From gdevenyi at gmail.com  Tue Dec  2 11:47:40 2014
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 2 Dec 2014 11:47:40 -0500
Subject: [MINC-users] mni.cortical.statistics download?
Message-ID: <CAFQOoOqU_YKUd2QEqVx6EbLtAwHsNN84NGzKcL2xFBzSgoJg-A@mail.gmail.com>

The main page of mni.cortical.statistics mentioned
http://www.bic.mni.mcgill.ca/users/jason/cortex/statistics.html

and at some points on the mailing list doesn't seem to exist anymore.

Does the download for mni.cortical.statistics still exist?

I know RMINC can do a lot of this now, but I've inherited some code that
already uses it, and I'll need to have that version working before I can
port it.

Can someone please share? Thanks

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

From claude at bic.mni.mcgill.ca  Tue Dec  2 12:03:58 2014
From: claude at bic.mni.mcgill.ca (Claude LEPAGE)
Date: Tue, 2 Dec 2014 12:03:58 -0500
Subject: [MINC-users] mni.cortical.statistics download?
In-Reply-To: <CAFQOoOqU_YKUd2QEqVx6EbLtAwHsNN84NGzKcL2xFBzSgoJg-A@mail.gmail.com>
Message-ID: <201412021703.sB2H3wNG017871@agrippa.bic.mni.mcgill.ca>

Hi,

I placed mni_cortical_statistics-0.9.4.tar.gz in:
http://packages.bic.mni.mcgill.ca/tgz/ with the other
archives. 

Claude

From gdevenyi at gmail.com  Tue Dec  2 12:06:59 2014
From: gdevenyi at gmail.com (Gabriel A. Devenyi)
Date: Tue, 2 Dec 2014 12:06:59 -0500
Subject: [MINC-users] mni.cortical.statistics download?
In-Reply-To: <201412021703.sB2H3wNG017871@agrippa.bic.mni.mcgill.ca>
References: <CAFQOoOqU_YKUd2QEqVx6EbLtAwHsNN84NGzKcL2xFBzSgoJg-A@mail.gmail.com>
	<201412021703.sB2H3wNG017871@agrippa.bic.mni.mcgill.ca>
Message-ID: <CAFQOoOreBvB9MddAuXz28EmVwc4EwG=MY9duYi+Om+w3+M3pkA@mail.gmail.com>

Thanks!

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

On Tue, Dec 2, 2014 at 12:03 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca>
wrote:

> Hi,
>
> I placed mni_cortical_statistics-0.9.4.tar.gz in:
> http://packages.bic.mni.mcgill.ca/tgz/ with the other
> archives.
>
> Claude
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From zijdenbos at gmail.com  Mon Dec  8 10:28:31 2014
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Mon, 8 Dec 2014 10:28:31 -0500
Subject: [MINC-users] Getopt::Tabular source distribution
Message-ID: <CABEEk14EcEKTVhsyF03Dy4OJ3Q5dX8VtwqR_yjq42HGywn=O-A@mail.gmail.com>

Hello all,

I was wondering if anybody knows where Getopt::Tabular lives; or rather,
how best to contribute to it. We've made a number of
improvements/extensions to it, so far implemented as wrappers or companion
subs (e.g., the ability to collect arbitrary-length lists, the ability to
suppress/expose options on the fly, or the ability to collect data into a
hashes) that I hope to integrate into Getopt::Tabular itself and contribute
back to the original distribution.

It's available on CPAN, but hasn't changed there since 1997. It also exists
on github as part of the MINC toolkit:

https://github.com/BIC-MNI/minc-toolkit/tree/master/perl-modules/Getopt-Tabular-0.3

Should the latter be *the* place to contribute to? If so, who updates CPAN,
and how?

Greg, you there? :-)

-- A

From bert at bic.mni.mcgill.ca  Mon Dec  8 10:56:31 2014
From: bert at bic.mni.mcgill.ca (Robert VINCENT)
Date: Mon, 8 Dec 2014 10:56:31 -0500 (EST)
Subject: [MINC-users] Getopt::Tabular source distribution
In-Reply-To: <CABEEk14EcEKTVhsyF03Dy4OJ3Q5dX8VtwqR_yjq42HGywn=O-A@mail.gmail.com>
References: <CABEEk14EcEKTVhsyF03Dy4OJ3Q5dX8VtwqR_yjq42HGywn=O-A@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.1412081054420.20267@agrippa.bic.mni.mcgill.ca>

Hi Alex,

I assume that the Github repository is the only active repository for the 
source code. I would be happy to add updating CPAN to my occasional todo 
list, esp. if somebody (Greg?) who knows how the process works can 
enlighten me.

     -bert

On Mon, 8 Dec 2014, Alex Zijdenbos wrote:

> Hello all,
>
> I was wondering if anybody knows where Getopt::Tabular lives; or rather,
> how best to contribute to it. We've made a number of
> improvements/extensions to it, so far implemented as wrappers or companion
> subs (e.g., the ability to collect arbitrary-length lists, the ability to
> suppress/expose options on the fly, or the ability to collect data into a
> hashes) that I hope to integrate into Getopt::Tabular itself and contribute
> back to the original distribution.
>
> It's available on CPAN, but hasn't changed there since 1997. It also exists
> on github as part of the MINC toolkit:
>
> https://github.com/BIC-MNI/minc-toolkit/tree/master/perl-modules/Getopt-Tabular-0.3
>
> Should the latter be *the* place to contribute to? If so, who updates CPAN,
> and how?
>
> Greg, you there? :-)
>
> -- A
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Mon Dec  8 11:00:20 2014
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Mon, 8 Dec 2014 11:00:20 -0500
Subject: [MINC-users] Getopt::Tabular source distribution
In-Reply-To: <Pine.LNX.4.64.1412081054420.20267@agrippa.bic.mni.mcgill.ca>
References: <CABEEk14EcEKTVhsyF03Dy4OJ3Q5dX8VtwqR_yjq42HGywn=O-A@mail.gmail.com>
	<Pine.LNX.4.64.1412081054420.20267@agrippa.bic.mni.mcgill.ca>
Message-ID: <C970CFE0-8E31-4EDD-83F6-3682419A3E9C@gmail.com>

Hello,

note that https://github.com/BIC-MNI/minc-toolkit/tree/master/perl-modules - is not a repository on it?s own - it is a part of minc-toolkit. I would think we need to move https://github.com/BIC-MNI/minc-toolkit/tree/master/perl-modules/Getopt-Tabular-0.3 into a  https://github.com/BIC-MNI/Getopt-Tabular and make it a separate git repository. 

On Dec 8, 2014, at 10:56 AM, Robert VINCENT <bert at bic.mni.mcgill.ca> wrote:

> Hi Alex,
> 
> I assume that the Github repository is the only active repository for the source code. I would be happy to add updating CPAN to my occasional todo list, esp. if somebody (Greg?) who knows how the process works can enlighten me.
> 
>    -bert
> 
> On Mon, 8 Dec 2014, Alex Zijdenbos wrote:
> 
>> Hello all,
>> 
>> I was wondering if anybody knows where Getopt::Tabular lives; or rather,
>> how best to contribute to it. We've made a number of
>> improvements/extensions to it, so far implemented as wrappers or companion
>> subs (e.g., the ability to collect arbitrary-length lists, the ability to
>> suppress/expose options on the fly, or the ability to collect data into a
>> hashes) that I hope to integrate into Getopt::Tabular itself and contribute
>> back to the original distribution.
>> 
>> It's available on CPAN, but hasn't changed there since 1997. It also exists
>> on github as part of the MINC toolkit:
>> 
>> https://github.com/BIC-MNI/minc-toolkit/tree/master/perl-modules/Getopt-Tabular-0.3
>> 
>> Should the latter be *the* place to contribute to? If so, who updates CPAN,
>> and how?
>> 
>> Greg, you there? :-)
>> 
>> -- A
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

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





From thomas.funck at mail.mcgill.ca  Fri Dec 12 20:41:55 2014
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Sat, 13 Dec 2014 01:41:55 +0000
Subject: [MINC-users] arguments to "miget_real_value_hyperslab"
Message-ID: <53F3FD0032C9CC4BA836E8F0FC2890653181C7B9@EXMBX2010-3.campus.MCGILL.CA>

Hi,

I recently updated my version of minc with the latest version on github and have come across the following problem. I want to read a hyperslab with '
miget_real_value_hyperslab", but I get this warning:

minc_helper.c:285:9: warning: passing argument 4 of ?miget_real_value_hyperslab? from incompatible pointer type [enabled by default]
         if(miget_real_value_hyperslab( img, MI_TYPE_DOUBLE, volume->wstarts, volume->wcount, volume->data) != MI_NOERROR) {
         ^
In file included from /usr/local/include/minc2.h:12:0,
                 from minc_helper.h:9,
                 from minc_helper.c:1:
/usr/local/include/minc2_api.h:1116:5: note: expected ?const misize_t *? but argument is of type ?long int *?


According to the documentation for the API (1), the "sizes" argument should be "long []", so why does the compiler complain that I'm not giving it a
?const misize_t *??


Thanks,

Thomas

(1) http://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_Application_Programmers_Interface#miget_real_value_hyperslab

From steve at sumost.ca  Sat Dec 13 18:54:28 2014
From: steve at sumost.ca (Steve M. Robbins)
Date: Sat, 13 Dec 2014 17:54:28 -0600
Subject: [MINC-users] arguments to "miget_real_value_hyperslab"
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC2890653181C7B9@EXMBX2010-3.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC2890653181C7B9@EXMBX2010-3.campus.MCGILL.CA>
Message-ID: <9786094.yBAPS9ZL4J@riemann>

On December 13, 2014 01:41:55 AM Thomas Funck wrote:
> Hi,
> 
> I recently updated my version of minc with the latest version on github and
> have come across the following problem. I want to read a hyperslab with '
> miget_real_value_hyperslab", but I get this warning:
> 
> minc_helper.c:285:9: warning: passing argument 4 of
> ?miget_real_value_hyperslab? from incompatible pointer type [enabled by
> default] if(miget_real_value_hyperslab( img, MI_TYPE_DOUBLE,
> volume->wstarts, volume->wcount, volume->data) != MI_NOERROR) { ^
> In file included from /usr/local/include/minc2.h:12:0,
>                  from minc_helper.h:9,
>                  from minc_helper.c:1:
> /usr/local/include/minc2_api.h:1116:5: note: expected ?const misize_t *? but
> argument is of type ?long int *?
> 
> 
> According to the documentation for the API (1), the "sizes" argument should
> be "long []", so why does the compiler complain that I'm not giving it a
> ?const misize_t *??

I guess the documentation is simply lagging the code: the header [1] does 
indicate that arguments 3 and 4 are type "const misize_t*".

-Steve

[1]  https://github.com/BIC-MNI/libminc/blob/master/libsrc2/minc2_api.h



From zijdenbos at gmail.com  Tue Dec 30 11:27:49 2014
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Tue, 30 Dec 2014 11:27:49 -0500
Subject: [MINC-users] mincresample -keep_real_range on float volume
Message-ID: <CABEEk16-c3mJuJ1PMsUPHun06JpD9ygjKiXBGMfXo1FCOa1bqA@mail.gmail.com>

Hi all,

It appears that running mincresample on a float volume while using
-keep_real_range, fails. A simple example:

$ mincreshape -float
/usr/local/bic/share/mni-models/icbm_avg_152_t1_tal_lin.mnc float.mnc
$ mincstats -quiet -min -max float.mnc
236.8016205
439776.2188

$ mincresample -keep_real_range float.mnc float_res.mnc
$ mincstats -quiet -min -max float_res.mnc
1.797693135e+308
-1.797693135e+308

Leaving aside why you'd want to use that option on a float volume (happened
buried in a script in my case); what should the correct behaviour be?
Ignore the -keep_real_range option for float volumes I'd imagine?

Happy 2015 in advance!

:-)

-- A