workdir features.

See https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L51 and
https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L34

There are a number of smaller things (job name larger than 15
characters == FAIL in PBS). This causes issues when tracking
dependencies as your unique job name may be longer than this. You can
either bomb and error out to the user (choose a shorter job name!) or
you have to track an internal database of jobnumbers (capture the
return value of qsub) and match these to input job names. Currently
in your implementation I think this will fail.

if we were using PBS?s awful qstat text outputs which are indeed
truncated, that would be the case, however, we?re parsing PBS?s XML
qstat output, which gives the full jobname properly (at least on our
version of 4.2.something)

See https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L138-L171

There are also issues around re-running jobs:

https://github.com/andrewjanke/qbatch/blob/master/qbatch#L103

As this can also screw up checking dependencies. In your case I think
this is handled better as you query based upon name. I didn?t see from
the code but can you specify a dependency as a job number?

I hadn?t thought at all about job re-running. Currently the dependency
support relies on the cluster, so I?m not sure of the heuristics of a
?soft failure? that allows a re-run, does it get back it?s old job
number? If it does, this should work, if it doesn?t I presume the
cluster kills the dependent job. Will need to investigate this
further.

See https://github.com/pipitone/qbatch/issues/94

As for depending on a job number, we don?t handle that right now,
easily added, noted here: https://github.com/pipitone/qbatch/issues/95

ta

Thanks for all your feedback!

>

a

On 10 May 2016 at 21:23, Gabriel A. Devenyi gdevenyi at gmail.com wrote:

Simon/Andrew, indeed this was written as an intended replacement for
sge_batch and/or the original qbatch (we at CoBrALab also had an earlier
internal qbatch which was not Andrew?s version).
Having said that, we didn?t ensure that it was a one-to-one drop in
replacement, so use may require some modification.

Andrew:
Yes, dependencies in PBS/SGE (and LSF, but I haven?t tested LSF at all yet)
are already implemented, just missing from the README, will add :) My
antsRegistration-MaGeT pipeline makes extensive use of them already.

For PBS we parse the XML joblist and do pattern matching on names:
https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L138-L171
And for SGE we use jobname pattern matching built into SGE:
https://github.com/pipitone/qbatch/blob/master/bin/qbatch#L381-L382

As for the queue, I have an in progress branch to specify ?other? batch
options, handled by environment variable, see
https://github.com/pipitone/qbatch/pull/80
I just need to solve the append vs. replace issue I?m having with argparse.
Thoughts here welcome :)

For bugs/feature requests/modifications, please feel free to request! Our
goal is to provide a maintained tool to support existing workflows and
enable new ones.

?
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Tue, May 10, 2016 at 9:07 AM, Andrew Janke a.janke at gmail.com wrote:
>

Very tasty.

Was it designed as a drop in replacement for qbatch?

https://github.com/andrewjanke/qbatch/blob/master/qbatch

I note a number of similarities in the C/L arguments. Any plans for
handling dependencies? I see code in there but no arguments to make
use of it? In particular to get around the hoops of tracking
dependencies via job numbers (that my qbatch returns) in PBS and/or
via names in gridengine? ie:

$ for i in .mnc; do qbatch ?name STEP1-$i ? ; done
$ qbatch ?name STEP2 ?depends ?STEP1-? ?

I ask as I use qbatch internally in things like volgenmodel in order
to abstract away from the various qsub?s. Currently I handle this via
some pretty horrendous perl code here:

https://github.com/andrewjanke/volgenmodel/blob/master/volgenmodel#L751

It?d be nice to be able to do away with it via your version!

I also find the notion of being able to define a queue via an ENV var
useful when you have a number of levels of scripts/perl/etc that don?t
always pass arguments through. ie:

https://github.com/andrewjanke/qbatch/blob/master/qbatch#L69

a

On 10 May 2016 at 03:38, Gabriel A. Devenyi gdevenyi at gmail.com wrote:

We (Gabriel A. Devenyi and Jon Pipitone) would like to announce the 1.0
release https://github.com/pipitone/qbatch/releases of qbatch, a
command-line tool for easily running a list of commands in parallel
(serial
farming) on a compute cluster. This tool takes the list of commands,
divides them up into batches of arbitrary size, and then submits each
batch
as a separate job or as part of an array job. qbatch also gives you a
consistent interface to use to submit commands on PBS and SGE clusters
or
locally, (support for others are planned/in testing, PRs welcome) while
setting requirements for processors, walltime, memory and job
dependencies.
This tool can be used as a quick interface to spread work out on a
cluster,
or as the glue for for connecting a simple pipeline to a cluster (see
https://github.com/CobraLab/antsRegistration-MAGeT for a sample
implementation)

The target audience of qbatch is two-fold: it is immediately available
for
users of PBS or SGE clusters to simplify their job construction, in
addition, through the use of environment variables, cluster
administrations
can craft a default qbatch deployment which allows new cluster users to
quickly submit jobs which honours the cluster?s policies.

For more information, check out our github webpage here:
http://github.com/pipitone/qbatch
qbatch is also available in pypi via pip install qbatch

?
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

________________________________

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

________________________________

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

From a.janke at gmail.com  Wed May 11 21:54:24 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 12 May 2016 09:54:24 +0800
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAFQOoOqS3OvPpACU1Qhi4r4-L0XqG5=Hhf68ymHjbsvRgbQG8g@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
	<CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>
	<CAFQOoOrgE5Xz4yULyhg4r7T-fnfmGMfRqnsQiTEDsKWz00FDtg@mail.gmail.com>
	<CAG0CB20g-JtWcXGDAdnXZj4Ys=+N3ihABJZk0TEDZKB5cj7f4g@mail.gmail.com>
	<CAFQOoOqS3OvPpACU1Qhi4r4-L0XqG5=Hhf68ymHjbsvRgbQG8g@mail.gmail.com>
Message-ID: <CAG0CB22grf7VVO89S=y=oMkLdYv5yPf_zdEnKmH+Ckc1ZsfCfw@mail.gmail.com>

> Whereas qbatch(python) expects commands to be in a file, this makes it
> difficult to use things like globs with qbatch:
>
> $ qbatch ?logfile blah.log ? do_something_args.pl *.mnc
>
> How hard would it be to support a single command after ???? I note
> that you can pipe things to qbatch via echo but this is a real pain to
> use in things like perl and python scripts. OK in shell though.
>
> We do support job lists input via STDIN
>
> #From this:
> $ for i in *.mnc; do process_something.sh -args *.mnc; done
> #To this
> $ for i in *.mnc; do echo process_something.sh -args *.mnc; done | qbatch -
>
> Would this work for you?

In most cases yes. If I'm just bashing away at the command line it'll
work. It gets hard when you try to use this incantation style in a
perl/python. (but OK in sh/bash).

ie you'd have to do this:

   system("for i in *.mnc; do echo process_something.sh -args *.mnc;
done | qbatch -")

Which is fraught with danger regarding quoting. Pipes are a pain
unless you are on a command line. It would mean that for me to use
this in a perl script I'd first have to create a commands.txt file (in
a temp dir -- and clean it up) and then call it. This to me seems
annoying as it's yet more tiny file everywhere. I also think it's
going to bite many users in the rear as how do you handle quoting?

print FH "mincmath \"dumb mincfile with space in name.mnc\"
\"Macintosh HD/out.mnc\"";

And then what happens if you are using a variable? just quote always?

print FH "mincmath \"$infile\" \"$outfile\"\n";

?

I much prefer using system's array format (in both perl and python) as
it gets around this. note that I still have to attempt to "fortify"
input commands as such:

   https://github.com/andrewjanke/qbatch/blob/master/qbatch#L59

There's no easy answer to this stuff.

> On our main PBS cluster the prolog and epilog scripts provide this for
> us, I?ve actually been scraping the net for prolog and epilog examples
> for SGE and yet to find them.

Short version: don't. I remember trying this also and giving up and
going back to doing it myself.

> Would you be amenable to allowing ?header-file and ?footer-file
> inserts into the joblist? I?m not sure about hard coding that kind of
> status lines into the tool.

By all means, so long as I can make it default in my ~/.config/qbatch.cfg :)

> if we were using PBS?s awful qstat text outputs which are indeed
> truncated, that would be the case, however, we?re parsing PBS?s XML
> qstat output, which gives the full jobname properly (at least on our
> version of 4.2.something)

Ah, OK, makes sense.

> I hadn?t thought at all about job re-running. Currently the dependency
> support relies on the cluster, so I?m not sure of the heuristics of a
> ?soft failure? that allows a re-run, does it get back it?s old job
> number? If it does, this should work, if it doesn?t I presume the
> cluster kills the dependent job. Will need to investigate this
> further.

Your grepping for job ID's should get you around this. There are also
interesting PBSPro installs on HPC systems that will crash the
scheduler if you specify a jobID as a dependency that doesn't exist!
it's a known issue that they are "working on". This is about 5 years
since I reported the bug...



a

From gdevenyi at gmail.com  Wed May 11 21:57:59 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 11 May 2016 21:57:59 -0400
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAG0CB22grf7VVO89S=y=oMkLdYv5yPf_zdEnKmH+Ckc1ZsfCfw@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
	<CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>
	<CAFQOoOrgE5Xz4yULyhg4r7T-fnfmGMfRqnsQiTEDsKWz00FDtg@mail.gmail.com>
	<CAG0CB20g-JtWcXGDAdnXZj4Ys=+N3ihABJZk0TEDZKB5cj7f4g@mail.gmail.com>
	<CAFQOoOqS3OvPpACU1Qhi4r4-L0XqG5=Hhf68ymHjbsvRgbQG8g@mail.gmail.com>
	<CAG0CB22grf7VVO89S=y=oMkLdYv5yPf_zdEnKmH+Ckc1ZsfCfw@mail.gmail.com>
Message-ID: <CAFQOoOo5DAjE+pH36Mq4dwx5xf_yOXoN5GiQG79mffa0ifWBTg@mail.gmail.com>

On Wed, May 11, 2016 at 9:54 PM, Andrew Janke <a.janke at gmail.com> wrote:

>
> Your grepping for job ID's should get you around this. There are also
> interesting PBSPro installs on HPC systems that will crash the
> scheduler if you specify a jobID as a dependency that doesn't exist!
> it's a known issue that they are "working on". This is about 5 years
> since I reported the bug...


Jon and I are well known for crashing SciNet on a regular basis :)

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From gdevenyi at gmail.com  Wed May 11 22:06:04 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 11 May 2016 22:06:04 -0400
Subject: [MINC-users] Announce - qbatch 1.0 - Execute shell command
 lines in parallel (serial farm) on SGE/PBS clusters
In-Reply-To: <CAG0CB22grf7VVO89S=y=oMkLdYv5yPf_zdEnKmH+Ckc1ZsfCfw@mail.gmail.com>
References: <CAFQOoOr2XXFDuLkDz+VFZNVPWr9kHWg+Jc63ef1VJEQ1PPgEiw@mail.gmail.com>
	<CAG0CB22w32290jSzp2cMscXOuYEwDRJdU3EaS-dxof+QG7ye4A@mail.gmail.com>
	<CAFQOoOrgE5Xz4yULyhg4r7T-fnfmGMfRqnsQiTEDsKWz00FDtg@mail.gmail.com>
	<CAG0CB20g-JtWcXGDAdnXZj4Ys=+N3ihABJZk0TEDZKB5cj7f4g@mail.gmail.com>
	<CAFQOoOqS3OvPpACU1Qhi4r4-L0XqG5=Hhf68ymHjbsvRgbQG8g@mail.gmail.com>
	<CAG0CB22grf7VVO89S=y=oMkLdYv5yPf_zdEnKmH+Ckc1ZsfCfw@mail.gmail.com>
Message-ID: <CAFQOoOqwJb2eFEQA62iA1Ds+QT5n7UYMq3MjyWWrswj4TsKV8g@mail.gmail.com>

On Wed, May 11, 2016 at 9:54 PM, Andrew Janke <a.janke at gmail.com> wrote:

> > Whereas qbatch(python) expects commands to be in a file, this makes it
> > difficult to use things like globs with qbatch:
> >
> > $ qbatch ?logfile blah.log ? do_something_args.pl *.mnc
> >
> > How hard would it be to support a single command after ???? I note
> > that you can pipe things to qbatch via echo but this is a real pain to
> > use in things like perl and python scripts. OK in shell though.
> >
> > We do support job lists input via STDIN
> >
> > #From this:
> > $ for i in *.mnc; do process_something.sh -args *.mnc; done
> > #To this
> > $ for i in *.mnc; do echo process_something.sh -args *.mnc; done |
> qbatch -
> >
> > Would this work for you?
>
> In most cases yes. If I'm just bashing away at the command line it'll
> work. It gets hard when you try to use this incantation style in a
> perl/python. (but OK in sh/bash).
>
> ie you'd have to do this:
>
>    system("for i in *.mnc; do echo process_something.sh -args *.mnc;
> done | qbatch -")
>
> Which is fraught with danger regarding quoting. Pipes are a pain
> unless you are on a command line. It would mean that for me to use
> this in a perl script I'd first have to create a commands.txt file (in
> a temp dir -- and clean it up) and then call it. This to me seems
> annoying as it's yet more tiny file everywhere. I also think it's
> going to bite many users in the rear as how do you handle quoting?
>
> print FH "mincmath \"dumb mincfile with space in name.mnc\"
> \"Macintosh HD/out.mnc\"";
>
> And then what happens if you are using a variable? just quote always?
>
> print FH "mincmath \"$infile\" \"$outfile\"\n";
>
> ?
>
> I much prefer using system's array format (in both perl and python) as
> it gets around this. note that I still have to attempt to "fortify"
> input commands as such:
>
>    https://github.com/andrewjanke/qbatch/blob/master/qbatch#L59
>
> There's no easy answer to this stuff.
>


I see the problem with just allowing piping, we will definitely add the
"--" method I see the benefits for non-shell uses.


>
> > On our main PBS cluster the prolog and epilog scripts provide this for
> > us, I?ve actually been scraping the net for prolog and epilog examples
> > for SGE and yet to find them.
>
> Short version: don't. I remember trying this also and giving up and
> going back to doing it myself.
>
> > Would you be amenable to allowing ?header-file and ?footer-file
> > inserts into the joblist? I?m not sure about hard coding that kind of
> > status lines into the tool.
>
> By all means, so long as I can make it default in my ~/.config/qbatch.cfg
> :)
>

So far, we handle defaults via environment variables, we may add another
ENV var, or we might do a config, need to discuss.


>
> > if we were using PBS?s awful qstat text outputs which are indeed
> > truncated, that would be the case, however, we?re parsing PBS?s XML
> > qstat output, which gives the full jobname properly (at least on our
> > version of 4.2.something)
>
> Ah, OK, makes sense.
>
> > I hadn?t thought at all about job re-running. Currently the dependency
> > support relies on the cluster, so I?m not sure of the heuristics of a
> > ?soft failure? that allows a re-run, does it get back it?s old job
> > number? If it does, this should work, if it doesn?t I presume the
> > cluster kills the dependent job. Will need to investigate this
> > further.
>
> Your grepping for job ID's should get you around this. There are also
> interesting PBSPro installs on HPC systems that will crash the
> scheduler if you specify a jobID as a dependency that doesn't exist!
> it's a known issue that they are "working on". This is about 5 years
> since I reported the bug...
>
>
>
> a
>

From zijdenbos at gmail.com  Fri May 13 15:35:37 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 13 May 2016 15:35:37 -0400
Subject: [MINC-users] minccomplete's completeness
Message-ID: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>

Hi all,

I managed to generate a large number of broken MINC files; possibly/likely
due to a filesystem problem. The processes that created them (e.g.,
mincaverage) did not produce any warnings and completed successfully; in
addition, minccomplete tells me that the files are complete.

Unfortunately, trying to read these files throws HDF5 and miicv errors (see
below) and they are obviously corrupt.

I am thinking that it would be useful to complete minccomplete by having it
actually test-read the data, such that it would report on file integrity?
This would make it easy to find these kinds of corruptions - and could even
tack that end the end of scripts to make sure outputs are intact. I'm
currently using 'mincstats -quiet -min' to locate them, but it seems the
natural place for this test would actually be minccomplete.

-- A

HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
  #000: H5Dio.c line 174 in H5Dread(): can't read data
    major: Dataset
    minor: Read failed
  #001: H5Dio.c line 449 in H5D_read(): can't read data
    major: Dataset
    minor: Read failed
  #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
chunk
    major: Low-level I/O
    minor: Read failed
  #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed
    major: Data filters
    minor: Filter operation failed
  #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
read
    major: Data filters
    minor: Read failed
  #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
    major: Data filters
    minor: Unable to initialize object
mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image

From zijdenbos at gmail.com  Fri May 13 16:15:09 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 13 May 2016 16:15:09 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
Message-ID: <CABEEk16tWHQX6qm8fM9zK24g8vipiKR9DcY_WrGyvK8d5Ss_vA@mail.gmail.com>

PS I should also note that most, if not all, standard MINC tools are happy
to process these files. They will print these HDF5 errors, but they will
generate an output file and produce an image (that is of course bad). For
example:

mincmath -add -const 0 corrupt.mnc corrupt2.mnc

results in these two images:
?
 corrupt.png
<https://drive.google.com/file/d/0B5fOtqpIs4sKUlotMGg4XzdQN28/view?usp=drive_web>
?
and, unless you troll through log files, a processing pipeline may happily
complete without any explicit failures.

I'd say that HDF5 read errors should at the very least trigger a non-zero
exit status in all MINC tools.

Since somebody might ask, here is this example file (I have a few hundred
more):
?
 corrupt.mnc
<https://drive.google.com/file/d/0B5fOtqpIs4sKdVphRGtfTVF0SWM/view?usp=drive_web>
?
-- A


On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi all,
>
> I managed to generate a large number of broken MINC files; possibly/likely
> due to a filesystem problem. The processes that created them (e.g.,
> mincaverage) did not produce any warnings and completed successfully; in
> addition, minccomplete tells me that the files are complete.
>
> Unfortunately, trying to read these files throws HDF5 and miicv errors
> (see below) and they are obviously corrupt.
>
> I am thinking that it would be useful to complete minccomplete by having
> it actually test-read the data, such that it would report on file
> integrity? This would make it easy to find these kinds of corruptions - and
> could even tack that end the end of scripts to make sure outputs are
> intact. I'm currently using 'mincstats -quiet -min' to locate them, but it
> seems the natural place for this test would actually be minccomplete.
>
> -- A
>
> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>   #000: H5Dio.c line 174 in H5Dread(): can't read data
>     major: Dataset
>     minor: Read failed
>   #001: H5Dio.c line 449 in H5D_read(): can't read data
>     major: Dataset
>     minor: Read failed
>   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
> chunk
>     major: Low-level I/O
>     minor: Read failed
>   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed
>     major: Data filters
>     minor: Filter operation failed
>   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
> read
>     major: Data filters
>     minor: Read failed
>   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>     major: Data filters
>     minor: Unable to initialize object
> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
>
>
>

From claude at bic.mni.mcgill.ca  Fri May 13 16:25:13 2016
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Fri, 13 May 2016 16:25:13 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
Message-ID: <201605132025.u4DKPDVR003016@login1.bic.mni.mcgill.ca>

Alex,

Here is what I've been doing to check for completeness of minc2 files
(for BigBrain 7404 slices):

sub minc_valid {

  my $input = shift;

  my $ret = `h5ls -r $input`;
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/info/ ) );
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image/ ) );
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-min/ ) );
  return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-max/ ) );

  return( 1 );
}

h5ls is a HDF5 tool.

Claude

>
> Hi all,
>
> I managed to generate a large number of broken MINC files; possibly/likely
> due to a filesystem problem. The processes that created them (e.g.,
> mincaverage) did not produce any warnings and completed successfully; in
> addition, minccomplete tells me that the files are complete.
>
> Unfortunately, trying to read these files throws HDF5 and miicv errors (see
> below) and they are obviously corrupt.
>
> I am thinking that it would be useful to complete minccomplete by having it
> actually test-read the data, such that it would report on file integrity?
> This would make it easy to find these kinds of corruptions - and could even
> tack that end the end of scripts to make sure outputs are intact. I'm
> currently using 'mincstats -quiet -min' to locate them, but it seems the
> natural place for this test would actually be minccomplete.
>
> -- A
>
> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>   #000: H5Dio.c line 174 in H5Dread(): can't read data
>     major: Dataset
>     minor: Read failed
>   #001: H5Dio.c line 449 in H5D_read(): can't read data
>     major: Dataset
>     minor: Read failed
>   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
> chunk
>     major: Low-level I/O
>     minor: Read failed
>   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed
>     major: Data filters
>     minor: Filter operation failed
>   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
> read
>     major: Data filters
>     minor: Read failed
>   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>     major: Data filters
>     minor: Unable to initialize object
> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From zijdenbos at gmail.com  Fri May 13 16:35:24 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 13 May 2016 16:35:24 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <201605132025.u4DKPDVR003016@login1.bic.mni.mcgill.ca>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<201605132025.u4DKPDVR003016@login1.bic.mni.mcgill.ca>
Message-ID: <CABEEk17WjmdTaVwMYM_DUp1W8R4uH-JKYtOKw+SL8TAVbhoj3A@mail.gmail.com>

Hi Claude,

That's a useful idea; but this specific test doesn't actually find the
errors in the volumes I have
so still incomplete :-)

-- A

On Fri, May 13, 2016 at 4:25 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>
wrote:

> Alex,
>
> Here is what I've been doing to check for completeness of minc2 files
> (for BigBrain 7404 slices):
>
> sub minc_valid {
>
>   my $input = shift;
>
>   my $ret = `h5ls -r $input`;
>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/info/ ) );
>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image/ ) );
>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-min/ ) );
>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-max/ ) );
>
>   return( 1 );
> }
>
> h5ls is a HDF5 tool.
>
> Claude
>
> >
> > Hi all,
> >
> > I managed to generate a large number of broken MINC files;
> possibly/likely
> > due to a filesystem problem. The processes that created them (e.g.,
> > mincaverage) did not produce any warnings and completed successfully; in
> > addition, minccomplete tells me that the files are complete.
> >
> > Unfortunately, trying to read these files throws HDF5 and miicv errors
> (see
> > below) and they are obviously corrupt.
> >
> > I am thinking that it would be useful to complete minccomplete by having
> it
> > actually test-read the data, such that it would report on file integrity?
> > This would make it easy to find these kinds of corruptions - and could
> even
> > tack that end the end of scripts to make sure outputs are intact. I'm
> > currently using 'mincstats -quiet -min' to locate them, but it seems the
> > natural place for this test would actually be minccomplete.
> >
> > -- A
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> >   #000: H5Dio.c line 174 in H5Dread(): can't read data
> >     major: Dataset
> >     minor: Read failed
> >   #001: H5Dio.c line 449 in H5D_read(): can't read data
> >     major: Dataset
> >     minor: Read failed
> >   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
> > chunk
> >     major: Low-level I/O
> >     minor: Read failed
> >   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
> failed
> >     major: Data filters
> >     minor: Filter operation failed
> >   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
> > read
> >     major: Data filters
> >     minor: Read failed
> >   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
> >     major: Data filters
> >     minor: Unable to initialize object
> > mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From a.janke at gmail.com  Sat May 14 06:49:09 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 14 May 2016 18:49:09 +0800
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CABEEk17WjmdTaVwMYM_DUp1W8R4uH-JKYtOKw+SL8TAVbhoj3A@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<201605132025.u4DKPDVR003016@login1.bic.mni.mcgill.ca>
	<CABEEk17WjmdTaVwMYM_DUp1W8R4uH-JKYtOKw+SL8TAVbhoj3A@mail.gmail.com>
Message-ID: <CAG0CB23ApL7vsJkWNRF9=bR4SQqZXannMpgrSGrXp_58hKDypQ@mail.gmail.com>

Hi Alex (and others)

Peter and I talked about checksums in MINC many years back and I think
I had subsequent discussions with Bert. At the time we were looking at
creating md5 signatures of both the data and the header and a joint
md5, predominately for reasons of data integrity, a prototype of this
was implemented at one point but I don't think it ever made it into
the main distribution. No idea where it is now, possibly in a
directory of Peter Neelins somewhere.

Part of the discussion then turned to a better way of how to determine
if the file was complete and the best we could come up with is the
current "write a flag when done" approach. I have seen a similar thing
to the error you are seeing but I tended to find that it was related
to reading broken MINC1 files with MINC2. Your problem looks different
though. It seems to be missing data chunks?

There is no good way that I can think of to determine if a minc file's
data is "good" other than to write an MD5 at the time of write along
with the complete flag. From memory the plan was

   image:md5_data   -- md5 of the data part only, minccmp/mincdiff
could make use of it.
   image:md5_header -- md5 of just the header
   image:md5_file  -- md5 of all of it.

We could then add a -md5 option to minccmp to check that what you have
in your file is indeed what you had in RAM while writing it out. It
would make minccmp slower as we'd have to read through the whole file
but it would achieve your aim. In your case the call of mincmd5 would
then bomb on the broken file which would achieve your aim but also a
perhaps achieve a more noble goal also.

And then of course do we get all meta and also check the value of the
md5 after we have written it to make sure it's been written correctly?
and then again in case we read it wrong?

And should we restrict to md5?  image:checksum_data?

I'm all for this extra functionality, it seems a logical extension for
a file format that aims to be as reproducible as possible. There were
also plans to use this as part of checking the provenance of a MINC
file but in favour of pragmatism we went for :ident as implemented by
Bert many years ago.


a

PS: Claude, yes your suggestion is also be a good heuristic!

On 14 May 2016 at 04:35, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Hi Claude,
>
> That's a useful idea; but this specific test doesn't actually find the
> errors in the volumes I have
> so still incomplete :-)
>
> -- A
>
> On Fri, May 13, 2016 at 4:25 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>
> wrote:
>
>> Alex,
>>
>> Here is what I've been doing to check for completeness of minc2 files
>> (for BigBrain 7404 slices):
>>
>> sub minc_valid {
>>
>>   my $input = shift;
>>
>>   my $ret = `h5ls -r $input`;
>>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/info/ ) );
>>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image/ ) );
>>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-min/ ) );
>>   return( 0 ) if( !( $ret =~ m/\/minc-2.0\/image\/0\/image-max/ ) );
>>
>>   return( 1 );
>> }
>>
>> h5ls is a HDF5 tool.
>>
>> Claude
>>
>> >
>> > Hi all,
>> >
>> > I managed to generate a large number of broken MINC files;
>> possibly/likely
>> > due to a filesystem problem. The processes that created them (e.g.,
>> > mincaverage) did not produce any warnings and completed successfully; in
>> > addition, minccomplete tells me that the files are complete.
>> >
>> > Unfortunately, trying to read these files throws HDF5 and miicv errors
>> (see
>> > below) and they are obviously corrupt.
>> >
>> > I am thinking that it would be useful to complete minccomplete by having
>> it
>> > actually test-read the data, such that it would report on file integrity?
>> > This would make it easy to find these kinds of corruptions - and could
>> even
>> > tack that end the end of scripts to make sure outputs are intact. I'm
>> > currently using 'mincstats -quiet -min' to locate them, but it seems the
>> > natural place for this test would actually be minccomplete.
>> >
>> > -- A
>> >
>> > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>> >   #000: H5Dio.c line 174 in H5Dread(): can't read data
>> >     major: Dataset
>> >     minor: Read failed
>> >   #001: H5Dio.c line 449 in H5D_read(): can't read data
>> >     major: Dataset
>> >     minor: Read failed
>> >   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
>> > chunk
>> >     major: Low-level I/O
>> >     minor: Read failed
>> >   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
>> failed
>> >     major: Data filters
>> >     minor: Filter operation failed
>> >   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
>> > read
>> >     major: Data filters
>> >     minor: Read failed
>> >   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>> >     major: Data filters
>> >     minor: Unable to initialize object
>> > mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From vladimir.fonov at gmail.com  Sat May 14 06:53:27 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Sat, 14 May 2016 06:53:27 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
Message-ID: <CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>

Hello,

the only thing minccomplete does is read the contents of the image:complete
attribute. Which is not even respected by all minc tools.
One real way to check the consistency of the minc file would be to enable
checksum , integrated into HDF5 file format.

Currently it can be enabled by setting the environment variable
MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
works only with MINC2 file format and it was not tested very well yet.

On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi all,
>
> I managed to generate a large number of broken MINC files; possibly/likely
> due to a filesystem problem. The processes that created them (e.g.,
> mincaverage) did not produce any warnings and completed successfully; in
> addition, minccomplete tells me that the files are complete.
>
> Unfortunately, trying to read these files throws HDF5 and miicv errors (see
> below) and they are obviously corrupt.
>
> I am thinking that it would be useful to complete minccomplete by having it
> actually test-read the data, such that it would report on file integrity?
> This would make it easy to find these kinds of corruptions - and could even
> tack that end the end of scripts to make sure outputs are intact. I'm
> currently using 'mincstats -quiet -min' to locate them, but it seems the
> natural place for this test would actually be minccomplete.
>
> -- A
>
> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>   #000: H5Dio.c line 174 in H5Dread(): can't read data
>     major: Dataset
>     minor: Read failed
>   #001: H5Dio.c line 449 in H5D_read(): can't read data
>     major: Dataset
>     minor: Read failed
>   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
> chunk
>     major: Low-level I/O
>     minor: Read failed
>   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed
>     major: Data filters
>     minor: Filter operation failed
>   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
> read
>     major: Data filters
>     minor: Read failed
>   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>     major: Data filters
>     minor: Unable to initialize object
> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>



-- 
Best regards,

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

From a.janke at gmail.com  Sat May 14 06:59:06 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Sat, 14 May 2016 18:59:06 +0800
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
Message-ID: <CAG0CB21gmqnNt3CRRdTD1XcyGDYAZwt98GC-xkbFibS-g1uLCA@mail.gmail.com>

And that sounds even better.  Never realised it was part of HDF5.


a

On 14 May 2016 at 18:53, Vladimir S. FONOV <vladimir.fonov at gmail.com> wrote:
> Hello,
>
> the only thing minccomplete does is read the contents of the image:complete
> attribute. Which is not even respected by all minc tools.
> One real way to check the consistency of the minc file would be to enable
> checksum , integrated into HDF5 file format.
>
> Currently it can be enabled by setting the environment variable
> MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
> works only with MINC2 file format and it was not tested very well yet.
>
> On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
>
>> Hi all,
>>
>> I managed to generate a large number of broken MINC files; possibly/likely
>> due to a filesystem problem. The processes that created them (e.g.,
>> mincaverage) did not produce any warnings and completed successfully; in
>> addition, minccomplete tells me that the files are complete.
>>
>> Unfortunately, trying to read these files throws HDF5 and miicv errors (see
>> below) and they are obviously corrupt.
>>
>> I am thinking that it would be useful to complete minccomplete by having it
>> actually test-read the data, such that it would report on file integrity?
>> This would make it easy to find these kinds of corruptions - and could even
>> tack that end the end of scripts to make sure outputs are intact. I'm
>> currently using 'mincstats -quiet -min' to locate them, but it seems the
>> natural place for this test would actually be minccomplete.
>>
>> -- A
>>
>> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>>   #000: H5Dio.c line 174 in H5Dread(): can't read data
>>     major: Dataset
>>     minor: Read failed
>>   #001: H5Dio.c line 449 in H5D_read(): can't read data
>>     major: Dataset
>>     minor: Read failed
>>   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
>> chunk
>>     major: Low-level I/O
>>     minor: Read failed
>>   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed
>>     major: Data filters
>>     minor: Filter operation failed
>>   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
>> read
>>     major: Data filters
>>     minor: Read failed
>>   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>>     major: Data filters
>>     minor: Unable to initialize object
>> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From robert.d.vincent at mcgill.ca  Sat May 14 07:02:55 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Sat, 14 May 2016 07:02:55 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
Message-ID: <CAAd5DeS4dgAZ=DPq3t+nvDXmm3tZc4kXuw2xSoVTNuoVeV6q+g@mail.gmail.com>

Hi all,

In any case, Alex is entirely correct HDF5 errors should be better handled
in a few key places - outright read errors should cause obvious things like
"exit(-1)" or something. The format is so full of redundancy that it's
quite unlikely you would successfully read a broken file, with or without
checksumming the data (there are already checksums built into most HDF5
data structures, e.g.).

I'll make these changes asap.

    -bert

On Sat, May 14, 2016 at 6:53 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Hello,
>
> the only thing minccomplete does is read the contents of the image:complete
> attribute. Which is not even respected by all minc tools.
> One real way to check the consistency of the minc file would be to enable
> checksum , integrated into HDF5 file format.
>
> Currently it can be enabled by setting the environment variable
> MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
> works only with MINC2 file format and it was not tested very well yet.
>
> On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi all,
> >
> > I managed to generate a large number of broken MINC files;
> possibly/likely
> > due to a filesystem problem. The processes that created them (e.g.,
> > mincaverage) did not produce any warnings and completed successfully; in
> > addition, minccomplete tells me that the files are complete.
> >
> > Unfortunately, trying to read these files throws HDF5 and miicv errors
> (see
> > below) and they are obviously corrupt.
> >
> > I am thinking that it would be useful to complete minccomplete by having
> it
> > actually test-read the data, such that it would report on file integrity?
> > This would make it easy to find these kinds of corruptions - and could
> even
> > tack that end the end of scripts to make sure outputs are intact. I'm
> > currently using 'mincstats -quiet -min' to locate them, but it seems the
> > natural place for this test would actually be minccomplete.
> >
> > -- A
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> >   #000: H5Dio.c line 174 in H5Dread(): can't read data
> >     major: Dataset
> >     minor: Read failed
> >   #001: H5Dio.c line 449 in H5D_read(): can't read data
> >     major: Dataset
> >     minor: Read failed
> >   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
> > chunk
> >     major: Low-level I/O
> >     minor: Read failed
> >   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
> failed
> >     major: Data filters
> >     minor: Filter operation failed
> >   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
> > read
> >     major: Data filters
> >     minor: Read failed
> >   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
> >     major: Data filters
> >     minor: Unable to initialize object
> > mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From zijdenbos at gmail.com  Sat May 14 07:13:42 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sat, 14 May 2016 07:13:42 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CAG0CB21gmqnNt3CRRdTD1XcyGDYAZwt98GC-xkbFibS-g1uLCA@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
	<CAG0CB21gmqnNt3CRRdTD1XcyGDYAZwt98GC-xkbFibS-g1uLCA@mail.gmail.com>
Message-ID: <CABEEk14xtch2DShYGVPci0hLW47SRr8peN6j4nGW_HhA5gdaWA@mail.gmail.com>

That sounds promising (and if it works an easy solution) for completing
minccomplete!

However, what concerns me the most about all of this is that a "bad" volume
may go entirely unnoticed as the standard MINC tools do not seem to care
about HDF5 errors. The volumes that I have are happily read by the MINC
tools, ignoring the HDF5 errors, and subsequently will produce output that
is "good" (see the the snapshot I sent). Ergo, if for whatever reason a bad
volume is created somewhere in a processing pipeline (which might even be a
temporary volume), it will be "fixed" by the downstream steps but you will
end up with bad data downstream. Unless visual QC picks it up or you
explicitly check all the logs for HDF5 warnings, you'd never know. This is
a very real problem IMHO that may have been affecting any of us...

-- A

On Sat, May 14, 2016 at 6:59 AM, Andrew Janke <a.janke at gmail.com> wrote:

> And that sounds even better.  Never realised it was part of HDF5.
>
>
> a
>
> On 14 May 2016 at 18:53, Vladimir S. FONOV <vladimir.fonov at gmail.com>
> wrote:
> > Hello,
> >
> > the only thing minccomplete does is read the contents of the
> image:complete
> > attribute. Which is not even respected by all minc tools.
> > One real way to check the consistency of the minc file would be to enable
> > checksum , integrated into HDF5 file format.
> >
> > Currently it can be enabled by setting the environment variable
> > MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
> > works only with MINC2 file format and it was not tested very well yet.
> >
> > On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
> >
> >> Hi all,
> >>
> >> I managed to generate a large number of broken MINC files;
> possibly/likely
> >> due to a filesystem problem. The processes that created them (e.g.,
> >> mincaverage) did not produce any warnings and completed successfully; in
> >> addition, minccomplete tells me that the files are complete.
> >>
> >> Unfortunately, trying to read these files throws HDF5 and miicv errors
> (see
> >> below) and they are obviously corrupt.
> >>
> >> I am thinking that it would be useful to complete minccomplete by
> having it
> >> actually test-read the data, such that it would report on file
> integrity?
> >> This would make it easy to find these kinds of corruptions - and could
> even
> >> tack that end the end of scripts to make sure outputs are intact. I'm
> >> currently using 'mincstats -quiet -min' to locate them, but it seems the
> >> natural place for this test would actually be minccomplete.
> >>
> >> -- A
> >>
> >> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> >>   #000: H5Dio.c line 174 in H5Dread(): can't read data
> >>     major: Dataset
> >>     minor: Read failed
> >>   #001: H5Dio.c line 449 in H5D_read(): can't read data
> >>     major: Dataset
> >>     minor: Read failed
> >>   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw
> data
> >> chunk
> >>     major: Low-level I/O
> >>     minor: Read failed
> >>   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
> failed
> >>     major: Data filters
> >>     minor: Filter operation failed
> >>   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure
> during
> >> read
> >>     major: Data filters
> >>     minor: Read failed
> >>   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
> >>     major: Data filters
> >>     minor: Unable to initialize object
> >> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >
> >
> >
> > --
> > Best regards,
> >
> >  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> > _______________________________________________
> > 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  Sat May 14 07:15:43 2016
From: vladimir.fonov at gmail.com (vladimir.fonov at gmail.com)
Date: Sat, 14 May 2016 07:15:43 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CAAd5DeS4dgAZ=DPq3t+nvDXmm3tZc4kXuw2xSoVTNuoVeV6q+g@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
	<CAAd5DeS4dgAZ=DPq3t+nvDXmm3tZc4kXuw2xSoVTNuoVeV6q+g@mail.gmail.com>
Message-ID: <9EB56324-39ED-48D9-9DA7-B76915DF7434@gmail.com>

The reason these errors are not handled properly, perhaps, is because we have calls like that:

https://github.com/BIC-MNI/libminc/blob/master/libsrc/voxel_loop.c#L1505

- notice the absence of checking for the return value. 

> On May 14, 2016, at 07:02, Robert D. Vincent <robert.d.vincent at mcgill.ca> wrote:
> 
> Hi all,
> 
> In any case, Alex is entirely correct HDF5 errors should be better handled
> in a few key places - outright read errors should cause obvious things like
> "exit(-1)" or something. The format is so full of redundancy that it's
> quite unlikely you would successfully read a broken file, with or without
> checksumming the data (there are already checksums built into most HDF5
> data structures, e.g.).
> 
> I'll make these changes asap.
> 
>    -bert
> 
> On Sat, May 14, 2016 at 6:53 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>> wrote:
> 
>> Hello,
>> 
>> the only thing minccomplete does is read the contents of the image:complete
>> attribute. Which is not even respected by all minc tools.
>> One real way to check the consistency of the minc file would be to enable
>> checksum , integrated into HDF5 file format.
>> 
>> Currently it can be enabled by setting the environment variable
>> MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
>> works only with MINC2 file format and it was not tested very well yet.
>> 
>> On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
>> wrote:
>> 
>>> Hi all,
>>> 
>>> I managed to generate a large number of broken MINC files;
>> possibly/likely
>>> due to a filesystem problem. The processes that created them (e.g.,
>>> mincaverage) did not produce any warnings and completed successfully; in
>>> addition, minccomplete tells me that the files are complete.
>>> 
>>> Unfortunately, trying to read these files throws HDF5 and miicv errors
>> (see
>>> below) and they are obviously corrupt.
>>> 
>>> I am thinking that it would be useful to complete minccomplete by having
>> it
>>> actually test-read the data, such that it would report on file integrity?
>>> This would make it easy to find these kinds of corruptions - and could
>> even
>>> tack that end the end of scripts to make sure outputs are intact. I'm
>>> currently using 'mincstats -quiet -min' to locate them, but it seems the
>>> natural place for this test would actually be minccomplete.
>>> 
>>> -- A
>>> 
>>> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>>>  #000: H5Dio.c line 174 in H5Dread(): can't read data
>>>    major: Dataset
>>>    minor: Read failed
>>>  #001: H5Dio.c line 449 in H5D_read(): can't read data
>>>    major: Dataset
>>>    minor: Read failed
>>>  #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
>>> chunk
>>>    major: Low-level I/O
>>>    minor: Read failed
>>>  #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
>> failed
>>>    major: Data filters
>>>    minor: Filter operation failed
>>>  #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
>>> read
>>>    major: Data filters
>>>    minor: Read failed
>>>  #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>>>    major: Data filters
>>>    minor: Unable to initialize object
>>> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>> 
>> 
>> 
>> 
>> --
>> Best regards,
>> 
>> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

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





From zijdenbos at gmail.com  Sat May 14 07:17:37 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sat, 14 May 2016 07:17:37 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CABEEk14xtch2DShYGVPci0hLW47SRr8peN6j4nGW_HhA5gdaWA@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
	<CAG0CB21gmqnNt3CRRdTD1XcyGDYAZwt98GC-xkbFibS-g1uLCA@mail.gmail.com>
	<CABEEk14xtch2DShYGVPci0hLW47SRr8peN6j4nGW_HhA5gdaWA@mail.gmail.com>
Message-ID: <CABEEk16oUYEgJ05XNEMtd1Engi41+nojGAKJbtMe9iK=3DvaQA@mail.gmail.com>

Ah - Bert was on the same page - thanks!!

On Sat, May 14, 2016 at 7:13 AM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> That sounds promising (and if it works an easy solution) for completing
> minccomplete!
>
> However, what concerns me the most about all of this is that a "bad"
> volume may go entirely unnoticed as the standard MINC tools do not seem to
> care about HDF5 errors. The volumes that I have are happily read by the
> MINC tools, ignoring the HDF5 errors, and subsequently will produce output
> that is "good" (see the the snapshot I sent). Ergo, if for whatever reason
> a bad volume is created somewhere in a processing pipeline (which might
> even be a temporary volume), it will be "fixed" by the downstream steps but
> you will end up with bad data downstream. Unless visual QC picks it up or
> you explicitly check all the logs for HDF5 warnings, you'd never know. This
> is a very real problem IMHO that may have been affecting any of us...
>
> -- A
>
> On Sat, May 14, 2016 at 6:59 AM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> And that sounds even better.  Never realised it was part of HDF5.
>>
>>
>> a
>>
>> On 14 May 2016 at 18:53, Vladimir S. FONOV <vladimir.fonov at gmail.com>
>> wrote:
>> > Hello,
>> >
>> > the only thing minccomplete does is read the contents of the
>> image:complete
>> > attribute. Which is not even respected by all minc tools.
>> > One real way to check the consistency of the minc file would be to
>> enable
>> > checksum , integrated into HDF5 file format.
>> >
>> > Currently it can be enabled by setting the environment variable
>> > MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
>> > works only with MINC2 file format and it was not tested very well yet.
>> >
>> > On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
>> wrote:
>> >
>> >> Hi all,
>> >>
>> >> I managed to generate a large number of broken MINC files;
>> possibly/likely
>> >> due to a filesystem problem. The processes that created them (e.g.,
>> >> mincaverage) did not produce any warnings and completed successfully;
>> in
>> >> addition, minccomplete tells me that the files are complete.
>> >>
>> >> Unfortunately, trying to read these files throws HDF5 and miicv errors
>> (see
>> >> below) and they are obviously corrupt.
>> >>
>> >> I am thinking that it would be useful to complete minccomplete by
>> having it
>> >> actually test-read the data, such that it would report on file
>> integrity?
>> >> This would make it easy to find these kinds of corruptions - and could
>> even
>> >> tack that end the end of scripts to make sure outputs are intact. I'm
>> >> currently using 'mincstats -quiet -min' to locate them, but it seems
>> the
>> >> natural place for this test would actually be minccomplete.
>> >>
>> >> -- A
>> >>
>> >> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>> >>   #000: H5Dio.c line 174 in H5Dread(): can't read data
>> >>     major: Dataset
>> >>     minor: Read failed
>> >>   #001: H5Dio.c line 449 in H5D_read(): can't read data
>> >>     major: Dataset
>> >>     minor: Read failed
>> >>   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw
>> data
>> >> chunk
>> >>     major: Low-level I/O
>> >>     minor: Read failed
>> >>   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
>> failed
>> >>     major: Data filters
>> >>     minor: Filter operation failed
>> >>   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure
>> during
>> >> read
>> >>     major: Data filters
>> >>     minor: Read failed
>> >>   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>> >>     major: Data filters
>> >>     minor: Unable to initialize object
>> >> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
>> >> _______________________________________________
>> >> MINC-users at bic.mni.mcgill.ca
>> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >>
>> >
>> >
>> >
>> > --
>> > Best regards,
>> >
>> >  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>> > _______________________________________________
>> > 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  Sat May 14 07:24:04 2016
From: vladimir.fonov at gmail.com (vladimir.fonov at gmail.com)
Date: Sat, 14 May 2016 07:24:04 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <9EB56324-39ED-48D9-9DA7-B76915DF7434@gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
	<CAAd5DeS4dgAZ=DPq3t+nvDXmm3tZc4kXuw2xSoVTNuoVeV6q+g@mail.gmail.com>
	<9EB56324-39ED-48D9-9DA7-B76915DF7434@gmail.com>
Message-ID: <33423F05-3F67-4DE3-8A11-BFFA4FA85F9A@gmail.com>

By the way, if you run something like 

volume_pol corrupt.mnc /opt/minc/share/icbm152_model_09a/mni_icbm152_t1_tal_nlin_sym_09a.mnc 

it will crash, end the return code is set to 1 , because of this: https://github.com/BIC-MNI/libminc/blob/develop/ezminc/minc_1_rw.cpp#L1297 but this method works only in C++


> On May 14, 2016, at 07:15, vladimir.fonov at gmail.com wrote:
> 
> The reason these errors are not handled properly, perhaps, is because we have calls like that:
> 
> https://github.com/BIC-MNI/libminc/blob/master/libsrc/voxel_loop.c#L1505
> 
> - notice the absence of checking for the return value. 
> 
>> On May 14, 2016, at 07:02, Robert D. Vincent <robert.d.vincent at mcgill.ca> wrote:
>> 
>> Hi all,
>> 
>> In any case, Alex is entirely correct HDF5 errors should be better handled
>> in a few key places - outright read errors should cause obvious things like
>> "exit(-1)" or something. The format is so full of redundancy that it's
>> quite unlikely you would successfully read a broken file, with or without
>> checksumming the data (there are already checksums built into most HDF5
>> data structures, e.g.).
>> 
>> I'll make these changes asap.
>> 
>>   -bert
>> 
>> On Sat, May 14, 2016 at 6:53 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
>>> wrote:
>> 
>>> Hello,
>>> 
>>> the only thing minccomplete does is read the contents of the image:complete
>>> attribute. Which is not even respected by all minc tools.
>>> One real way to check the consistency of the minc file would be to enable
>>> checksum , integrated into HDF5 file format.
>>> 
>>> Currently it can be enabled by setting the environment variable
>>> MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
>>> works only with MINC2 file format and it was not tested very well yet.
>>> 
>>> On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
>>> wrote:
>>> 
>>>> Hi all,
>>>> 
>>>> I managed to generate a large number of broken MINC files;
>>> possibly/likely
>>>> due to a filesystem problem. The processes that created them (e.g.,
>>>> mincaverage) did not produce any warnings and completed successfully; in
>>>> addition, minccomplete tells me that the files are complete.
>>>> 
>>>> Unfortunately, trying to read these files throws HDF5 and miicv errors
>>> (see
>>>> below) and they are obviously corrupt.
>>>> 
>>>> I am thinking that it would be useful to complete minccomplete by having
>>> it
>>>> actually test-read the data, such that it would report on file integrity?
>>>> This would make it easy to find these kinds of corruptions - and could
>>> even
>>>> tack that end the end of scripts to make sure outputs are intact. I'm
>>>> currently using 'mincstats -quiet -min' to locate them, but it seems the
>>>> natural place for this test would actually be minccomplete.
>>>> 
>>>> -- A
>>>> 
>>>> HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
>>>> #000: H5Dio.c line 174 in H5Dread(): can't read data
>>>>   major: Dataset
>>>>   minor: Read failed
>>>> #001: H5Dio.c line 449 in H5D_read(): can't read data
>>>>   major: Dataset
>>>>   minor: Read failed
>>>> #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
>>>> chunk
>>>>   major: Low-level I/O
>>>>   minor: Read failed
>>>> #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
>>> failed
>>>>   major: Data filters
>>>>   minor: Filter operation failed
>>>> #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
>>>> read
>>>>   major: Data filters
>>>>   minor: Read failed
>>>> #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
>>>>   major: Data filters
>>>>   minor: Unable to initialize object
>>>> mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
>>>> _______________________________________________
>>>> MINC-users at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> Best regards,
>>> 
>>> Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>> 
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> 
> Best regards, Vladimir S. FONOV ~ v.s.fonov <at> ilmarin.info
> 
> 
> 
> 

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





From zijdenbos at gmail.com  Sat May 14 17:04:16 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Sat, 14 May 2016 17:04:16 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
Message-ID: <CABEEk16JJOgLewbz4qppLioMAcC-nR0jYoWqW7ptEKQMoLHONg@mail.gmail.com>

On this note: nii2mnc is one of the tools that doesn't appear to set the
image:complete attribute. I haven't found any others yet but since I
started running minccomplete on anything I generate, I may come up with
more :)

On Sat, May 14, 2016 at 6:53 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Hello,
>
> the only thing minccomplete does is read the contents of the image:complete
> attribute. Which is not even respected by all minc tools.
> One real way to check the consistency of the minc file would be to enable
> checksum , integrated into HDF5 file format.
>
> Currently it can be enabled by setting the environment variable
> MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
> works only with MINC2 file format and it was not tested very well yet.
>
> On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi all,
> >
> > I managed to generate a large number of broken MINC files;
> possibly/likely
> > due to a filesystem problem. The processes that created them (e.g.,
> > mincaverage) did not produce any warnings and completed successfully; in
> > addition, minccomplete tells me that the files are complete.
> >
> > Unfortunately, trying to read these files throws HDF5 and miicv errors
> (see
> > below) and they are obviously corrupt.
> >
> > I am thinking that it would be useful to complete minccomplete by having
> it
> > actually test-read the data, such that it would report on file integrity?
> > This would make it easy to find these kinds of corruptions - and could
> even
> > tack that end the end of scripts to make sure outputs are intact. I'm
> > currently using 'mincstats -quiet -min' to locate them, but it seems the
> > natural place for this test would actually be minccomplete.
> >
> > -- A
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> >   #000: H5Dio.c line 174 in H5Dread(): can't read data
> >     major: Dataset
> >     minor: Read failed
> >   #001: H5Dio.c line 449 in H5D_read(): can't read data
> >     major: Dataset
> >     minor: Read failed
> >   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data
> > chunk
> >     major: Low-level I/O
> >     minor: Read failed
> >   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
> failed
> >     major: Data filters
> >     minor: Filter operation failed
> >   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure during
> > read
> >     major: Data filters
> >     minor: Read failed
> >   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
> >     major: Data filters
> >     minor: Unable to initialize object
> > mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From robert.d.vincent at mcgill.ca  Mon May 16 12:38:50 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Mon, 16 May 2016 12:38:50 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CABEEk16JJOgLewbz4qppLioMAcC-nR0jYoWqW7ptEKQMoLHONg@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
	<CABEEk16JJOgLewbz4qppLioMAcC-nR0jYoWqW7ptEKQMoLHONg@mail.gmail.com>
Message-ID: <CAAd5DeQC6+T-aZBhNJv+n-NJ-ZzbdY6oG=DUvrX6CiYu8_bp6w@mail.gmail.com>

Hi all,

I have just checked in changes to volume_io, voxel_loop and the following
minc tools:

mincaverage, minccalc, minccmp, mincconcat, mincconvert, minccopy,
mincextract, minclookup, mincmakescalar, mincmakevector, mincmath,
mincresample, mincreshape, mincsample, mincstats, minctoraw, mincwindow.

These tools will still behave as before, in that they will run to
completion with a corrupt file. However, they will report the error as a
non-zero exit code (EXIT_FAILURE), in addition to whatever messages are
currently displayed by the libraries.

Two existing tools, mincinfo and mincdump, seem to already have correct
handling of read errors. At least two others, mincblob and mincmorph,
should pick up the changes via volume_io.

This covers the majority of the command line tools. It may also make sense
to reflect these changes in some of the basic scripts (e.g. mincpik,
mincdiff) - let me know if there are any particularly salient cases we
should take care of.

    -bert

On Sat, May 14, 2016 at 5:04 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> On this note: nii2mnc is one of the tools that doesn't appear to set the
> image:complete attribute. I haven't found any others yet but since I
> started running minccomplete on anything I generate, I may come up with
> more :)
>
> On Sat, May 14, 2016 at 6:53 AM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com
> > wrote:
>
> > Hello,
> >
> > the only thing minccomplete does is read the contents of the
> image:complete
> > attribute. Which is not even respected by all minc tools.
> > One real way to check the consistency of the minc file would be to enable
> > checksum , integrated into HDF5 file format.
> >
> > Currently it can be enabled by setting the environment variable
> > MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
> > works only with MINC2 file format and it was not tested very well yet.
> >
> > On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> > wrote:
> >
> > > Hi all,
> > >
> > > I managed to generate a large number of broken MINC files;
> > possibly/likely
> > > due to a filesystem problem. The processes that created them (e.g.,
> > > mincaverage) did not produce any warnings and completed successfully;
> in
> > > addition, minccomplete tells me that the files are complete.
> > >
> > > Unfortunately, trying to read these files throws HDF5 and miicv errors
> > (see
> > > below) and they are obviously corrupt.
> > >
> > > I am thinking that it would be useful to complete minccomplete by
> having
> > it
> > > actually test-read the data, such that it would report on file
> integrity?
> > > This would make it easy to find these kinds of corruptions - and could
> > even
> > > tack that end the end of scripts to make sure outputs are intact. I'm
> > > currently using 'mincstats -quiet -min' to locate them, but it seems
> the
> > > natural place for this test would actually be minccomplete.
> > >
> > > -- A
> > >
> > > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> > >   #000: H5Dio.c line 174 in H5Dread(): can't read data
> > >     major: Dataset
> > >     minor: Read failed
> > >   #001: H5Dio.c line 449 in H5D_read(): can't read data
> > >     major: Dataset
> > >     minor: Read failed
> > >   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw
> data
> > > chunk
> > >     major: Low-level I/O
> > >     minor: Read failed
> > >   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
> > failed
> > >     major: Data filters
> > >     minor: Filter operation failed
> > >   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure
> during
> > > read
> > >     major: Data filters
> > >     minor: Read failed
> > >   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate() failed
> > >     major: Data filters
> > >     minor: Unable to initialize object
> > > mincstats (from miicv_get): Can't read dataset /minc-2.0/image/0/image
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > >
> >
> >
> >
> > --
> > Best regards,
> >
> >  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> > _______________________________________________
> > 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 gdevenyi at gmail.com  Tue May 17 16:24:33 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 17 May 2016 16:24:33 -0400
Subject: [MINC-users] Handling conversion from SPM "analyze" format?
Message-ID: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>

Hi minc-users,

I've inherited some data I think was touched by SPM at some point, as I
have a hdr/img/mat for each.

Upon conversion (with ana2mnc) they're not oriented properly. I suspect I
can rectify this with information in the .mat file?

Does anyone know how I can do this with the minc tools? Or will I have to
figure out something with SPM?

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

From a.janke at gmail.com  Tue May 17 16:53:42 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 18 May 2016 06:53:42 +1000
Subject: [MINC-users] Handling conversion from SPM "analyze" format?
In-Reply-To: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
Message-ID: <CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>

Hi Gabriel,

If you call ana2mnc as spm2mnc (make a symlink) it will attempt to
make a MINC file with the correct orientation. There is also a spm2xfm
that will convert the .mat to a .xfm file. It uses mat1dump (something
I wrote in Perl many years ago).


a

On 18 May 2016 at 06:24, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> Hi minc-users,
>
> I've inherited some data I think was touched by SPM at some point, as I
> have a hdr/img/mat for each.
>
> Upon conversion (with ana2mnc) they're not oriented properly. I suspect I
> can rectify this with information in the .mat file?
>
> Does anyone know how I can do this with the minc tools? Or will I have to
> figure out something with SPM?
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From pgravel at bic.mni.mcgill.ca  Tue May 17 21:58:48 2016
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 17 May 2016 21:58:48 -0400 (EDT)
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
Message-ID: <alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>

Dear All,

I want to prepare a virtual machine for VirtualBox that includes a linux 
version with the minc tools. But being lazy (;-)!), I was wondering if 
anyone already had that and be willing to share.
Otherwise, any pointers on how to go about it (of course I would be 
willing to share the finished product!)?

Many thanks!

Paul


From a.janke at gmail.com  Tue May 17 22:01:34 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 18 May 2016 12:01:34 +1000
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
Message-ID: <CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>

I'm sure I saw one pass through the minc-users mailing list a while back?

I use the neurodebian VM and then

   apt-get install minc-toolkit     (thanks Vlad!)

a


On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> Dear All,
>
> I want to prepare a virtual machine for VirtualBox that includes a linux
> version with the minc tools. But being lazy (;-)!), I was wondering if
> anyone already had that and be willing to share.
> Otherwise, any pointers on how to go about it (of course I would be willing
> to share the finished product!)?
>
> Many thanks!
>
> Paul
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From zijdenbos at gmail.com  Tue May 17 22:10:36 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Tue, 17 May 2016 22:10:36 -0400
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
Message-ID: <CABEEk17CA=SiRq96b8HjU7yVhBDBg7PQrjSgUmh60-qfGhX=-w@mail.gmail.com>

I once built a VM "MINCbuntu" (still available at
http://packages.bic.mni.mcgill.ca/virtual-machines/), but that hasn't been
updated since 2009, so I'd suggest to follow Andrew's suggestion at this
point :-)

-- A



On Tue, May 17, 2016 at 10:01 PM, Andrew Janke <a.janke at gmail.com> wrote:

> I'm sure I saw one pass through the minc-users mailing list a while back?
>
> I use the neurodebian VM and then
>
>    apt-get install minc-toolkit     (thanks Vlad!)
>
> a
>
>
> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> > Dear All,
> >
> > I want to prepare a virtual machine for VirtualBox that includes a linux
> > version with the minc tools. But being lazy (;-)!), I was wondering if
> > anyone already had that and be willing to share.
> > Otherwise, any pointers on how to go about it (of course I would be
> willing
> > to share the finished product!)?
> >
> > Many thanks!
> >
> > Paul
> >
> > _______________________________________________
> > 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  Tue May 17 22:10:40 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 17 May 2016 22:10:40 -0400
Subject: [MINC-users] WQC - simple QC tool with web interface
Message-ID: <CAMCwi7PcURxUZPbVNr2UCkNiPKSRLUj-AFzDWQxSQ3E5yhOKEA@mail.gmail.com>

Hello Everybody,

this is yet another QC helper script, similar idea to
https://github.com/CobraLab/PyQC , but using your browser for user
interface instead of QT.
It can function either locally, or tunnel over SSH , when your data is
actually located somewhere else.

The user interface is very simple - you either click on links with your
mouse , or press '1' to give image 'pass' flag or '2' for 'fail' , arrow
keys maybe used for navigation.

The new tool lives in https://github.com/vfonov/wqc

This tool have minimal dependencies - it is written in python and uses
CherryPY , which can be installed without sudo access by running "pip
install cherrypy --user"

-- 
Best regards,

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

From pierre.bellec at criugm.qc.ca  Tue May 17 22:29:51 2016
From: pierre.bellec at criugm.qc.ca (Pierre Bellec)
Date: Tue, 17 May 2016 22:29:51 -0400
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CABEEk17CA=SiRq96b8HjU7yVhBDBg7PQrjSgUmh60-qfGhX=-w@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<CABEEk17CA=SiRq96b8HjU7yVhBDBg7PQrjSgUmh60-qfGhX=-w@mail.gmail.com>
Message-ID: <CADPHwxAbdmoTwf2vH--PWtun7+_4fhJ+Qmf9=0=hN93OWr9LjA@mail.gmail.com>

Hi Paul,

Not sure this will fit your objectives, but using a docker container may be
an alternative to a VM (or you can deploy the container inside a VM as
well, it's easier to update). Here is the minc-toolkit image we use in the
lab, it's derived from an old Ubuntu 12.04. I don't think there is an
official minc-toolkit repo on docker hub at this point
https://hub.docker.com/r/simexp/minc-toolkit/

FYI the build file is here:
https://github.com/SIMEXP/Projects/tree/master/docker/minc-toolkit/1.9.2

Best,

Pierre

Pierre Bellec
Assistant professor ("adjoint sous octroi"), Department of computer science
and operational research (DIRO <http://diro.umontreal.ca/>)
Member, Centre de recherche de l'institut Universitaire de g?riatrie de
Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
Member, Institute of Biomedical Engineering <http://www.igb.umontreal.ca/>
Universit? de Montr?al, Montr?al, Canada
Phone +1 514 713 5596
Full coordinates on my home page
<http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
Laboratory website <http://simexp-lab.org>.

On Tue, May 17, 2016 at 10:10 PM, Alex Zijdenbos <zijdenbos at gmail.com>
wrote:

> I once built a VM "MINCbuntu" (still available at
> http://packages.bic.mni.mcgill.ca/virtual-machines/), but that hasn't been
> updated since 2009, so I'd suggest to follow Andrew's suggestion at this
> point :-)
>
> -- A
>
>
>
> On Tue, May 17, 2016 at 10:01 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
> > I'm sure I saw one pass through the minc-users mailing list a while back?
> >
> > I use the neurodebian VM and then
> >
> >    apt-get install minc-toolkit     (thanks Vlad!)
> >
> > a
> >
> >
> > On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> > > Dear All,
> > >
> > > I want to prepare a virtual machine for VirtualBox that includes a
> linux
> > > version with the minc tools. But being lazy (;-)!), I was wondering if
> > > anyone already had that and be willing to share.
> > > Otherwise, any pointers on how to go about it (of course I would be
> > willing
> > > to share the finished product!)?
> > >
> > > Many thanks!
> > >
> > > Paul
> > >
> > > _______________________________________________
> > > 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 pgravel at bic.mni.mcgill.ca  Tue May 17 22:39:52 2016
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 17 May 2016 22:39:52 -0400 (EDT)
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CADPHwxAbdmoTwf2vH--PWtun7+_4fhJ+Qmf9=0=hN93OWr9LjA@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<CABEEk17CA=SiRq96b8HjU7yVhBDBg7PQrjSgUmh60-qfGhX=-w@mail.gmail.com>
	<CADPHwxAbdmoTwf2vH--PWtun7+_4fhJ+Qmf9=0=hN93OWr9LjA@mail.gmail.com>
Message-ID: <alpine.DEB.2.02.1605172238010.15533@login1.bic.mni.mcgill.ca>

Thanks Andrew, Alex and Pierre for such quick replies!

I am currently trying Andrew's suggestion; before reading you replies, I 
actually noticed Andrew's comment on the http://neuro.debian.net/ web 
page. Coincidence? I think not ;-)!

Best,

Paul


On Tue, 17 May 2016, Pierre Bellec wrote:

> Hi Paul,
>
> Not sure this will fit your objectives, but using a docker container may be
> an alternative to a VM (or you can deploy the container inside a VM as
> well, it's easier to update). Here is the minc-toolkit image we use in the
> lab, it's derived from an old Ubuntu 12.04. I don't think there is an
> official minc-toolkit repo on docker hub at this point
> https://hub.docker.com/r/simexp/minc-toolkit/
>
> FYI the build file is here:
> https://github.com/SIMEXP/Projects/tree/master/docker/minc-toolkit/1.9.2
>
> Best,
>
> Pierre
>
> Pierre Bellec
> Assistant professor ("adjoint sous octroi"), Department of computer science
> and operational research (DIRO <http://diro.umontreal.ca/>)
> Member, Centre de recherche de l'institut Universitaire de g?riatrie de
> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
> Member, Institute of Biomedical Engineering <http://www.igb.umontreal.ca/>
> Universit? de Montr?al, Montr?al, Canada
> Phone +1 514 713 5596
> Full coordinates on my home page
> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
> Laboratory website <http://simexp-lab.org>.
>
> On Tue, May 17, 2016 at 10:10 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
>> I once built a VM "MINCbuntu" (still available at
>> http://packages.bic.mni.mcgill.ca/virtual-machines/), but that hasn't been
>> updated since 2009, so I'd suggest to follow Andrew's suggestion at this
>> point :-)
>>
>> -- A
>>
>>
>>
>> On Tue, May 17, 2016 at 10:01 PM, Andrew Janke <a.janke at gmail.com> wrote:
>>
>> > I'm sure I saw one pass through the minc-users mailing list a while back?
>> >
>> > I use the neurodebian VM and then
>> >
>> >    apt-get install minc-toolkit     (thanks Vlad!)
>> >
>> > a
>> >
>> >
>> > On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> > > Dear All,
>> > >
>> > > I want to prepare a virtual machine for VirtualBox that includes a
>> linux
>> > > version with the minc tools. But being lazy (;-)!), I was wondering if
>> > > anyone already had that and be willing to share.
>> > > Otherwise, any pointers on how to go about it (of course I would be
>> > willing
>> > > to share the finished product!)?
>> > >
>> > > Many thanks!
>> > >
>> > > Paul
>> > >
>> > > _______________________________________________
>> > > 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 pgravel at bic.mni.mcgill.ca  Tue May 17 22:56:03 2016
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 17 May 2016 22:56:03 -0400 (EDT)
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
Message-ID: <alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>

So I installed:
NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.

After importing the "Applicance" in VirtualBox and configuring, I can 
start the virtual machine, so far so good, but when I come to install the 
minctools; I had to use:
sudo apt-get install minc-toolkit

I get the following:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package minc-toolkit

any ideas?

Thanks again!

Paul


On Wed, 18 May 2016, Andrew Janke wrote:

> I'm sure I saw one pass through the minc-users mailing list a while back?
>
> I use the neurodebian VM and then
>
>   apt-get install minc-toolkit     (thanks Vlad!)
>
> a
>
>
> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> Dear All,
>>
>> I want to prepare a virtual machine for VirtualBox that includes a linux
>> version with the minc tools. But being lazy (;-)!), I was wondering if
>> anyone already had that and be willing to share.
>> Otherwise, any pointers on how to go about it (of course I would be willing
>> to share the finished product!)?
>>
>> Many thanks!
>>
>> Paul
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue May 17 23:01:26 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 18 May 2016 13:01:26 +1000
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
Message-ID: <CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>

In my case I add my own private apt repository that mirrors things
from the new a shiny source here:

   http://bic-mni.github.io/

In your case, just download the appropriate .deb file and then install
using dpkg.

This should do it:

   $ wget http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb

   $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb


a

On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> So I installed:
> NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>
> After importing the "Applicance" in VirtualBox and configuring, I can start
> the virtual machine, so far so good, but when I come to install the
> minctools; I had to use:
> sudo apt-get install minc-toolkit
>
> I get the following:
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> E: Unable to locate package minc-toolkit
>
> any ideas?
>
> Thanks again!
>
> Paul
>
>
>
> On Wed, 18 May 2016, Andrew Janke wrote:
>
>> I'm sure I saw one pass through the minc-users mailing list a while back?
>>
>> I use the neurodebian VM and then
>>
>>   apt-get install minc-toolkit     (thanks Vlad!)
>>
>> a
>>
>>
>> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>>>
>>> Dear All,
>>>
>>> I want to prepare a virtual machine for VirtualBox that includes a linux
>>> version with the minc tools. But being lazy (;-)!), I was wondering if
>>> anyone already had that and be willing to share.
>>> Otherwise, any pointers on how to go about it (of course I would be
>>> willing
>>> to share the finished product!)?
>>>
>>> Many thanks!
>>>
>>> Paul
>>>
>>> _______________________________________________
>>> 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 pierre.bellec at criugm.qc.ca  Tue May 17 23:05:17 2016
From: pierre.bellec at criugm.qc.ca (Pierre Bellec)
Date: Tue, 17 May 2016 23:05:17 -0400
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
Message-ID: <CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>

Paul, you may also want to look at dependencies and sourcing
environment variables (paragraph "using") in the documentation:
http://bic-mni.github.io/#installing

Pierre Bellec
Assistant professor ("adjoint sous octroi"), Department of computer science
and operational research (DIRO <http://diro.umontreal.ca/>)
Member, Centre de recherche de l'institut Universitaire de g?riatrie de
Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
Member, Institute of Biomedical Engineering <http://www.igb.umontreal.ca/>
Universit? de Montr?al, Montr?al, Canada
Phone +1 514 713 5596
Full coordinates on my home page
<http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
Laboratory website <http://simexp-lab.org>.

On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com> wrote:

> In my case I add my own private apt repository that mirrors things
> from the new a shiny source here:
>
>    http://bic-mni.github.io/
>
> In your case, just download the appropriate .deb file and then install
> using dpkg.
>
> This should do it:
>
>    $ wget
> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>
>    $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>
>
> a
>
> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> > So I installed:
> > NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
> >
> > After importing the "Applicance" in VirtualBox and configuring, I can
> start
> > the virtual machine, so far so good, but when I come to install the
> > minctools; I had to use:
> > sudo apt-get install minc-toolkit
> >
> > I get the following:
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > E: Unable to locate package minc-toolkit
> >
> > any ideas?
> >
> > Thanks again!
> >
> > Paul
> >
> >
> >
> > On Wed, 18 May 2016, Andrew Janke wrote:
> >
> >> I'm sure I saw one pass through the minc-users mailing list a while
> back?
> >>
> >> I use the neurodebian VM and then
> >>
> >>   apt-get install minc-toolkit     (thanks Vlad!)
> >>
> >> a
> >>
> >>
> >> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> >>>
> >>> Dear All,
> >>>
> >>> I want to prepare a virtual machine for VirtualBox that includes a
> linux
> >>> version with the minc tools. But being lazy (;-)!), I was wondering if
> >>> anyone already had that and be willing to share.
> >>> Otherwise, any pointers on how to go about it (of course I would be
> >>> willing
> >>> to share the finished product!)?
> >>>
> >>> Many thanks!
> >>>
> >>> Paul
> >>>
> >>> _______________________________________________
> >>> 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 pgravel at bic.mni.mcgill.ca  Tue May 17 23:38:03 2016
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Tue, 17 May 2016 23:38:03 -0400 (EDT)
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
Message-ID: <alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>

Once again many thanks Andrew and Pierre!

It seems to have worked after sourcing /opt/minc/minc-toolkit-config.sh .

I will give it a try (using MINC files) tomorrow.

@Andrew: have a good day!

@Pierre: Have a good night!

Best,

Paul

On Tue, 17 May 2016, Pierre Bellec wrote:

> Paul, you may also want to look at dependencies and sourcing
> environment variables (paragraph "using") in the documentation:
> http://bic-mni.github.io/#installing
>
> Pierre Bellec
> Assistant professor ("adjoint sous octroi"), Department of computer science
> and operational research (DIRO <http://diro.umontreal.ca/>)
> Member, Centre de recherche de l'institut Universitaire de g?riatrie de
> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
> Member, Institute of Biomedical Engineering <http://www.igb.umontreal.ca/>
> Universit? de Montr?al, Montr?al, Canada
> Phone +1 514 713 5596
> Full coordinates on my home page
> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
> Laboratory website <http://simexp-lab.org>.
>
> On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> In my case I add my own private apt repository that mirrors things
>> from the new a shiny source here:
>>
>>    http://bic-mni.github.io/
>>
>> In your case, just download the appropriate .deb file and then install
>> using dpkg.
>>
>> This should do it:
>>
>>    $ wget
>> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>
>>    $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>
>>
>> a
>>
>> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> > So I installed:
>> > NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>> >
>> > After importing the "Applicance" in VirtualBox and configuring, I can
>> start
>> > the virtual machine, so far so good, but when I come to install the
>> > minctools; I had to use:
>> > sudo apt-get install minc-toolkit
>> >
>> > I get the following:
>> > Reading package lists... Done
>> > Building dependency tree
>> > Reading state information... Done
>> > E: Unable to locate package minc-toolkit
>> >
>> > any ideas?
>> >
>> > Thanks again!
>> >
>> > Paul
>> >
>> >
>> >
>> > On Wed, 18 May 2016, Andrew Janke wrote:
>> >
>> >> I'm sure I saw one pass through the minc-users mailing list a while
>> back?
>> >>
>> >> I use the neurodebian VM and then
>> >>
>> >>   apt-get install minc-toolkit     (thanks Vlad!)
>> >>
>> >> a
>> >>
>> >>
>> >> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> >>>
>> >>> Dear All,
>> >>>
>> >>> I want to prepare a virtual machine for VirtualBox that includes a
>> linux
>> >>> version with the minc tools. But being lazy (;-)!), I was wondering if
>> >>> anyone already had that and be willing to share.
>> >>> Otherwise, any pointers on how to go about it (of course I would be
>> >>> willing
>> >>> to share the finished product!)?
>> >>>
>> >>> Many thanks!
>> >>>
>> >>> Paul
>> >>>
>> >>> _______________________________________________
>> >>> 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 dante.denigris at gmail.com  Wed May 18 10:42:40 2016
From: dante.denigris at gmail.com (Dante De Nigris)
Date: Wed, 18 May 2016 14:42:40 +0000
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
	<alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
Message-ID: <CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>

Hi all,

Similar to Pierre's previous proposal, I recently built a docker image with
the minc-toolkit.  I was personally interested in building a very small
image so I use the Alpine Linux Base image and build everything from
scratch.

Thiis might not correspond directly to your current needs, but it was
pretty reasonable for me.

https://hub.docker.com/r/dantino19/minc-toolkit/



On Tue, May 17, 2016 at 11:39 PM Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
wrote:

> Once again many thanks Andrew and Pierre!
>
> It seems to have worked after sourcing /opt/minc/minc-toolkit-config.sh .
>
> I will give it a try (using MINC files) tomorrow.
>
> @Andrew: have a good day!
>
> @Pierre: Have a good night!
>
> Best,
>
> Paul
>
> On Tue, 17 May 2016, Pierre Bellec wrote:
>
> > Paul, you may also want to look at dependencies and sourcing
> > environment variables (paragraph "using") in the documentation:
> > http://bic-mni.github.io/#installing
> >
> > Pierre Bellec
> > Assistant professor ("adjoint sous octroi"), Department of computer
> science
> > and operational research (DIRO <http://diro.umontreal.ca/>)
> > Member, Centre de recherche de l'institut Universitaire de g?riatrie de
> > Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
> > Member, Institute of Biomedical Engineering <
> http://www.igb.umontreal.ca/>
> > Universit? de Montr?al, Montr?al, Canada
> > Phone +1 514 713 5596
> > Full coordinates on my home page
> > <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
> > Laboratory website <http://simexp-lab.org>.
> >
> > On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com>
> wrote:
> >
> >> In my case I add my own private apt repository that mirrors things
> >> from the new a shiny source here:
> >>
> >>    http://bic-mni.github.io/
> >>
> >> In your case, just download the appropriate .deb file and then install
> >> using dpkg.
> >>
> >> This should do it:
> >>
> >>    $ wget
> >>
> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
> >>
> >>    $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
> >>
> >>
> >> a
> >>
> >> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
> >> > So I installed:
> >> > NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
> >> >
> >> > After importing the "Applicance" in VirtualBox and configuring, I can
> >> start
> >> > the virtual machine, so far so good, but when I come to install the
> >> > minctools; I had to use:
> >> > sudo apt-get install minc-toolkit
> >> >
> >> > I get the following:
> >> > Reading package lists... Done
> >> > Building dependency tree
> >> > Reading state information... Done
> >> > E: Unable to locate package minc-toolkit
> >> >
> >> > any ideas?
> >> >
> >> > Thanks again!
> >> >
> >> > Paul
> >> >
> >> >
> >> >
> >> > On Wed, 18 May 2016, Andrew Janke wrote:
> >> >
> >> >> I'm sure I saw one pass through the minc-users mailing list a while
> >> back?
> >> >>
> >> >> I use the neurodebian VM and then
> >> >>
> >> >>   apt-get install minc-toolkit     (thanks Vlad!)
> >> >>
> >> >> a
> >> >>
> >> >>
> >> >> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> wrote:
> >> >>>
> >> >>> Dear All,
> >> >>>
> >> >>> I want to prepare a virtual machine for VirtualBox that includes a
> >> linux
> >> >>> version with the minc tools. But being lazy (;-)!), I was wondering
> if
> >> >>> anyone already had that and be willing to share.
> >> >>> Otherwise, any pointers on how to go about it (of course I would be
> >> >>> willing
> >> >>> to share the finished product!)?
> >> >>>
> >> >>> Many thanks!
> >> >>>
> >> >>> Paul
> >> >>>
> >> >>> _______________________________________________
> >> >>> 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 vladimir.fonov at gmail.com  Wed May 18 11:05:58 2016
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 18 May 2016 11:05:58 -0400
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
	<alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
	<CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>
Message-ID: <573C84D6.8040208@gmail.com>

Hello,

On 16-05-18 10:42 AM, Dante De Nigris wrote:
> Similar to Pierre's previous proposal, I recently built a docker image with
> the minc-toolkit.  I was personally interested in building a very small
> image so I use the Alpine Linux Base image and build everything from
> scratch.
So, you want to run minc-toolkit on your embedded device?



>
> Thiis might not correspond directly to your current needs, but it was
> pretty reasonable for me.
>
> https://hub.docker.com/r/dantino19/minc-toolkit/
>
>
>
> On Tue, May 17, 2016 at 11:39 PM Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> wrote:
>
>> Once again many thanks Andrew and Pierre!
>>
>> It seems to have worked after sourcing /opt/minc/minc-toolkit-config.sh .
>>
>> I will give it a try (using MINC files) tomorrow.
>>
>> @Andrew: have a good day!
>>
>> @Pierre: Have a good night!
>>
>> Best,
>>
>> Paul
>>
>> On Tue, 17 May 2016, Pierre Bellec wrote:
>>
>>> Paul, you may also want to look at dependencies and sourcing
>>> environment variables (paragraph "using") in the documentation:
>>> http://bic-mni.github.io/#installing
>>>
>>> Pierre Bellec
>>> Assistant professor ("adjoint sous octroi"), Department of computer
>> science
>>> and operational research (DIRO <http://diro.umontreal.ca/>)
>>> Member, Centre de recherche de l'institut Universitaire de g?riatrie de
>>> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
>>> Member, Institute of Biomedical Engineering <
>> http://www.igb.umontreal.ca/>
>>> Universit? de Montr?al, Montr?al, Canada
>>> Phone +1 514 713 5596
>>> Full coordinates on my home page
>>> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
>>> Laboratory website <http://simexp-lab.org>.
>>>
>>> On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com>
>> wrote:
>>>
>>>> In my case I add my own private apt repository that mirrors things
>>>> from the new a shiny source here:
>>>>
>>>>     http://bic-mni.github.io/
>>>>
>>>> In your case, just download the appropriate .deb file and then install
>>>> using dpkg.
>>>>
>>>> This should do it:
>>>>
>>>>     $ wget
>>>>
>> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>
>>>>     $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>
>>>>
>>>> a
>>>>
>>>> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>>>>> So I installed:
>>>>> NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>>>>>
>>>>> After importing the "Applicance" in VirtualBox and configuring, I can
>>>> start
>>>>> the virtual machine, so far so good, but when I come to install the
>>>>> minctools; I had to use:
>>>>> sudo apt-get install minc-toolkit
>>>>>
>>>>> I get the following:
>>>>> Reading package lists... Done
>>>>> Building dependency tree
>>>>> Reading state information... Done
>>>>> E: Unable to locate package minc-toolkit
>>>>>
>>>>> any ideas?
>>>>>
>>>>> Thanks again!
>>>>>
>>>>> Paul
>>>>>
>>>>>
>>>>>
>>>>> On Wed, 18 May 2016, Andrew Janke wrote:
>>>>>
>>>>>> I'm sure I saw one pass through the minc-users mailing list a while
>>>> back?
>>>>>>
>>>>>> I use the neurodebian VM and then
>>>>>>
>>>>>>    apt-get install minc-toolkit     (thanks Vlad!)
>>>>>>
>>>>>> a
>>>>>>
>>>>>>
>>>>>> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>> wrote:
>>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>> I want to prepare a virtual machine for VirtualBox that includes a
>>>> linux
>>>>>>> version with the minc tools. But being lazy (;-)!), I was wondering
>> if
>>>>>>> anyone already had that and be willing to share.
>>>>>>> Otherwise, any pointers on how to go about it (of course I would be
>>>>>>> willing
>>>>>>> to share the finished product!)?


-- 
Best regards,

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

From gdevenyi at gmail.com  Wed May 18 11:20:12 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Wed, 18 May 2016 11:20:12 -0400
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <573C84D6.8040208@gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
	<alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
	<CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>
	<573C84D6.8040208@gmail.com>
Message-ID: <CAFQOoOrPWwCXMWt+P0Lo88S6wu+fZ5zUbJQEmd5PF-q-kat0nw@mail.gmail.com>

One more option:

I built a Lubuntu-based VirtualBox image with minc-toolikit/R/RMINC and
brain-view2 for doing cortical-thickness like analysis.

https://drive.google.com/file/d/0B9gIQxu-xaI6NVE4bGxhUzRvYlE/view?usp=sharing

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Wed, May 18, 2016 at 11:05 AM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:

> Hello,
>
> On 16-05-18 10:42 AM, Dante De Nigris wrote:
>
>> Similar to Pierre's previous proposal, I recently built a docker image
>> with
>> the minc-toolkit.  I was personally interested in building a very small
>> image so I use the Alpine Linux Base image and build everything from
>> scratch.
>>
> So, you want to run minc-toolkit on your embedded device?
>
>
>
>
>
>> Thiis might not correspond directly to your current needs, but it was
>> pretty reasonable for me.
>>
>> https://hub.docker.com/r/dantino19/minc-toolkit/
>>
>>
>>
>> On Tue, May 17, 2016 at 11:39 PM Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>> wrote:
>>
>> Once again many thanks Andrew and Pierre!
>>>
>>> It seems to have worked after sourcing /opt/minc/minc-toolkit-config.sh .
>>>
>>> I will give it a try (using MINC files) tomorrow.
>>>
>>> @Andrew: have a good day!
>>>
>>> @Pierre: Have a good night!
>>>
>>> Best,
>>>
>>> Paul
>>>
>>> On Tue, 17 May 2016, Pierre Bellec wrote:
>>>
>>> Paul, you may also want to look at dependencies and sourcing
>>>> environment variables (paragraph "using") in the documentation:
>>>> http://bic-mni.github.io/#installing
>>>>
>>>> Pierre Bellec
>>>> Assistant professor ("adjoint sous octroi"), Department of computer
>>>>
>>> science
>>>
>>>> and operational research (DIRO <http://diro.umontreal.ca/>)
>>>> Member, Centre de recherche de l'institut Universitaire de g?riatrie de
>>>> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
>>>> Member, Institute of Biomedical Engineering <
>>>>
>>> http://www.igb.umontreal.ca/>
>>>
>>>> Universit? de Montr?al, Montr?al, Canada
>>>> Phone +1 514 713 5596
>>>> Full coordinates on my home page
>>>> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
>>>> Laboratory website <http://simexp-lab.org>.
>>>>
>>>> On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com>
>>>>
>>> wrote:
>>>
>>>>
>>>> In my case I add my own private apt repository that mirrors things
>>>>> from the new a shiny source here:
>>>>>
>>>>>     http://bic-mni.github.io/
>>>>>
>>>>> In your case, just download the appropriate .deb file and then install
>>>>> using dpkg.
>>>>>
>>>>> This should do it:
>>>>>
>>>>>     $ wget
>>>>>
>>>>>
>>> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>
>>>>
>>>>>     $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>>
>>>>>
>>>>> a
>>>>>
>>>>> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>> wrote:
>>>>>
>>>>>> So I installed:
>>>>>> NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>>>>>>
>>>>>> After importing the "Applicance" in VirtualBox and configuring, I can
>>>>>>
>>>>> start
>>>>>
>>>>>> the virtual machine, so far so good, but when I come to install the
>>>>>> minctools; I had to use:
>>>>>> sudo apt-get install minc-toolkit
>>>>>>
>>>>>> I get the following:
>>>>>> Reading package lists... Done
>>>>>> Building dependency tree
>>>>>> Reading state information... Done
>>>>>> E: Unable to locate package minc-toolkit
>>>>>>
>>>>>> any ideas?
>>>>>>
>>>>>> Thanks again!
>>>>>>
>>>>>> Paul
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, 18 May 2016, Andrew Janke wrote:
>>>>>>
>>>>>> I'm sure I saw one pass through the minc-users mailing list a while
>>>>>>>
>>>>>> back?
>>>>>
>>>>>>
>>>>>>> I use the neurodebian VM and then
>>>>>>>
>>>>>>>    apt-get install minc-toolkit     (thanks Vlad!)
>>>>>>>
>>>>>>> a
>>>>>>>
>>>>>>>
>>>>>>> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>>>>
>>>>>> wrote:
>>>
>>>>
>>>>>>>> Dear All,
>>>>>>>>
>>>>>>>> I want to prepare a virtual machine for VirtualBox that includes a
>>>>>>>>
>>>>>>> linux
>>>>>
>>>>>> version with the minc tools. But being lazy (;-)!), I was wondering
>>>>>>>>
>>>>>>> if
>>>
>>>> anyone already had that and be willing to share.
>>>>>>>> Otherwise, any pointers on how to go about it (of course I would be
>>>>>>>> willing
>>>>>>>> to share the finished product!)?
>>>>>>>>
>>>>>>>
>
> --
> 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 pgravel at bic.mni.mcgill.ca  Wed May 18 11:24:02 2016
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 18 May 2016 11:24:02 -0400 (EDT)
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <573C84D6.8040208@gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
	<alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
	<CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>
	<573C84D6.8040208@gmail.com>
Message-ID: <alpine.DEB.2.02.1605181109070.5848@login1.bic.mni.mcgill.ca>

Dear All,

So I am now trying Alex's method, which is working so far, but I would 
need a username and a password, Alex?

The reason for these questions is that I am preparing a hands-on training 
session as part of the PET Workshop happening in a couple of weeks, and I 
would have liked to have a virtual machine file with all the necessary 
tools, in order to make it easier for the participants to install the 
package.

Best,

Paul


On Wed, 18 May 2016, Vladimir S. FONOV wrote:

> Hello,
>
> On 16-05-18 10:42 AM, Dante De Nigris wrote:
>> Similar to Pierre's previous proposal, I recently built a docker image with
>> the minc-toolkit.  I was personally interested in building a very small
>> image so I use the Alpine Linux Base image and build everything from
>> scratch.
> So, you want to run minc-toolkit on your embedded device?
>
>
>
>>
>> Thiis might not correspond directly to your current needs, but it was
>> pretty reasonable for me.
>>
>> https://hub.docker.com/r/dantino19/minc-toolkit/
>>
>>
>>
>> On Tue, May 17, 2016 at 11:39 PM Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>> wrote:
>>
>>> Once again many thanks Andrew and Pierre!
>>>
>>> It seems to have worked after sourcing /opt/minc/minc-toolkit-config.sh .
>>>
>>> I will give it a try (using MINC files) tomorrow.
>>>
>>> @Andrew: have a good day!
>>>
>>> @Pierre: Have a good night!
>>>
>>> Best,
>>>
>>> Paul
>>>
>>> On Tue, 17 May 2016, Pierre Bellec wrote:
>>>
>>>> Paul, you may also want to look at dependencies and sourcing
>>>> environment variables (paragraph "using") in the documentation:
>>>> http://bic-mni.github.io/#installing
>>>>
>>>> Pierre Bellec
>>>> Assistant professor ("adjoint sous octroi"), Department of computer
>>> science
>>>> and operational research (DIRO <http://diro.umontreal.ca/>)
>>>> Member, Centre de recherche de l'institut Universitaire de g?riatrie de
>>>> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
>>>> Member, Institute of Biomedical Engineering <
>>> http://www.igb.umontreal.ca/>
>>>> Universit? de Montr?al, Montr?al, Canada
>>>> Phone +1 514 713 5596
>>>> Full coordinates on my home page
>>>> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
>>>> Laboratory website <http://simexp-lab.org>.
>>>>
>>>> On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com>
>>> wrote:
>>>>
>>>>> In my case I add my own private apt repository that mirrors things
>>>>> from the new a shiny source here:
>>>>>
>>>>>     http://bic-mni.github.io/
>>>>>
>>>>> In your case, just download the appropriate .deb file and then install
>>>>> using dpkg.
>>>>>
>>>>> This should do it:
>>>>>
>>>>>     $ wget
>>>>>
>>> 
> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>>
>>>>>     $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>>
>>>>>
>>>>> a
>>>>>
>>>>> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>>>>>> So I installed:
>>>>>> NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>>>>>>
>>>>>> After importing the "Applicance" in VirtualBox and configuring, I can
>>>>> start
>>>>>> the virtual machine, so far so good, but when I come to install the
>>>>>> minctools; I had to use:
>>>>>> sudo apt-get install minc-toolkit
>>>>>>
>>>>>> I get the following:
>>>>>> Reading package lists... Done
>>>>>> Building dependency tree
>>>>>> Reading state information... Done
>>>>>> E: Unable to locate package minc-toolkit
>>>>>>
>>>>>> any ideas?
>>>>>>
>>>>>> Thanks again!
>>>>>>
>>>>>> Paul
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, 18 May 2016, Andrew Janke wrote:
>>>>>>
>>>>>>> I'm sure I saw one pass through the minc-users mailing list a while
>>>>> back?
>>>>>>>
>>>>>>> I use the neurodebian VM and then
>>>>>>>
>>>>>>>    apt-get install minc-toolkit     (thanks Vlad!)
>>>>>>>
>>>>>>> a
>>>>>>>
>>>>>>>
>>>>>>> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>> wrote:
>>>>>>>>
>>>>>>>> Dear All,
>>>>>>>>
>>>>>>>> I want to prepare a virtual machine for VirtualBox that includes a
>>>>> linux
>>>>>>>> version with the minc tools. But being lazy (;-)!), I was wondering
>>> if
>>>>>>>> anyone already had that and be willing to share.
>>>>>>>> Otherwise, any pointers on how to go about it (of course I would be
>>>>>>>> willing
>>>>>>>> to share the finished product!)?
>
>
> -- 
> 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 zijdenbos at gmail.com  Wed May 18 11:30:34 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 18 May 2016 11:30:34 -0400
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <alpine.DEB.2.02.1605181109070.5848@login1.bic.mni.mcgill.ca>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
	<alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
	<CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>
	<573C84D6.8040208@gmail.com>
	<alpine.DEB.2.02.1605181109070.5848@login1.bic.mni.mcgill.ca>
Message-ID: <CABEEk14oAc-OacNgirHmgu+z0Uhz69q6bGtZGumBhiLUNiY9xg@mail.gmail.com>

Hi Paul - user/pass are in the instructions on that page I sent:

User: minc pass: minc

that user has full sudo privileges iirc.

On Wed, May 18, 2016 at 11:24 AM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
wrote:

> Dear All,
>
> So I am now trying Alex's method, which is working so far, but I would
> need a username and a password, Alex?
>
> The reason for these questions is that I am preparing a hands-on training
> session as part of the PET Workshop happening in a couple of weeks, and I
> would have liked to have a virtual machine file with all the necessary
> tools, in order to make it easier for the participants to install the
> package.
>
> Best,
>
> Paul
>
>
>
> On Wed, 18 May 2016, Vladimir S. FONOV wrote:
>
> Hello,
>>
>> On 16-05-18 10:42 AM, Dante De Nigris wrote:
>>
>>> Similar to Pierre's previous proposal, I recently built a docker image
>>> with
>>> the minc-toolkit.  I was personally interested in building a very small
>>> image so I use the Alpine Linux Base image and build everything from
>>> scratch.
>>>
>> So, you want to run minc-toolkit on your embedded device?
>>
>>
>>
>>
>>> Thiis might not correspond directly to your current needs, but it was
>>> pretty reasonable for me.
>>>
>>> https://hub.docker.com/r/dantino19/minc-toolkit/
>>>
>>>
>>>
>>> On Tue, May 17, 2016 at 11:39 PM Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>> wrote:
>>>
>>> Once again many thanks Andrew and Pierre!
>>>>
>>>> It seems to have worked after sourcing /opt/minc/minc-toolkit-config.sh
>>>> .
>>>>
>>>> I will give it a try (using MINC files) tomorrow.
>>>>
>>>> @Andrew: have a good day!
>>>>
>>>> @Pierre: Have a good night!
>>>>
>>>> Best,
>>>>
>>>> Paul
>>>>
>>>> On Tue, 17 May 2016, Pierre Bellec wrote:
>>>>
>>>> Paul, you may also want to look at dependencies and sourcing
>>>>> environment variables (paragraph "using") in the documentation:
>>>>> http://bic-mni.github.io/#installing
>>>>>
>>>>> Pierre Bellec
>>>>> Assistant professor ("adjoint sous octroi"), Department of computer
>>>>>
>>>> science
>>>>
>>>>> and operational research (DIRO <http://diro.umontreal.ca/>)
>>>>> Member, Centre de recherche de l'institut Universitaire de g?riatrie de
>>>>> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
>>>>> Member, Institute of Biomedical Engineering <
>>>>>
>>>> http://www.igb.umontreal.ca/>
>>>>
>>>>> Universit? de Montr?al, Montr?al, Canada
>>>>> Phone +1 514 713 5596
>>>>> Full coordinates on my home page
>>>>> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
>>>>> Laboratory website <http://simexp-lab.org>.
>>>>>
>>>>> On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com>
>>>>>
>>>> wrote:
>>>>
>>>>>
>>>>> In my case I add my own private apt repository that mirrors things
>>>>>> from the new a shiny source here:
>>>>>>
>>>>>>     http://bic-mni.github.io/
>>>>>>
>>>>>> In your case, just download the appropriate .deb file and then install
>>>>>> using dpkg.
>>>>>>
>>>>>> This should do it:
>>>>>>
>>>>>>     $ wget
>>>>>>
>>>>>>
>>>>
>> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>
>>>
>>>>>>     $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>>>
>>>>>>
>>>>>> a
>>>>>>
>>>>>> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>>> wrote:
>>>>>>
>>>>>>> So I installed:
>>>>>>> NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>>>>>>>
>>>>>>> After importing the "Applicance" in VirtualBox and configuring, I can
>>>>>>>
>>>>>> start
>>>>>>
>>>>>>> the virtual machine, so far so good, but when I come to install the
>>>>>>> minctools; I had to use:
>>>>>>> sudo apt-get install minc-toolkit
>>>>>>>
>>>>>>> I get the following:
>>>>>>> Reading package lists... Done
>>>>>>> Building dependency tree
>>>>>>> Reading state information... Done
>>>>>>> E: Unable to locate package minc-toolkit
>>>>>>>
>>>>>>> any ideas?
>>>>>>>
>>>>>>> Thanks again!
>>>>>>>
>>>>>>> Paul
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, 18 May 2016, Andrew Janke wrote:
>>>>>>>
>>>>>>> I'm sure I saw one pass through the minc-users mailing list a while
>>>>>>>>
>>>>>>> back?
>>>>>>
>>>>>>>
>>>>>>>> I use the neurodebian VM and then
>>>>>>>>
>>>>>>>>    apt-get install minc-toolkit     (thanks Vlad!)
>>>>>>>>
>>>>>>>> a
>>>>>>>>
>>>>>>>>
>>>>>>>> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>>>>>
>>>>>>> wrote:
>>>>
>>>>>
>>>>>>>>> Dear All,
>>>>>>>>>
>>>>>>>>> I want to prepare a virtual machine for VirtualBox that includes a
>>>>>>>>>
>>>>>>>> linux
>>>>>>
>>>>>>> version with the minc tools. But being lazy (;-)!), I was wondering
>>>>>>>>>
>>>>>>>> if
>>>>
>>>>> anyone already had that and be willing to share.
>>>>>>>>> Otherwise, any pointers on how to go about it (of course I would be
>>>>>>>>> willing
>>>>>>>>> to share the finished product!)?
>>>>>>>>>
>>>>>>>>
>>
>> --
>> 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
>>
>
> _______________________________________________
> 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 18 13:11:21 2016
From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL)
Date: Wed, 18 May 2016 13:11:21 -0400 (EDT)
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <CABEEk14oAc-OacNgirHmgu+z0Uhz69q6bGtZGumBhiLUNiY9xg@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
	<alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
	<CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>
	<573C84D6.8040208@gmail.com>
	<alpine.DEB.2.02.1605181109070.5848@login1.bic.mni.mcgill.ca>
	<CABEEk14oAc-OacNgirHmgu+z0Uhz69q6bGtZGumBhiLUNiY9xg@mail.gmail.com>
Message-ID: <alpine.DEB.2.02.1605181254240.22290@login1.bic.mni.mcgill.ca>

Thanks Alex!

I should have read the instructions more carefully!

Actually, this package would be in essence what I was looking for.
Unfortunately, I had different outcomes with NeuroDebian installation on a 
laptop and on my desktop at work (I of course acknowledge that this is 
most lokely due to my limitations in such matters ;-)!)

That being said, if need be, would it be ok Alex if I distribute your 
virtual machine for a workshop?
I would of course acknowledge you!

Many thanks to All who replied!

Best Regards,

Paul


On Wed, 18 May 2016, Alex Zijdenbos wrote:

> Hi Paul - user/pass are in the instructions on that page I sent:
>
> User: minc pass: minc
>
> that user has full sudo privileges iirc.
>
> On Wed, May 18, 2016 at 11:24 AM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> wrote:
>
>> Dear All,
>>
>> So I am now trying Alex's method, which is working so far, but I would
>> need a username and a password, Alex?
>>
>> The reason for these questions is that I am preparing a hands-on training
>> session as part of the PET Workshop happening in a couple of weeks, and I
>> would have liked to have a virtual machine file with all the necessary
>> tools, in order to make it easier for the participants to install the
>> package.
>>
>> Best,
>>
>> Paul
>>
>>
>>
>> On Wed, 18 May 2016, Vladimir S. FONOV wrote:
>>
>> Hello,
>>>
>>> On 16-05-18 10:42 AM, Dante De Nigris wrote:
>>>
>>>> Similar to Pierre's previous proposal, I recently built a docker image
>>>> with
>>>> the minc-toolkit.  I was personally interested in building a very small
>>>> image so I use the Alpine Linux Base image and build everything from
>>>> scratch.
>>>>
>>> So, you want to run minc-toolkit on your embedded device?
>>>
>>>
>>>
>>>
>>>> Thiis might not correspond directly to your current needs, but it was
>>>> pretty reasonable for me.
>>>>
>>>> https://hub.docker.com/r/dantino19/minc-toolkit/
>>>>
>>>>
>>>>
>>>> On Tue, May 17, 2016 at 11:39 PM Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>> wrote:
>>>>
>>>> Once again many thanks Andrew and Pierre!
>>>>>
>>>>> It seems to have worked after sourcing /opt/minc/minc-toolkit-config.sh
>>>>> .
>>>>>
>>>>> I will give it a try (using MINC files) tomorrow.
>>>>>
>>>>> @Andrew: have a good day!
>>>>>
>>>>> @Pierre: Have a good night!
>>>>>
>>>>> Best,
>>>>>
>>>>> Paul
>>>>>
>>>>> On Tue, 17 May 2016, Pierre Bellec wrote:
>>>>>
>>>>> Paul, you may also want to look at dependencies and sourcing
>>>>>> environment variables (paragraph "using") in the documentation:
>>>>>> http://bic-mni.github.io/#installing
>>>>>>
>>>>>> Pierre Bellec
>>>>>> Assistant professor ("adjoint sous octroi"), Department of computer
>>>>>>
>>>>> science
>>>>>
>>>>>> and operational research (DIRO <http://diro.umontreal.ca/>)
>>>>>> Member, Centre de recherche de l'institut Universitaire de g?riatrie de
>>>>>> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
>>>>>> Member, Institute of Biomedical Engineering <
>>>>>>
>>>>> http://www.igb.umontreal.ca/>
>>>>>
>>>>>> Universit? de Montr?al, Montr?al, Canada
>>>>>> Phone +1 514 713 5596
>>>>>> Full coordinates on my home page
>>>>>> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
>>>>>> Laboratory website <http://simexp-lab.org>.
>>>>>>
>>>>>> On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com>
>>>>>>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> In my case I add my own private apt repository that mirrors things
>>>>>>> from the new a shiny source here:
>>>>>>>
>>>>>>>     http://bic-mni.github.io/
>>>>>>>
>>>>>>> In your case, just download the appropriate .deb file and then install
>>>>>>> using dpkg.
>>>>>>>
>>>>>>> This should do it:
>>>>>>>
>>>>>>>     $ wget
>>>>>>>
>>>>>>>
>>>>>
>>> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>
>>>>
>>>>>>>     $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>>>>
>>>>>>>
>>>>>>> a
>>>>>>>
>>>>>>> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> So I installed:
>>>>>>>> NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>>>>>>>>
>>>>>>>> After importing the "Applicance" in VirtualBox and configuring, I can
>>>>>>>>
>>>>>>> start
>>>>>>>
>>>>>>>> the virtual machine, so far so good, but when I come to install the
>>>>>>>> minctools; I had to use:
>>>>>>>> sudo apt-get install minc-toolkit
>>>>>>>>
>>>>>>>> I get the following:
>>>>>>>> Reading package lists... Done
>>>>>>>> Building dependency tree
>>>>>>>> Reading state information... Done
>>>>>>>> E: Unable to locate package minc-toolkit
>>>>>>>>
>>>>>>>> any ideas?
>>>>>>>>
>>>>>>>> Thanks again!
>>>>>>>>
>>>>>>>> Paul
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, 18 May 2016, Andrew Janke wrote:
>>>>>>>>
>>>>>>>> I'm sure I saw one pass through the minc-users mailing list a while
>>>>>>>>>
>>>>>>>> back?
>>>>>>>
>>>>>>>>
>>>>>>>>> I use the neurodebian VM and then
>>>>>>>>>
>>>>>>>>>    apt-get install minc-toolkit     (thanks Vlad!)
>>>>>>>>>
>>>>>>>>> a
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>>>>>>
>>>>>>>> wrote:
>>>>>
>>>>>>
>>>>>>>>>> Dear All,
>>>>>>>>>>
>>>>>>>>>> I want to prepare a virtual machine for VirtualBox that includes a
>>>>>>>>>>
>>>>>>>>> linux
>>>>>>>
>>>>>>>> version with the minc tools. But being lazy (;-)!), I was wondering
>>>>>>>>>>
>>>>>>>>> if
>>>>>
>>>>>> anyone already had that and be willing to share.
>>>>>>>>>> Otherwise, any pointers on how to go about it (of course I would be
>>>>>>>>>> willing
>>>>>>>>>> to share the finished product!)?
>>>>>>>>>>
>>>>>>>>>
>>>
>>> --
>>> 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
>>>
>>
>> _______________________________________________
>> 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 May 18 13:39:51 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 18 May 2016 13:39:51 -0400
Subject: [MINC-users] Virtual machine that includes minc tools
In-Reply-To: <alpine.DEB.2.02.1605181254240.22290@login1.bic.mni.mcgill.ca>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172154520.6495@login1.bic.mni.mcgill.ca>
	<CAG0CB21wm1hBpWjUxAU-t33ThemXMfX9e83Xd20Vf_2Uys3+gQ@mail.gmail.com>
	<alpine.DEB.2.02.1605172252450.15533@login1.bic.mni.mcgill.ca>
	<CAG0CB20UPgAEg96fnA6T9CbyVGmGW9EQ9WD2mXp_69iA2H0Q3A@mail.gmail.com>
	<CADPHwxBjsFpM_B-BAjijpTz3zbFpkf6i1WQ8mZHL6dpOGK=dNA@mail.gmail.com>
	<alpine.DEB.2.02.1605172336090.22479@login1.bic.mni.mcgill.ca>
	<CALz388nX-GY2dTyXjFwtcFHogNiTgdZLDG20BBhau-3saN2KOg@mail.gmail.com>
	<573C84D6.8040208@gmail.com>
	<alpine.DEB.2.02.1605181109070.5848@login1.bic.mni.mcgill.ca>
	<CABEEk14oAc-OacNgirHmgu+z0Uhz69q6bGtZGumBhiLUNiY9xg@mail.gmail.com>
	<alpine.DEB.2.02.1605181254240.22290@login1.bic.mni.mcgill.ca>
Message-ID: <CABEEk14VcVN0WaS4zKVEJTVCA8GcFD+u1N=jDs9q7wqtP4qGXQ@mail.gmail.com>

Sure - it's freely available as it is. It's just rather ancient so it's
missing the past 6-7 years of MINC development

-- A

On Wed, May 18, 2016 at 1:11 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
wrote:

> Thanks Alex!
>
> I should have read the instructions more carefully!
>
> Actually, this package would be in essence what I was looking for.
> Unfortunately, I had different outcomes with NeuroDebian installation on a
> laptop and on my desktop at work (I of course acknowledge that this is most
> lokely due to my limitations in such matters ;-)!)
>
> That being said, if need be, would it be ok Alex if I distribute your
> virtual machine for a workshop?
> I would of course acknowledge you!
>
> Many thanks to All who replied!
>
> Best Regards,
>
> Paul
>
>
>
> On Wed, 18 May 2016, Alex Zijdenbos wrote:
>
> Hi Paul - user/pass are in the instructions on that page I sent:
>>
>> User: minc pass: minc
>>
>> that user has full sudo privileges iirc.
>>
>> On Wed, May 18, 2016 at 11:24 AM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>> wrote:
>>
>> Dear All,
>>>
>>> So I am now trying Alex's method, which is working so far, but I would
>>> need a username and a password, Alex?
>>>
>>> The reason for these questions is that I am preparing a hands-on training
>>> session as part of the PET Workshop happening in a couple of weeks, and I
>>> would have liked to have a virtual machine file with all the necessary
>>> tools, in order to make it easier for the participants to install the
>>> package.
>>>
>>> Best,
>>>
>>> Paul
>>>
>>>
>>>
>>> On Wed, 18 May 2016, Vladimir S. FONOV wrote:
>>>
>>> Hello,
>>>
>>>>
>>>> On 16-05-18 10:42 AM, Dante De Nigris wrote:
>>>>
>>>> Similar to Pierre's previous proposal, I recently built a docker image
>>>>> with
>>>>> the minc-toolkit.  I was personally interested in building a very small
>>>>> image so I use the Alpine Linux Base image and build everything from
>>>>> scratch.
>>>>>
>>>>> So, you want to run minc-toolkit on your embedded device?
>>>>
>>>>
>>>>
>>>>
>>>> Thiis might not correspond directly to your current needs, but it was
>>>>> pretty reasonable for me.
>>>>>
>>>>> https://hub.docker.com/r/dantino19/minc-toolkit/
>>>>>
>>>>>
>>>>>
>>>>> On Tue, May 17, 2016 at 11:39 PM Paul GRAVEL <
>>>>> pgravel at bic.mni.mcgill.ca>
>>>>> wrote:
>>>>>
>>>>> Once again many thanks Andrew and Pierre!
>>>>>
>>>>>>
>>>>>> It seems to have worked after sourcing
>>>>>> /opt/minc/minc-toolkit-config.sh
>>>>>> .
>>>>>>
>>>>>> I will give it a try (using MINC files) tomorrow.
>>>>>>
>>>>>> @Andrew: have a good day!
>>>>>>
>>>>>> @Pierre: Have a good night!
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Paul
>>>>>>
>>>>>> On Tue, 17 May 2016, Pierre Bellec wrote:
>>>>>>
>>>>>> Paul, you may also want to look at dependencies and sourcing
>>>>>>
>>>>>>> environment variables (paragraph "using") in the documentation:
>>>>>>> http://bic-mni.github.io/#installing
>>>>>>>
>>>>>>> Pierre Bellec
>>>>>>> Assistant professor ("adjoint sous octroi"), Department of computer
>>>>>>>
>>>>>>> science
>>>>>>
>>>>>> and operational research (DIRO <http://diro.umontreal.ca/>)
>>>>>>> Member, Centre de recherche de l'institut Universitaire de g?riatrie
>>>>>>> de
>>>>>>> Montr?al (CRIUGM <http://www.criugm.qc.ca/>)
>>>>>>> Member, Institute of Biomedical Engineering <
>>>>>>>
>>>>>>> http://www.igb.umontreal.ca/>
>>>>>>
>>>>>> Universit? de Montr?al, Montr?al, Canada
>>>>>>> Phone +1 514 713 5596
>>>>>>> Full coordinates on my home page
>>>>>>> <http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec>
>>>>>>> Laboratory website <http://simexp-lab.org>.
>>>>>>>
>>>>>>> On Tue, May 17, 2016 at 11:01 PM, Andrew Janke <a.janke at gmail.com>
>>>>>>>
>>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>> In my case I add my own private apt repository that mirrors things
>>>>>>>
>>>>>>>> from the new a shiny source here:
>>>>>>>>
>>>>>>>>     http://bic-mni.github.io/
>>>>>>>>
>>>>>>>> In your case, just download the appropriate .deb file and then
>>>>>>>> install
>>>>>>>> using dpkg.
>>>>>>>>
>>>>>>>> This should do it:
>>>>>>>>
>>>>>>>>     $ wget
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>> http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>
>>>>
>>>>>     $ sudo dpkg -i minc-toolkit-1.9.11-20160202-Debian_7.3-x86_64.deb
>>>>>>>>
>>>>>>>>
>>>>>>>> a
>>>>>>>>
>>>>>>>> On 18 May 2016 at 12:56, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> So I installed:
>>>>>>>>> NeuroDebian 7.8.0 image (64bit) for Windows 7 64 bit.
>>>>>>>>>
>>>>>>>>> After importing the "Applicance" in VirtualBox and configuring, I
>>>>>>>>> can
>>>>>>>>>
>>>>>>>>> start
>>>>>>>>
>>>>>>>> the virtual machine, so far so good, but when I come to install the
>>>>>>>>> minctools; I had to use:
>>>>>>>>> sudo apt-get install minc-toolkit
>>>>>>>>>
>>>>>>>>> I get the following:
>>>>>>>>> Reading package lists... Done
>>>>>>>>> Building dependency tree
>>>>>>>>> Reading state information... Done
>>>>>>>>> E: Unable to locate package minc-toolkit
>>>>>>>>>
>>>>>>>>> any ideas?
>>>>>>>>>
>>>>>>>>> Thanks again!
>>>>>>>>>
>>>>>>>>> Paul
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, 18 May 2016, Andrew Janke wrote:
>>>>>>>>>
>>>>>>>>> I'm sure I saw one pass through the minc-users mailing list a while
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> back?
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> I use the neurodebian VM and then
>>>>>>>>>>
>>>>>>>>>>    apt-get install minc-toolkit     (thanks Vlad!)
>>>>>>>>>>
>>>>>>>>>> a
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 18 May 2016 at 11:58, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
>>>>>>>>>>
>>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>> Dear All,
>>>>>>>>>>>
>>>>>>>>>>> I want to prepare a virtual machine for VirtualBox that includes
>>>>>>>>>>> a
>>>>>>>>>>>
>>>>>>>>>>> linux
>>>>>>>>>>
>>>>>>>>>
>>>>>>>> version with the minc tools. But being lazy (;-)!), I was wondering
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> if
>>>>>>>>>>
>>>>>>>>>
>>>>>> anyone already had that and be willing to share.
>>>>>>>
>>>>>>>> Otherwise, any pointers on how to go about it (of course I would be
>>>>>>>>>>> willing
>>>>>>>>>>> to share the finished product!)?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>> --
>>>> 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
>>>>
>>>>
>>> _______________________________________________
>>> 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 caroline.paquette at mcgill.ca  Sun May 22 19:32:25 2016
From: caroline.paquette at mcgill.ca (Caroline Paquette)
Date: Sun, 22 May 2016 19:32:25 -0400
Subject: [MINC-users] mincmath
Message-ID: <57424189.3020602@mcgill.ca>

Hello,
We are using mincmath to multiply a volume (PET acquired with HRRT) by a 
brain mask, which should be simple. Some outputs are non-zero outside 
the brain (although these same voxels are zero in the mask file!). Error 
is random as some of the files multiplied by the same mask are zero 
while others are non-zero (e.g., 3 trials for the same subject, images 
are realigned so we use the same brain mask).
Any advice? Is this a known problem? We tried writing the files float 
and using different combinations of file formats without success. Files 
were converted from ecat (original) to nifti in matlab using the 
spm_ecattonii function. Preprocessing was done with SPM12 and then 
converted to minc with nii2mnc (we also tried some options with the 
import without success).
Thank you,
Caroline

From a.janke at gmail.com  Sun May 22 22:00:07 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 23 May 2016 12:00:07 +1000
Subject: [MINC-users] mincmath
In-Reply-To: <57424189.3020602@mcgill.ca>
References: <57424189.3020602@mcgill.ca>
Message-ID: <CAG0CB23rGeDbMesrTbstrxo++qj5EFYAdj0JrHcqrni8C2xWzw@mail.gmail.com>

Hi Caroline,

My guess is that discretisation of your mask volume is causing the
issue. Meaning instead of 0 being stored a very small number is
instead. What datatype is your mask volume and how are you determining
that the values in the mask are zero?

If you want mask calculations to be robust to this issue then you can
use minccalc to treat voxels with a mask value of less than 0.5 as 0.


   $ minccalc -expression "if(A[1] < 0.5) ? 0 : A[0]" input.mnc
mask.mnc output.mnc


a


On 23 May 2016 at 09:32, Caroline Paquette <caroline.paquette at mcgill.ca> wrote:
> Hello,
> We are using mincmath to multiply a volume (PET acquired with HRRT) by a
> brain mask, which should be simple. Some outputs are non-zero outside the
> brain (although these same voxels are zero in the mask file!). Error is
> random as some of the files multiplied by the same mask are zero while
> others are non-zero (e.g., 3 trials for the same subject, images are
> realigned so we use the same brain mask).
> Any advice? Is this a known problem? We tried writing the files float and
> using different combinations of file formats without success. Files were
> converted from ecat (original) to nifti in matlab using the spm_ecattonii
> function. Preprocessing was done with SPM12 and then converted to minc with
> nii2mnc (we also tried some options with the import without success).
> Thank you,
> Caroline
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From gdevenyi at gmail.com  Tue May 24 10:10:06 2016
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 24 May 2016 10:10:06 -0400
Subject: [MINC-users] Handling conversion from SPM "analyze" format?
In-Reply-To: <CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
Message-ID: <CAFQOoOqtQdeO4p=rGHF2oS7QoYDfPWs23QHfz6jbVaMa7NrUQw@mail.gmail.com>

Thanks Andrew,

It looks like mat1dump doesn?t support the .mat format these files are in.

$ spm2xfm 1001794_wba_001.mat /tmp/test.xfm
Use of uninitialized value $P in hash element at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 61.
Use of uninitialized value in multiplication (*) at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 61.
Use of uninitialized value $P in hash element at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 62.
Use of uninitialized value in concatenation (.) or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 62.
Invalid type '1' in unpack at
/opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 70.
Use of uninitialized value $dump[1] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
Use of uninitialized value $dump[2] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
Use of uninitialized value $dump[3] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
Use of uninitialized value $dump[3] in substitution (s///) at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 230.
Use of uninitialized value $dump[1] in join or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.
Use of uninitialized value $dump[2] in join or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.
Use of uninitialized value $dump[3] in join or string at
/opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.

Do you think octave may be able to parse out the matrix?
?

--
Gabriel A. Devenyi B.Eng. Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gdevenyi at gmail.com

On Tue, May 17, 2016 at 4:53 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Gabriel,
>
> If you call ana2mnc as spm2mnc (make a symlink) it will attempt to
> make a MINC file with the correct orientation. There is also a spm2xfm
> that will convert the .mat to a .xfm file. It uses mat1dump (something
> I wrote in Perl many years ago).
>
>
> a
>
> On 18 May 2016 at 06:24, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> > Hi minc-users,
> >
> > I've inherited some data I think was touched by SPM at some point, as I
> > have a hdr/img/mat for each.
> >
> > Upon conversion (with ana2mnc) they're not oriented properly. I suspect I
> > can rectify this with information in the .mat file?
> >
> > Does anyone know how I can do this with the minc tools? Or will I have to
> > figure out something with SPM?
> >
> > --
> > Gabriel A. Devenyi B.Eng. Ph.D.
> > Research Computing Associate
> > Computational Brain Anatomy Laboratory
> > Cerebral Imaging Center
> > Douglas Mental Health University Institute
> > Affiliate, Department of Psychiatry
> > McGill University
> > t: 514.761.6131x4781
> > e: gdevenyi at gmail.com
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue May 24 16:18:37 2016
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 25 May 2016 04:18:37 +0800
Subject: [MINC-users] Handling conversion from SPM "analyze" format?
In-Reply-To: <CAFQOoOqtQdeO4p=rGHF2oS7QoYDfPWs23QHfz6jbVaMa7NrUQw@mail.gmail.com>
References: <CAFQOoOoQxuv-5Eth5GXqQXC2SE9vxF4AtGU-gd7gbWSQRJGKoQ@mail.gmail.com>
	<CAG0CB21cBHXXjrizS5=TSp_sXi9_+pbnObX9A1pEq1fWFq5nMQ@mail.gmail.com>
	<CAFQOoOqtQdeO4p=rGHF2oS7QoYDfPWs23QHfz6jbVaMa7NrUQw@mail.gmail.com>
Message-ID: <CAG0CB230VdV9z3SjGFGXAMG0XsDMgwM4yC9q68u=yum+YpCAag@mail.gmail.com>

Yes mat1dump will only parse older MATLAB .mat files. Someone else
wrote a another one for newer ones out there somewhere...  however I
see you are using octave which is a far better solution.


a


On 24 May 2016 at 22:10, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
> Thanks Andrew,
>
> It looks like mat1dump doesn?t support the .mat format these files are in.
>
> $ spm2xfm 1001794_wba_001.mat /tmp/test.xfm
> Use of uninitialized value $P in hash element at
> /opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 61.
> Use of uninitialized value in multiplication (*) at
> /opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 61.
> Use of uninitialized value $P in hash element at
> /opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 62.
> Use of uninitialized value in concatenation (.) or string at
> /opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 62.
> Invalid type '1' in unpack at
> /opt/quarantine/minc-toolkit-extras/1.0/build/mat1dump line 70.
> Use of uninitialized value $dump[1] in substitution (s///) at
> /opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
> Use of uninitialized value $dump[2] in substitution (s///) at
> /opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
> Use of uninitialized value $dump[3] in substitution (s///) at
> /opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 228.
> Use of uninitialized value $dump[3] in substitution (s///) at
> /opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 230.
> Use of uninitialized value $dump[1] in join or string at
> /opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.
> Use of uninitialized value $dump[2] in join or string at
> /opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.
> Use of uninitialized value $dump[3] in join or string at
> /opt/quarantine/minc-toolkit-extras/1.0/build/spm2xfm line 235.
>
> Do you think octave may be able to parse out the matrix?
>
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> Affiliate, Department of Psychiatry
> McGill University
> t: 514.761.6131x4781
> e: gdevenyi at gmail.com
>
> On Tue, May 17, 2016 at 4:53 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Hi Gabriel,
>>
>> If you call ana2mnc as spm2mnc (make a symlink) it will attempt to
>> make a MINC file with the correct orientation. There is also a spm2xfm
>> that will convert the .mat to a .xfm file. It uses mat1dump (something
>> I wrote in Perl many years ago).
>>
>>
>> a
>>
>> On 18 May 2016 at 06:24, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
>> > Hi minc-users,
>> >
>> > I've inherited some data I think was touched by SPM at some point, as I
>> > have a hdr/img/mat for each.
>> >
>> > Upon conversion (with ana2mnc) they're not oriented properly. I suspect I
>> > can rectify this with information in the .mat file?
>> >
>> > Does anyone know how I can do this with the minc tools? Or will I have to
>> > figure out something with SPM?
>> >
>> > --
>> > Gabriel A. Devenyi B.Eng. Ph.D.
>> > Research Computing Associate
>> > Computational Brain Anatomy Laboratory
>> > Cerebral Imaging Center
>> > Douglas Mental Health University Institute
>> > Affiliate, Department of Psychiatry
>> > McGill University
>> > t: 514.761.6131x4781
>> > e: gdevenyi at gmail.com
>> > _______________________________________________
>> > 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  Mon May 30 11:37:20 2016
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Mon, 30 May 2016 11:37:20 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CAAd5DeQC6+T-aZBhNJv+n-NJ-ZzbdY6oG=DUvrX6CiYu8_bp6w@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
	<CABEEk16JJOgLewbz4qppLioMAcC-nR0jYoWqW7ptEKQMoLHONg@mail.gmail.com>
	<CAAd5DeQC6+T-aZBhNJv+n-NJ-ZzbdY6oG=DUvrX6CiYu8_bp6w@mail.gmail.com>
Message-ID: <CABEEk14N7QH2HPvCE2KG+7wj78hZ4z60z+VNHbQBUtcj0nzopA@mail.gmail.com>

Nice work, Bert!

I have since built in some paranoid checking in all of my scripts, and one
thing that keeps turning up is that nii2mnc doesn't actually set the
'complete' flag. Iow, anything created by nii2mnc fails minccomplete. Any
chance you fixed that as well?

Thanks,

-- A

On Mon, May 16, 2016 at 12:38 PM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi all,
>
> I have just checked in changes to volume_io, voxel_loop and the following
> minc tools:
>
> mincaverage, minccalc, minccmp, mincconcat, mincconvert, minccopy,
> mincextract, minclookup, mincmakescalar, mincmakevector, mincmath,
> mincresample, mincreshape, mincsample, mincstats, minctoraw, mincwindow.
>
> These tools will still behave as before, in that they will run to
> completion with a corrupt file. However, they will report the error as a
> non-zero exit code (EXIT_FAILURE), in addition to whatever messages are
> currently displayed by the libraries.
>
> Two existing tools, mincinfo and mincdump, seem to already have correct
> handling of read errors. At least two others, mincblob and mincmorph,
> should pick up the changes via volume_io.
>
> This covers the majority of the command line tools. It may also make sense
> to reflect these changes in some of the basic scripts (e.g. mincpik,
> mincdiff) - let me know if there are any particularly salient cases we
> should take care of.
>
>     -bert
>
> On Sat, May 14, 2016 at 5:04 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > On this note: nii2mnc is one of the tools that doesn't appear to set the
> > image:complete attribute. I haven't found any others yet but since I
> > started running minccomplete on anything I generate, I may come up with
> > more :)
> >
> > On Sat, May 14, 2016 at 6:53 AM, Vladimir S. FONOV <
> > vladimir.fonov at gmail.com
> > > wrote:
> >
> > > Hello,
> > >
> > > the only thing minccomplete does is read the contents of the
> > image:complete
> > > attribute. Which is not even respected by all minc tools.
> > > One real way to check the consistency of the minc file would be to
> enable
> > > checksum , integrated into HDF5 file format.
> > >
> > > Currently it can be enabled by setting the environment variable
> > > MINC_CHECKSUM to 1 , at the time when file is created. Obviously, this
> > > works only with MINC2 file format and it was not tested very well yet.
> > >
> > > On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> > > wrote:
> > >
> > > > Hi all,
> > > >
> > > > I managed to generate a large number of broken MINC files;
> > > possibly/likely
> > > > due to a filesystem problem. The processes that created them (e.g.,
> > > > mincaverage) did not produce any warnings and completed successfully;
> > in
> > > > addition, minccomplete tells me that the files are complete.
> > > >
> > > > Unfortunately, trying to read these files throws HDF5 and miicv
> errors
> > > (see
> > > > below) and they are obviously corrupt.
> > > >
> > > > I am thinking that it would be useful to complete minccomplete by
> > having
> > > it
> > > > actually test-read the data, such that it would report on file
> > integrity?
> > > > This would make it easy to find these kinds of corruptions - and
> could
> > > even
> > > > tack that end the end of scripts to make sure outputs are intact. I'm
> > > > currently using 'mincstats -quiet -min' to locate them, but it seems
> > the
> > > > natural place for this test would actually be minccomplete.
> > > >
> > > > -- A
> > > >
> > > > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> > > >   #000: H5Dio.c line 174 in H5Dread(): can't read data
> > > >     major: Dataset
> > > >     minor: Read failed
> > > >   #001: H5Dio.c line 449 in H5D_read(): can't read data
> > > >     major: Dataset
> > > >     minor: Read failed
> > > >   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw
> > data
> > > > chunk
> > > >     major: Low-level I/O
> > > >     minor: Read failed
> > > >   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read
> > > failed
> > > >     major: Data filters
> > > >     minor: Filter operation failed
> > > >   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure
> > during
> > > > read
> > > >     major: Data filters
> > > >     minor: Read failed
> > > >   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate()
> failed
> > > >     major: Data filters
> > > >     minor: Unable to initialize object
> > > > mincstats (from miicv_get): Can't read dataset
> /minc-2.0/image/0/image
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > >
> > >
> > >
> > > --
> > > Best regards,
> > >
> > >  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> > > _______________________________________________
> > > 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 robert.d.vincent at mcgill.ca  Mon May 30 11:41:59 2016
From: robert.d.vincent at mcgill.ca (Robert D. Vincent)
Date: Mon, 30 May 2016 11:41:59 -0400
Subject: [MINC-users] minccomplete's completeness
In-Reply-To: <CABEEk14N7QH2HPvCE2KG+7wj78hZ4z60z+VNHbQBUtcj0nzopA@mail.gmail.com>
References: <CABEEk17TXVkmC9D=ZQWccGVufvUcC0FDi3zN=5CXQXSUb=tRew@mail.gmail.com>
	<CAMCwi7OtT0JuGZkR1fdruOViK5vGOKG6g8_wuFTdpUk4XpsXRw@mail.gmail.com>
	<CABEEk16JJOgLewbz4qppLioMAcC-nR0jYoWqW7ptEKQMoLHONg@mail.gmail.com>
	<CAAd5DeQC6+T-aZBhNJv+n-NJ-ZzbdY6oG=DUvrX6CiYu8_bp6w@mail.gmail.com>
	<CABEEk14N7QH2HPvCE2KG+7wj78hZ4z60z+VNHbQBUtcj0nzopA@mail.gmail.com>
Message-ID: <CAAd5DeSA2buDEY_B6dctmGT1XtSvM3yqsV93M10Vb8F=AuBCOw@mail.gmail.com>

Not yet. I'll try to fix it soon.

On Mon, May 30, 2016 at 11:37 AM, Alex Zijdenbos <zijdenbos at gmail.com>
wrote:

> Nice work, Bert!
>
> I have since built in some paranoid checking in all of my scripts, and one
> thing that keeps turning up is that nii2mnc doesn't actually set the
> 'complete' flag. Iow, anything created by nii2mnc fails minccomplete. Any
> chance you fixed that as well?
>
> Thanks,
>
> -- A
>
> On Mon, May 16, 2016 at 12:38 PM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi all,
> >
> > I have just checked in changes to volume_io, voxel_loop and the following
> > minc tools:
> >
> > mincaverage, minccalc, minccmp, mincconcat, mincconvert, minccopy,
> > mincextract, minclookup, mincmakescalar, mincmakevector, mincmath,
> > mincresample, mincreshape, mincsample, mincstats, minctoraw, mincwindow.
> >
> > These tools will still behave as before, in that they will run to
> > completion with a corrupt file. However, they will report the error as a
> > non-zero exit code (EXIT_FAILURE), in addition to whatever messages are
> > currently displayed by the libraries.
> >
> > Two existing tools, mincinfo and mincdump, seem to already have correct
> > handling of read errors. At least two others, mincblob and mincmorph,
> > should pick up the changes via volume_io.
> >
> > This covers the majority of the command line tools. It may also make
> sense
> > to reflect these changes in some of the basic scripts (e.g. mincpik,
> > mincdiff) - let me know if there are any particularly salient cases we
> > should take care of.
> >
> >     -bert
> >
> > On Sat, May 14, 2016 at 5:04 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> > wrote:
> >
> > > On this note: nii2mnc is one of the tools that doesn't appear to set
> the
> > > image:complete attribute. I haven't found any others yet but since I
> > > started running minccomplete on anything I generate, I may come up with
> > > more :)
> > >
> > > On Sat, May 14, 2016 at 6:53 AM, Vladimir S. FONOV <
> > > vladimir.fonov at gmail.com
> > > > wrote:
> > >
> > > > Hello,
> > > >
> > > > the only thing minccomplete does is read the contents of the
> > > image:complete
> > > > attribute. Which is not even respected by all minc tools.
> > > > One real way to check the consistency of the minc file would be to
> > enable
> > > > checksum , integrated into HDF5 file format.
> > > >
> > > > Currently it can be enabled by setting the environment variable
> > > > MINC_CHECKSUM to 1 , at the time when file is created. Obviously,
> this
> > > > works only with MINC2 file format and it was not tested very well
> yet.
> > > >
> > > > On Fri, May 13, 2016 at 3:35 PM, Alex Zijdenbos <zijdenbos at gmail.com
> >
> > > > wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I managed to generate a large number of broken MINC files;
> > > > possibly/likely
> > > > > due to a filesystem problem. The processes that created them (e.g.,
> > > > > mincaverage) did not produce any warnings and completed
> successfully;
> > > in
> > > > > addition, minccomplete tells me that the files are complete.
> > > > >
> > > > > Unfortunately, trying to read these files throws HDF5 and miicv
> > errors
> > > > (see
> > > > > below) and they are obviously corrupt.
> > > > >
> > > > > I am thinking that it would be useful to complete minccomplete by
> > > having
> > > > it
> > > > > actually test-read the data, such that it would report on file
> > > integrity?
> > > > > This would make it easy to find these kinds of corruptions - and
> > could
> > > > even
> > > > > tack that end the end of scripts to make sure outputs are intact.
> I'm
> > > > > currently using 'mincstats -quiet -min' to locate them, but it
> seems
> > > the
> > > > > natural place for this test would actually be minccomplete.
> > > > >
> > > > > -- A
> > > > >
> > > > > HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:
> > > > >   #000: H5Dio.c line 174 in H5Dread(): can't read data
> > > > >     major: Dataset
> > > > >     minor: Read failed
> > > > >   #001: H5Dio.c line 449 in H5D_read(): can't read data
> > > > >     major: Dataset
> > > > >     minor: Read failed
> > > > >   #002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read
> raw
> > > data
> > > > > chunk
> > > > >     major: Low-level I/O
> > > > >     minor: Read failed
> > > > >   #003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline
> read
> > > > failed
> > > > >     major: Data filters
> > > > >     minor: Filter operation failed
> > > > >   #004: H5Z.c line 1120 in H5Z_pipeline(): filter returned failure
> > > during
> > > > > read
> > > > >     major: Data filters
> > > > >     minor: Read failed
> > > > >   #005: H5Zdeflate.c line 125 in H5Z_filter_deflate(): inflate()
> > failed
> > > > >     major: Data filters
> > > > >     minor: Unable to initialize object
> > > > > mincstats (from miicv_get): Can't read dataset
> > /minc-2.0/image/0/image
> > > > > _______________________________________________
> > > > > MINC-users at bic.mni.mcgill.ca
> > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Best regards,
> > > >
> > > >  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> > > > _______________________________________________
> > > > 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
> >
> >
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