From andrew at biospective.com  Thu Jul  3 10:13:34 2014
From: andrew at biospective.com (Andrew Wood)
Date: Thu, 3 Jul 2014 10:13:34 -0400
Subject: [MINC-users] DTI DICOM to Minc Conversion
Message-ID: <CABApf9G4aQ2rV2oJc8UMrb0H3vyoaygPkekDHCTP5FkfmJnb9g@mail.gmail.com>

Hi all,

I'm wondering if anyone out there has worked with ADNI DTI data. When I run
the DICOM through dcm2mnc, the time dimension gets lost.. I've had success
with other DTI datasets in the past (e.g. PPMI), where the different
directions are converted along the time dimension, so there is something
about this ADNI data is confusing the converter.

I've tried several different versions of dcm2mnc, and having no luck with
any of them.

I'd appreciate any advise on how to best get this conversion working.

Thanks,
Andrew

From a.janke at gmail.com  Thu Jul  3 12:29:04 2014
From: a.janke at gmail.com (Andrew Janke)
Date: Fri, 4 Jul 2014 02:29:04 +1000
Subject: [MINC-users] DTI DICOM to Minc Conversion
In-Reply-To: <CABApf9G4aQ2rV2oJc8UMrb0H3vyoaygPkekDHCTP5FkfmJnb9g@mail.gmail.com>
References: <CABApf9G4aQ2rV2oJc8UMrb0H3vyoaygPkekDHCTP5FkfmJnb9g@mail.gmail.com>
Message-ID: <CAG0CB21XXVzmvO0kHpsbNk_qtikCXiyybDFfdm4NbXkT7ZVCTQ@mail.gmail.com>

Hi Andrew,

While I probably should fix dcm2mnc to handle this case I've always
been of the opinion that converters should be written in scripting
languages to allow quick hackery, so my usual fix for such things is
to write something dodgy in perl.

I once wrote something called dcmsort that lives in here:

   https://github.com/andrewjanke/mnc2dcm

That will give you a quick idea of all the DICOM files in a directory.
It uses a version of DICOM.pm from John Harlap (and others), I should
get around to changing this to something like dcmtk but have never
found a need just yet. Yes, there is a version of my mythical mnc2dcm
converter there that will sort of work but I wouldn't recommend anyone
uses it for anything real...

The idea is that you run this on your input series of DICOM files,
that are then renamed to something sensical and put into folders in a
reasonably organised structure. At which point you pass the series of
folders into dcm2mnc and then play mincconcat after if that is what
you want. I tend to store Diffusion data in separate files (one for
each direction, B0 image) as this allows me to do quick math across
them if needs be.


a

On 4 July 2014 00:13, Andrew Wood <andrew at biospective.com> wrote:
> Hi all,
>
> I'm wondering if anyone out there has worked with ADNI DTI data. When I run
> the DICOM through dcm2mnc, the time dimension gets lost.. I've had success
> with other DTI datasets in the past (e.g. PPMI), where the different
> directions are converted along the time dimension, so there is something
> about this ADNI data is confusing the converter.
>
> I've tried several different versions of dcm2mnc, and having no luck with
> any of them.
>
> I'd appreciate any advise on how to best get this conversion working.
>
> Thanks,
> Andrew
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From zijdenbos at gmail.com  Fri Jul  4 14:00:06 2014
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Fri, 4 Jul 2014 14:00:06 -0400
Subject: [MINC-users] minccalc bug
Message-ID: <CABEEk140-Eu_D=y-Yhnorj2OX_7zqtLaVQNhcTbNcguxOLZkKA@mail.gmail.com>

This one is probably for AJ; I stumbled across some really bizarre
behaviour of minccalc:

minccalc -expression 'x=0; y=A[1]; if (y < 2) x=y; y' \
/usr/local/bic/share/mni-models/average305_t1_tal_lin_mask.mnc \
/usr/local/bic/share/mni-models/average305_t1_tal_lin.mnc \
y.mnc

I would have imagined that the output file y.mnc would be the same as the
second input file (A[1]), as y is never assigned to after y=A[1]; but that
is not the case. The 'if' condition combined with the x=y assignment,
somehow modifies y (rather significantly). If you play with the
conditional, the assignment, or for instance use y=A[0], things may work as
expected; but in the invocation above, it goes horribly wrong.

-- A

From a.janke at gmail.com  Mon Jul  7 07:18:57 2014
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 7 Jul 2014 21:18:57 +1000
Subject: [MINC-users] minccalc bug
In-Reply-To: <CABEEk140-Eu_D=y-Yhnorj2OX_7zqtLaVQNhcTbNcguxOLZkKA@mail.gmail.com>
References: <CABEEk140-Eu_D=y-Yhnorj2OX_7zqtLaVQNhcTbNcguxOLZkKA@mail.gmail.com>
Message-ID: <CAG0CB22ofScq-ra8KFNTAHXoGBzNjFSM_BAQ31DR4MLTFAVabQ@mail.gmail.com>

Hi Alex,

After fiddling with this for a bit I think it's a combination of two things.

1. Restriction of range and slice scaling. If you run this all in
double precision and clamp the output afterwards you can almost
recover your image. Something is strange in the logic as presented but
I can't quite figure out what is causing things to go haywire.

2. You are relying upon "magic" functionality for your output image,
(the last evaluated expression). It's also not clear upon a quick
glance that the final y is out of the if loop. Use braces! To avoid
confusion you are always best to use the outfile argument syntax in
these cases. ie:

    minccalc -expression 'x=0; y=A[1]; if (y < 2) x=y; y' \
      -outfile y y.mnc \
/usr/local/bic/share/mni-models/average305_t1_tal_lin_mask.mnc \
/usr/local/bic/share/mni-models/average305_t1_tal_lin.mnc

Still I think it's a bug but if its caused by restriction of range
then it isn't really. Not sure. You'd be best served to break your
file down to one voxel and check the output using the -debug argument
at which point you'll probably get a clue as to what is awry.

In the meantime, probably a good idea to file a bug here (preferably a
reduced version using rawtominc with a single voxel).


https://github.com/BIC-MNI/minc-tools/issues

ta


a

On 5 July 2014 04:00, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> This one is probably for AJ; I stumbled across some really bizarre
> behaviour of minccalc:
>
> minccalc -expression 'x=0; y=A[1]; if (y < 2) x=y; y' \
> /usr/local/bic/share/mni-models/average305_t1_tal_lin_mask.mnc \
> /usr/local/bic/share/mni-models/average305_t1_tal_lin.mnc \
> y.mnc
>
> I would have imagined that the output file y.mnc would be the same as the
> second input file (A[1]), as y is never assigned to after y=A[1]; but that
> is not the case. The 'if' condition combined with the x=y assignment,
> somehow modifies y (rather significantly). If you play with the
> conditional, the assignment, or for instance use y=A[0], things may work as
> expected; but in the invocation above, it goes horribly wrong.
>
> -- A
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From jon at pipitone.ca  Tue Jul  8 18:25:37 2014
From: jon at pipitone.ca (Jon Pipitone)
Date: Tue, 8 Jul 2014 18:25:37 -0400
Subject: [MINC-users] MINC virtual machine
Message-ID: <20140708222530.GA10955@kimsrv>

Hi all, 

Just letting you know that I've created a Ubuntu 12.04 virtual machine
with the minc-toolkit installed in it, along with R and RMINC. A link to
the machine is available here with instructions: 

  https://github.com/pipitone/minc-enabled-vm

I built this for a collaborator of ours but figure it may come in handy
for y'all too. 

Feel free to send me pull-requests for additions/changes. 

Jon.

From mallar.chak at gmail.com  Tue Jul  8 18:53:39 2014
From: mallar.chak at gmail.com (Mallar Chakravarty)
Date: Tue, 8 Jul 2014 18:53:39 -0400
Subject: [MINC-users] MINC virtual machine
In-Reply-To: <20140708222530.GA10955@kimsrv>
References: <20140708222530.GA10955@kimsrv>
Message-ID: <640487F7-C752-4109-8224-EF0DFF60761D@gmail.com>

So does this work for Erics work?  I guess it just needs to be reinstalled?

(Nice work posting this by the way)

Sent from my iPhone

> On Jul 8, 2014, at 6:25 PM, Jon Pipitone <jon at pipitone.ca> wrote:
> 
> Hi all, 
> 
> Just letting you know that I've created a Ubuntu 12.04 virtual machine
> with the minc-toolkit installed in it, along with R and RMINC. A link to
> the machine is available here with instructions: 
> 
>  https://github.com/pipitone/minc-enabled-vm
> 
> I built this for a collaborator of ours but figure it may come in handy
> for y'all too. 
> 
> Feel free to send me pull-requests for additions/changes. 
> 
> Jon.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From mallar.chak at gmail.com  Tue Jul  8 19:43:37 2014
From: mallar.chak at gmail.com (Mallar Chakravarty)
Date: Tue, 8 Jul 2014 19:43:37 -0400
Subject: [MINC-users] MINC virtual machine
In-Reply-To: <640487F7-C752-4109-8224-EF0DFF60761D@gmail.com>
References: <20140708222530.GA10955@kimsrv>
	<640487F7-C752-4109-8224-EF0DFF60761D@gmail.com>
Message-ID: <CAMrG8rP_oQhEBmB0XPH_jy4WV+-h_MvTeGmD6pwg8bk0YqFKMA@mail.gmail.com>

woops - sorry for the lack of selective reply.  Have a good night folks.

mallar


On Tue, Jul 8, 2014 at 6:53 PM, Mallar Chakravarty <mallar.chak at gmail.com>
wrote:

> So does this work for Erics work?  I guess it just needs to be reinstalled?
>
> (Nice work posting this by the way)
>
> Sent from my iPhone
>
> > On Jul 8, 2014, at 6:25 PM, Jon Pipitone <jon at pipitone.ca> wrote:
> >
> > Hi all,
> >
> > Just letting you know that I've created a Ubuntu 12.04 virtual machine
> > with the minc-toolkit installed in it, along with R and RMINC. A link to
> > the machine is available here with instructions:
> >
> >  https://github.com/pipitone/minc-enabled-vm
> >
> > I built this for a collaborator of ours but figure it may come in handy
> > for y'all too.
> >
> > Feel free to send me pull-requests for additions/changes.
> >
> > Jon.
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From a.janke at gmail.com  Tue Jul  8 19:47:50 2014
From: a.janke at gmail.com (Andrew Janke)
Date: Wed, 9 Jul 2014 09:47:50 +1000
Subject: [MINC-users] MINC virtual machine
In-Reply-To: <20140708222530.GA10955@kimsrv>
References: <20140708222530.GA10955@kimsrv>
Message-ID: <CAG0CB20Vee88Ev5BCfbUiFxkHhMXQ7VgSNHR0VQ83i=6KD-8YQ@mail.gmail.com>

Thanks Jon,

Should prove useful, if others are interested in this sort of approach
we have a CentOS version of this (plus a bunch of other tools)
available too. Why CentOS? The Oz research cloud mandated it. bah!


a

On 9 July 2014 08:25, Jon Pipitone <jon at pipitone.ca> wrote:
> Hi all,
>
> Just letting you know that I've created a Ubuntu 12.04 virtual machine
> with the minc-toolkit installed in it, along with R and RMINC. A link to
> the machine is available here with instructions:
>
>   https://github.com/pipitone/minc-enabled-vm
>
> I built this for a collaborator of ours but figure it may come in handy
> for y'all too.
>
> Feel free to send me pull-requests for additions/changes.
>
> Jon.
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From jon at pipitone.ca  Tue Jul  8 20:46:05 2014
From: jon at pipitone.ca (Jon Pipitone)
Date: Tue, 8 Jul 2014 20:46:05 -0400
Subject: [MINC-users] MINC virtual machine
In-Reply-To: <CAG0CB20Vee88Ev5BCfbUiFxkHhMXQ7VgSNHR0VQ83i=6KD-8YQ@mail.gmail.com>
References: <20140708222530.GA10955@kimsrv>
	<CAG0CB20Vee88Ev5BCfbUiFxkHhMXQ7VgSNHR0VQ83i=6KD-8YQ@mail.gmail.com>
Message-ID: <493EF0DA-03B9-4B41-9376-D12784A8F02B@pipitone.ca>

Andrew, if you send me you build file for your box I'll fold it into the ansible playbook and make it work for CentOS and Ubuntu. (We also need a CentOS VM for testing for our university supercomputer.)

On 2014-07-08, at 19:47, Andrew Janke <a.janke at gmail.com> wrote:

> Thanks Jon,
> 
> Should prove useful, if others are interested in this sort of approach
> we have a CentOS version of this (plus a bunch of other tools)
> available too. Why CentOS? The Oz research cloud mandated it. bah!
> 
> 
> a
> 
> On 9 July 2014 08:25, Jon Pipitone <jon at pipitone.ca> wrote:
>> Hi all,
>> 
>> Just letting you know that I've created a Ubuntu 12.04 virtual machine
>> with the minc-toolkit installed in it, along with R and RMINC. A link to
>> the machine is available here with instructions:
>> 
>>  https://github.com/pipitone/minc-enabled-vm
>> 
>> I built this for a collaborator of ours but figure it may come in handy
>> for y'all too.
>> 
>> Feel free to send me pull-requests for additions/changes.
>> 
>> Jon.
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From mishkind at gmail.com  Fri Jul 11 21:27:47 2014
From: mishkind at gmail.com (Mishkin Derakhshan)
Date: Fri, 11 Jul 2014 15:27:47 -1000
Subject: [MINC-users] MINC virtual machine
In-Reply-To: <493EF0DA-03B9-4B41-9376-D12784A8F02B@pipitone.ca>
References: <20140708222530.GA10955@kimsrv>
	<CAG0CB20Vee88Ev5BCfbUiFxkHhMXQ7VgSNHR0VQ83i=6KD-8YQ@mail.gmail.com>
	<493EF0DA-03B9-4B41-9376-D12784A8F02B@pipitone.ca>
Message-ID: <CAB-GmL04hXVObv_UKYfaWXT=fSyB4wX6QLmoJ+nGYpeBW4sLsw@mail.gmail.com>

Hi Jon,
FYI, I used the link on github to download the virtual machine
appliance but instead of finding box.ovf it has box-disk1.vmdk
of course you can still just create a new virtual box and select 'use
existing disk' to get it working but just thought you should update
the instructions, or, actually provide the box.ovf file.
mishkin

On Tue, Jul 8, 2014 at 2:46 PM, Jon Pipitone <jon at pipitone.ca> wrote:
> Andrew, if you send me you build file for your box I'll fold it into the ansible playbook and make it work for CentOS and Ubuntu. (We also need a CentOS VM for testing for our university supercomputer.)
>
> On 2014-07-08, at 19:47, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Thanks Jon,
>>
>> Should prove useful, if others are interested in this sort of approach
>> we have a CentOS version of this (plus a bunch of other tools)
>> available too. Why CentOS? The Oz research cloud mandated it. bah!
>>
>>
>> a
>>
>> On 9 July 2014 08:25, Jon Pipitone <jon at pipitone.ca> wrote:
>>> Hi all,
>>>
>>> Just letting you know that I've created a Ubuntu 12.04 virtual machine
>>> with the minc-toolkit installed in it, along with R and RMINC. A link to
>>> the machine is available here with instructions:
>>>
>>>  https://github.com/pipitone/minc-enabled-vm
>>>
>>> I built this for a collaborator of ours but figure it may come in handy
>>> for y'all too.
>>>
>>> Feel free to send me pull-requests for additions/changes.
>>>
>>> Jon.
>>> _______________________________________________
>>> 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 jon at pipitone.ca  Sat Jul 12 20:54:10 2014
From: jon at pipitone.ca (Jon Pipitone)
Date: Sat, 12 Jul 2014 20:54:10 -0400
Subject: [MINC-users] MINC virtual machine
In-Reply-To: <CAB-GmL04hXVObv_UKYfaWXT=fSyB4wX6QLmoJ+nGYpeBW4sLsw@mail.gmail.com>
References: <20140708222530.GA10955@kimsrv>
	<CAG0CB20Vee88Ev5BCfbUiFxkHhMXQ7VgSNHR0VQ83i=6KD-8YQ@mail.gmail.com>
	<493EF0DA-03B9-4B41-9376-D12784A8F02B@pipitone.ca>
	<CAB-GmL04hXVObv_UKYfaWXT=fSyB4wX6QLmoJ+nGYpeBW4sLsw@mail.gmail.com>
Message-ID: <20140713005410.GB24694@kimsrv.clarke-inst.on.ca>

Mishkin, 

Good catch. I've updated the link on github to point to a zip file with
the box.ovf file. 

Jon.

On 07/11, Mishkin Derakhshan wrote:
> Hi Jon,
> FYI, I used the link on github to download the virtual machine
> appliance but instead of finding box.ovf it has box-disk1.vmdk
> of course you can still just create a new virtual box and select 'use
> existing disk' to get it working but just thought you should update
> the instructions, or, actually provide the box.ovf file.
> mishkin

From jon at pipitone.ca  Fri Jul 18 17:01:13 2014
From: jon at pipitone.ca (Jon Pipitone)
Date: Fri, 18 Jul 2014 17:01:13 -0400
Subject: [MINC-users] debian brain-view2 package?
Message-ID: <20140718210103.GB26401@kandel.clarke-inst.on.ca>

Hey all, 

Has anyone gone through the trouble of packaging up brain-view2[1] and
dependencies for debian/ubuntu? 

I'd like to get some non-supertechnical collaborators using it and would
rather toss them .debs than anything else. 

What I'd really love is to find out is that there is a secret ubuntu ppa
out there which I could add as an apt repo. ;-)

Jon.

[1] https://wiki.mouseimaging.ca/display/MICePub/brain-view

From a.janke at gmail.com  Sun Jul 20 18:05:21 2014
From: a.janke at gmail.com (Andrew Janke)
Date: Mon, 21 Jul 2014 08:05:21 +1000
Subject: [MINC-users] debian brain-view2 package?
In-Reply-To: <20140718210103.GB26401@kandel.clarke-inst.on.ca>
References: <20140718210103.GB26401@kandel.clarke-inst.on.ca>
Message-ID: <CAG0CB21BcEcP3r831OAdO46GeVswqMqQL6Z90w9g31T_28umjw@mail.gmail.com>

> Has anyone gone through the trouble of packaging up brain-view2[1] and
> dependencies for debian/ubuntu?

Nope, not I. I used to be able to make a binary build of brain-view
(original flavour) going, but there were issues around Quarter, Coin
and bicInventor in later versions of Ubuntu.

Being CMake based Vladimir should find it a doddle to include in
minc-toolkit. :)


a

From vladimir.fonov at gmail.com  Wed Jul 23 00:26:58 2014
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 23 Jul 2014 00:26:58 -0400
Subject: [MINC-users] minc-toolkit 1.9.1 with ITK4.5 experimental release
Message-ID: <CAMCwi7PLyrapdLTtL+WrVkj4tas60n5zbLWKCFtk961-V+q-8Q@mail.gmail.com>

Hello Everybody,

I made a new experimental release of minc-toolkit with ITK 4.5 ,
available at : http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#1.9.1
ITK 4.5 was compiled with both minc1 and minc2 support.

The packaged  includes updated minctracc, which fixes slight
left-right bias in non-linear registration. Unfortunately it means
that results are going to be slightly different.

Also, it includes C3D, ANTS and Elastix.

-- 
Best regards,

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

From vladimir.fonov at gmail.com  Thu Jul 31 18:15:44 2014
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 31 Jul 2014 18:15:44 -0400
Subject: [MINC-users] bug fix in minc-toolkit with ITK4
Message-ID: <CAMCwi7N0F0ntCNy_Vf6iKq=bSuan+uwsG7mCCLyCvGOswOFmUg@mail.gmail.com>

Hello Everybody,

I fixed some bugs in my building scripts for compiling minc-toolkit
version with ITKv4 causing disabled optimization in compilation of
some libraries, most notably FFTW.

The updated version: binary packages and the source code is available
at  http://www.bic.mni.mcgill.ca/ServicesSoftware/ServicesSoftwareMincToolKit#1.9.2

-- 
Best regards,

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