From sylvain at bic.mni.mcgill.ca  Mon Mar  3 12:37:28 2014
From: sylvain at bic.mni.mcgill.ca (Sylvain Milot)
Date: Mon, 3 Mar 2014 12:37:28 -0500 (EST)
Subject: [MINC-users] MRI measurements (fwd)
Message-ID: <Pine.LNX.4.64.1403031235590.11522@nestor.bic.mni.mcgill.ca>


is there anyone out there that could offer some insight ?

---------- Forwarded message ----------
Date: Thu, 27 Feb 2014 15:36:50 -1000
From: Portia Resnick <portia at hawaii.edu>
To: bicadmin at bic.mni.mcgill.ca
Subject: MRI measurements

Aloha,

I am a current PhD student who is interested in MRI research. My area is
not the brain, but the hypodermis and superficial fascia. I have been
combing the literature looking for standardization of measurement protocols
and it was suggested by a radiologist to look at hippocampus research. I
came across your measurement software and was wondering if it could be used
for musculoskeletal research as well.  If not, is there any software that
you know of that would also take volume measurements or do similar
comparisons with the musculoskeletal system.

Mahalo for your time and consideration in this matter.

Portia

-- 
Portia B. Resnick, MA, ATC, LMT
Doctoral Graduate Assistant
Department of Kinesiology and Rehabilitation Science
University of Hawaii at Manoa
portia at hawaii.edu

From rick.hoge at linev.ca  Mon Mar  3 12:39:11 2014
From: rick.hoge at linev.ca (Rick Hoge)
Date: Mon, 3 Mar 2014 17:39:11 +0000
Subject: [MINC-users] MRI measurements (fwd)
In-Reply-To: <Pine.LNX.4.64.1403031235590.11522@nestor.bic.mni.mcgill.ca>
References: <Pine.LNX.4.64.1403031235590.11522@nestor.bic.mni.mcgill.ca>
Message-ID: <65331F85-2CA1-41C7-B8ED-2EFACB824E2A@linev.ca>


OsiriX?

> On Mar 3, 2014, at 12:38 PM, "Sylvain Milot" <sylvain at bic.mni.mcgill.ca> wrote:
> 
> 
> is there anyone out there that could offer some insight ?
> 
> ---------- Forwarded message ----------
> Date: Thu, 27 Feb 2014 15:36:50 -1000
> From: Portia Resnick <portia at hawaii.edu>
> To: bicadmin at bic.mni.mcgill.ca
> Subject: MRI measurements
> 
> Aloha,
> 
> I am a current PhD student who is interested in MRI research. My area is
> not the brain, but the hypodermis and superficial fascia. I have been
> combing the literature looking for standardization of measurement protocols
> and it was suggested by a radiologist to look at hippocampus research. I
> came across your measurement software and was wondering if it could be used
> for musculoskeletal research as well.  If not, is there any software that
> you know of that would also take volume measurements or do similar
> comparisons with the musculoskeletal system.
> 
> Mahalo for your time and consideration in this matter.
> 
> Portia
> 
> -- 
> Portia B. Resnick, MA, ATC, LMT
> Doctoral Graduate Assistant
> Department of Kinesiology and Rehabilitation Science
> University of Hawaii at Manoa
> portia at hawaii.edu
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From sorench at gmail.com  Mon Mar  3 12:45:40 2014
From: sorench at gmail.com (Soren Christensen)
Date: Mon, 3 Mar 2014 09:45:40 -0800
Subject: [MINC-users] MRI measurements (fwd)
In-Reply-To: <65331F85-2CA1-41C7-B8ED-2EFACB824E2A@linev.ca>
References: <Pine.LNX.4.64.1403031235590.11522@nestor.bic.mni.mcgill.ca>
	<65331F85-2CA1-41C7-B8ED-2EFACB824E2A@linev.ca>
Message-ID: <CAHfsrRa_0fFkVUWkbK3VkJkJmKVZm2VSWPw3B3w6rJ0H23TcQw@mail.gmail.com>

Hi Portia,
 You should probably sign up to group mails to get feed back.
Maybe a little more detail on what type of analysis you will be doing will
help too. Is it just measuring volumes?  Will you be doing registrations?
I'd be cautious with Osirix volumetrics - the volume calculation is not the
usual product of voxel volumes by voxel count, but rather the volume of the
ROIs interpolated in the z direction (with a rather unusual formula if you
check the source) - it is not intended for for scattered lesions for
example.

Soren



On Mon, Mar 3, 2014 at 9:39 AM, Rick Hoge <rick.hoge at linev.ca> wrote:

>
> OsiriX?
>
> > On Mar 3, 2014, at 12:38 PM, "Sylvain Milot" <sylvain at bic.mni.mcgill.ca>
> wrote:
> >
> >
> > is there anyone out there that could offer some insight ?
> >
> > ---------- Forwarded message ----------
> > Date: Thu, 27 Feb 2014 15:36:50 -1000
> > From: Portia Resnick <portia at hawaii.edu>
> > To: bicadmin at bic.mni.mcgill.ca
> > Subject: MRI measurements
> >
> > Aloha,
> >
> > I am a current PhD student who is interested in MRI research. My area is
> > not the brain, but the hypodermis and superficial fascia. I have been
> > combing the literature looking for standardization of measurement
> protocols
> > and it was suggested by a radiologist to look at hippocampus research. I
> > came across your measurement software and was wondering if it could be
> used
> > for musculoskeletal research as well.  If not, is there any software that
> > you know of that would also take volume measurements or do similar
> > comparisons with the musculoskeletal system.
> >
> > Mahalo for your time and consideration in this matter.
> >
> > Portia
> >
> > --
> > Portia B. Resnick, MA, ATC, LMT
> > Doctoral Graduate Assistant
> > Department of Kinesiology and Rehabilitation Science
> > University of Hawaii at Manoa
> > portia at hawaii.edu
> > _______________________________________________
> > 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 thomas.funck at mail.mcgill.ca  Tue Mar  4 17:16:17 2014
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Tue, 4 Mar 2014 22:16:17 +0000
Subject: [MINC-users] Shared minc libraries on BIC server
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065317BF46E@EXMBX2010-3.campus.MCGILL.CA>

Hi, 

I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?

Thanks,

Thomas

From vladimir.fonov at gmail.com  Tue Mar  4 17:28:02 2014
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Tue, 04 Mar 2014 17:28:02 -0500
Subject: [MINC-users] Shared minc libraries on BIC server
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065317BF46E@EXMBX2010-3.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065317BF46E@EXMBX2010-3.campus.MCGILL.CA>
Message-ID: <53165372.1080909@gmail.com>

Hello,


I prefer compiling it all statically to avoid conflicts between 
different versions of minc, HDF5 and NETCDF which are floating around.

If you decide to build latest minc yourself , then I suggest using cmake 
to build it.


On 14-03-04 05:16 PM, Thomas Funck wrote:
> I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?
>
> Thanks,


-- 
Best regards,

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

From ayman.oweida at mail.mcgill.ca  Wed Mar  5 13:34:43 2014
From: ayman.oweida at mail.mcgill.ca (Ayman Oweida)
Date: Wed, 5 Mar 2014 18:34:43 +0000
Subject: [MINC-users] mritotal
In-Reply-To: <53165372.1080909@gmail.com>
References: <53F3FD0032C9CC4BA836E8F0FC289065317BF46E@EXMBX2010-3.campus.MCGILL.CA>
	<53165372.1080909@gmail.com>
Message-ID: <C11EE90B-1A5E-49DE-B450-ECF328DED4A4@mail.mcgill.ca>


I would like to execute the command mritotal from MNI_Autoreg to multiple files. 
I'm currently using it file by file.  Is there a script or command to use for applying mritotal to multiple files?

Thank you,
Ayman
McGill University

From thomas.funck at mail.mcgill.ca  Wed Mar  5 13:38:04 2014
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Wed, 5 Mar 2014 18:38:04 +0000
Subject: [MINC-users] pyminc problem getting dimension sizes
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065317BF60D@EXMBX2010-3.campus.MCGILL.CA>

Hi again,

I'm trying to read in a minc file (minc 2, float) with pyminc, but I'm getting issues with the sizes of the dimensions. Using "libminc.miget_volumes_sizes" in volumes.py I get dimensions of [932007903413L, 181L, 0L]  instead of of [181, 217, 181]  (which is what mincinfo gives me) . There appears to have been earlier issues (https://github.com/mcvaneede/pyminc/pull/5) with a discrepancy between the data type used in libpyminc2.py and minc-2.2. I tried changing "misize_t" in libpyminc2.py to c_uint, c_ulong from the default of c_ulonglong, but to no avail. 

Thanks again for any help!

Thomas


________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Wednesday, March 05, 2014 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 104, Issue 2

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. Shared minc libraries on BIC server (Thomas Funck)
   2. Re: Shared minc libraries on BIC server (Vladimir S. FONOV)


----------------------------------------------------------------------

Message: 1
Date: Tue, 4 Mar 2014 22:16:17 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Subject: [MINC-users] Shared minc libraries on BIC server
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065317BF46E at EXMBX2010-3.campus.MCGILL.CA>

Content-Type: text/plain; charset="us-ascii"

Hi,

I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?

Thanks,

Thomas

------------------------------

Message: 2
Date: Tue, 04 Mar 2014 17:28:02 -0500
From: "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
To: minc-users at bic.mni.mcgill.ca
Subject: Re: [MINC-users] Shared minc libraries on BIC server
Message-ID: <53165372.1080909 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello,


I prefer compiling it all statically to avoid conflicts between
different versions of minc, HDF5 and NETCDF which are floating around.

If you decide to build latest minc yourself , then I suggest using cmake
to build it.


On 14-03-04 05:16 PM, Thomas Funck wrote:
> I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?
>
> Thanks,


--
Best regards,

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


------------------------------

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


End of MINC-users Digest, Vol 104, Issue 2
******************************************

From zijdenbos at gmail.com  Wed Mar  5 13:50:14 2014
From: zijdenbos at gmail.com (Alex Zijdenbos)
Date: Wed, 5 Mar 2014 13:50:14 -0500
Subject: [MINC-users] mritotal
In-Reply-To: <C11EE90B-1A5E-49DE-B450-ECF328DED4A4@mail.mcgill.ca>
References: <53F3FD0032C9CC4BA836E8F0FC289065317BF46E@EXMBX2010-3.campus.MCGILL.CA>
	<53165372.1080909@gmail.com>
	<C11EE90B-1A5E-49DE-B450-ECF328DED4A4@mail.mcgill.ca>
Message-ID: <CABEEk17QbTkHAkp1AJnXBjXdpFqV9wyDnZu9XmvCwkD1ZQUBqg@mail.gmail.com>

Hi Ayman,

This is really a generic unix question, not specific to MINC; but the
simplest way to do this is to just use a command line 'for' loop. You can
do that in any number of ways, but one would be:

for f in *mnc; do xfm=`basename $f .mnc`.xfm; mritotal $f $xfm; done

That will run them in sequence; if you want to submit them to SGE or some
such, you could for example put Andrew Janke's qbatch in from of mritotal
(assuming that is available on the system you are working on).

-- A



On Wed, Mar 5, 2014 at 1:34 PM, Ayman Oweida <ayman.oweida at mail.mcgill.ca>wrote:

>
> I would like to execute the command mritotal from MNI_Autoreg to multiple
> files.
> I'm currently using it file by file.  Is there a script or command to use
> for applying mritotal to multiple files?
>
> Thank you,
> Ayman
> McGill University
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>

From matthijs at mouseimaging.ca  Wed Mar  5 13:57:23 2014
From: matthijs at mouseimaging.ca (Matthijs van Eede)
Date: Wed, 5 Mar 2014 13:57:23 -0500 (EST)
Subject: [MINC-users] pyminc problem getting dimension sizes
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065317BF60D@EXMBX2010-3.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065317BF60D@EXMBX2010-3.campus.MCGILL.CA>
Message-ID: <1657285681.1143268.1394045843816.JavaMail.root@mouseimaging.ca>

Hi Thomas, 

What version of MINC are you using? Could you give me the output of the following:

mincresample -version

Thanks,
Matthijs

----- Original Message -----
From: "Thomas Funck" <thomas.funck at mail.mcgill.ca>
To: minc-users at bic.mni.mcgill.ca
Sent: Wednesday, March 5, 2014 1:38:04 PM
Subject: [MINC-users] pyminc problem getting dimension sizes

Hi again,

I'm trying to read in a minc file (minc 2, float) with pyminc, but I'm getting issues with the sizes of the dimensions. Using "libminc.miget_volumes_sizes" in volumes.py I get dimensions of [932007903413L, 181L, 0L]  instead of of [181, 217, 181]  (which is what mincinfo gives me) . There appears to have been earlier issues (https://github.com/mcvaneede/pyminc/pull/5) with a discrepancy between the data type used in libpyminc2.py and minc-2.2. I tried changing "misize_t" in libpyminc2.py to c_uint, c_ulong from the default of c_ulonglong, but to no avail. 

Thanks again for any help!

Thomas


________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Wednesday, March 05, 2014 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 104, Issue 2

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. Shared minc libraries on BIC server (Thomas Funck)
   2. Re: Shared minc libraries on BIC server (Vladimir S. FONOV)


----------------------------------------------------------------------

Message: 1
Date: Tue, 4 Mar 2014 22:16:17 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Subject: [MINC-users] Shared minc libraries on BIC server
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065317BF46E at EXMBX2010-3.campus.MCGILL.CA>

Content-Type: text/plain; charset="us-ascii"

Hi,

I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?

Thanks,

Thomas

------------------------------

Message: 2
Date: Tue, 04 Mar 2014 17:28:02 -0500
From: "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
To: minc-users at bic.mni.mcgill.ca
Subject: Re: [MINC-users] Shared minc libraries on BIC server
Message-ID: <53165372.1080909 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello,


I prefer compiling it all statically to avoid conflicts between
different versions of minc, HDF5 and NETCDF which are floating around.

If you decide to build latest minc yourself , then I suggest using cmake
to build it.


On 14-03-04 05:16 PM, Thomas Funck wrote:
> I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?
>
> Thanks,


--
Best regards,

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


------------------------------

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


End of MINC-users Digest, Vol 104, Issue 2
******************************************
_______________________________________________
MINC-users at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From thomas.funck at mail.mcgill.ca  Wed Mar  5 14:02:57 2014
From: thomas.funck at mail.mcgill.ca (Thomas Funck)
Date: Wed, 5 Mar 2014 19:02:57 +0000
Subject: [MINC-users] SOLVED: pyminc problem getting dimension sizes
Message-ID: <53F3FD0032C9CC4BA836E8F0FC289065317BF62B@EXMBX2010-3.campus.MCGILL.CA>

Fixed my problem.  Just had to change  <int_sizes = c_ulonglong * 5>  to <int_sizes = c_unit * 5> in libpyminc2.py

Thomas

________________________________________
From: Thomas Funck
Sent: Wednesday, March 05, 2014 1:38 PM
To: minc-users at bic.mni.mcgill.ca
Subject: pyminc problem getting dimension sizes

Hi again,

I'm trying to read in a minc file (minc 2, float) with pyminc, but I'm getting issues with the sizes of the dimensions. Using "libminc.miget_volumes_sizes" in volumes.py I get dimensions of [932007903413L, 181L, 0L]  instead of of [181, 217, 181]  (which is what mincinfo gives me) . There appears to have been earlier issues (https://github.com/mcvaneede/pyminc/pull/5) with a discrepancy between the data type used in libpyminc2.py and minc-2.2. I tried changing "misize_t" in libpyminc2.py to c_uint, c_ulong from the default of c_ulonglong, but to no avail.

Thanks again for any help!

Thomas


________________________________________
From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
Sent: Wednesday, March 05, 2014 12:00 PM
To: minc-users at bic.mni.mcgill.ca
Subject: MINC-users Digest, Vol 104, Issue 2

Send MINC-users mailing list submissions to
        minc-users at bic.mni.mcgill.ca

To subscribe or unsubscribe via the World Wide Web, visit
        http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
or, via email, send a message with subject or body 'help' to
        minc-users-request at bic.mni.mcgill.ca

You can reach the person managing the list at
        minc-users-owner at bic.mni.mcgill.ca

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MINC-users digest..."


Today's Topics:

   1. Shared minc libraries on BIC server (Thomas Funck)
   2. Re: Shared minc libraries on BIC server (Vladimir S. FONOV)


----------------------------------------------------------------------

Message: 1
Date: Tue, 4 Mar 2014 22:16:17 +0000
From: Thomas Funck <thomas.funck at mail.mcgill.ca>
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Subject: [MINC-users] Shared minc libraries on BIC server
Message-ID:
        <53F3FD0032C9CC4BA836E8F0FC289065317BF46E at EXMBX2010-3.campus.MCGILL.CA>

Content-Type: text/plain; charset="us-ascii"

Hi,

I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?

Thanks,

Thomas

------------------------------

Message: 2
Date: Tue, 04 Mar 2014 17:28:02 -0500
From: "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
To: minc-users at bic.mni.mcgill.ca
Subject: Re: [MINC-users] Shared minc libraries on BIC server
Message-ID: <53165372.1080909 at gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hello,


I prefer compiling it all statically to avoid conflicts between
different versions of minc, HDF5 and NETCDF which are floating around.

If you decide to build latest minc yourself , then I suggest using cmake
to build it.


On 14-03-04 05:16 PM, Thomas Funck wrote:
> I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?
>
> Thanks,


--
Best regards,

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


------------------------------

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


End of MINC-users Digest, Vol 104, Issue 2
******************************************

From vladimir.fonov at gmail.com  Wed Mar  5 15:11:32 2014
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 05 Mar 2014 15:11:32 -0500
Subject: [MINC-users] SOLVED: pyminc problem getting dimension sizes
In-Reply-To: <53F3FD0032C9CC4BA836E8F0FC289065317BF62B@EXMBX2010-3.campus.MCGILL.CA>
References: <53F3FD0032C9CC4BA836E8F0FC289065317BF62B@EXMBX2010-3.campus.MCGILL.CA>
Message-ID: <531784F4.7050107@gmail.com>

Hello,

I would imagine that pyminc was adapted to work with develop version of 
MINC2 ( https://github.com/BIC-MNI/libminc/tree/develop )

there : 
https://github.com/BIC-MNI/libminc/blob/develop/libsrc2/minc2_api.h#L552

which defined these parameters as misize_t , which is actually hsize_t 
from HDF5 
(http://www.hdfgroup.org/HDF5/doc/TechNotes/BigDataSmMach.html) which is 
in turn  unsigned long long


Previous version : 
https://github.com/BIC-MNI/libminc/blob/master/libsrc2/minc2.h#L315


On 14-03-05 02:02 PM, Thomas Funck wrote:
> Fixed my problem.  Just had to change  <int_sizes = c_ulonglong * 5>  to <int_sizes = c_unit * 5> in libpyminc2.py
>
> Thomas
>
> ________________________________________
> From: Thomas Funck
> Sent: Wednesday, March 05, 2014 1:38 PM
> To: minc-users at bic.mni.mcgill.ca
> Subject: pyminc problem getting dimension sizes
>
> Hi again,
>
> I'm trying to read in a minc file (minc 2, float) with pyminc, but I'm getting issues with the sizes of the dimensions. Using "libminc.miget_volumes_sizes" in volumes.py I get dimensions of [932007903413L, 181L, 0L]  instead of of [181, 217, 181]  (which is what mincinfo gives me) . There appears to have been earlier issues (https://github.com/mcvaneede/pyminc/pull/5) with a discrepancy between the data type used in libpyminc2.py and minc-2.2. I tried changing "misize_t" in libpyminc2.py to c_uint, c_ulong from the default of c_ulonglong, but to no avail.
>
> Thanks again for any help!
>
> Thomas
>
>
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca [minc-users-bounces at bic.mni.mcgill.ca] on behalf of minc-users-request at bic.mni.mcgill.ca [minc-users-request at bic.mni.mcgill.ca]
> Sent: Wednesday, March 05, 2014 12:00 PM
> To: minc-users at bic.mni.mcgill.ca
> Subject: MINC-users Digest, Vol 104, Issue 2
>
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> Today's Topics:
>
>     1. Shared minc libraries on BIC server (Thomas Funck)
>     2. Re: Shared minc libraries on BIC server (Vladimir S. FONOV)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 4 Mar 2014 22:16:17 +0000
> From: Thomas Funck <thomas.funck at mail.mcgill.ca>
> To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] Shared minc libraries on BIC server
> Message-ID:
>          <53F3FD0032C9CC4BA836E8F0FC289065317BF46E at EXMBX2010-3.campus.MCGILL.CA>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?
>
> Thanks,
>
> Thomas
>
> ------------------------------
>
> Message: 2
> Date: Tue, 04 Mar 2014 17:28:02 -0500
> From: "Vladimir S. FONOV" <vladimir.fonov at gmail.com>
> To: minc-users at bic.mni.mcgill.ca
> Subject: Re: [MINC-users] Shared minc libraries on BIC server
> Message-ID: <53165372.1080909 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello,
>
>
> I prefer compiling it all statically to avoid conflicts between
> different versions of minc, HDF5 and NETCDF which are floating around.
>
> If you decide to build latest minc yourself , then I suggest using cmake
> to build it.
>
>
> On 14-03-04 05:16 PM, Thomas Funck wrote:
>> I want to use pyminc, but I can't seem locate shared minc libraries on the BIC server. Do you I just need to recompile minc on my own terminal with the "--enable=shared" flag or there some way around this (maybe using pyminc with static libraries)?
>>
>> Thanks,
>
>
> --
> Best regards,
>
>    Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
>
>
> ------------------------------
>
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> End of MINC-users Digest, Vol 104, Issue 2
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-- 
Best regards,

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

From jon at pipitone.ca  Wed Mar 12 15:27:34 2014
From: jon at pipitone.ca (Jon Pipitone)
Date: Wed, 12 Mar 2014 15:27:34 -0400
Subject: [MINC-users] Software Carpentry workshops, Montreal, QC. April 14-15
Message-ID: <20140312192727.GB28735@kimsrv.clarke-inst.on.ca>

Hi all, 

This a project I've been involved with for a long time now. The goal is
to build up the computing skills of researchers in all disciplines so
that they can do better science. 

I thought I'd share this with you all, since I figure these workshops
may be of relevance to MINC users and perhaps your
colleagues/collaborators. 

Jon.

----- Forwarded message from Greg Wilson <gvwilson at software-carpentry.com> -----

> Hello,
> 
> I hope you don't mind mail out of the blue, but I was hoping you could let your graduate students and faculty know about some Software Carpentry workshops that are taking place in Montreal on April 14-15.  Our aim is to teach researchers in science, engineering, medicine, and related fields the basic computing skills they need to get more done in less time, and with less pain.  Founded in 1998, we are now part of the Mozilla Foundation, and in 2013 we ran almost 100 workshops for more than 3500 people in 12 countries - you can find out more at http://software-carpentry.org.
> 
> We will be running four separate events in Montreal:
> 
> * A two-workshop on April 14-15 that will cover the Unix shell, programming in Python, version control, and data management: http://www.eventbrite.com/e/montreal-software-carpentry-bootcamp-registration-10151376039
> 
> * A similar workshop on the same days for research librarians: http://www.eventbrite.com/e/software-skills-for-librarians-registration-10812972893
> 
> * A one-day master class in next-generation sequencing on April 14: http://www.eventbrite.com/e/master-class-in-next-generation-sequencing-registration-10151618765
> 
> * A one-day class on R for people who already know how to program in some other language on April 15: http://www.eventbrite.com/e/r-for-programmers-registration-10319320365
> 
> There are more details at http://pycon.blogspot.ca/2014/02/software-carpentry-at-pycon.html, and if you or your colleagues would like more information, please give us a shout at admin at software-carpentry.org.  (We'd also be happy to talk about putting on other events in the summer or fall if it would be helpful.)
> 
> Thanks for your time,
> Dr. Greg Wilson
> Mozilla Foundation / Software Carpentry

> Mes salutations,
> 
> J'esp?re que ?a ne vous d?range pas que je vous envoie un courriel ? l'improviste, mais je vous prie de notifier vos ?tudiants de cycles sup?rieurs ? assister aux ateliers Software Carpentry qui auront lieu le 14 et 15 avril ? Montr?al. Notre but est d'instruire des chercheurs en science, g?nie, m?decine, et des domaines connect?s les aptitudes informatiques de base n?cessaires pour faire plus, en moins de temps, et avec moins de douleur. Fond? en 1998, nous faisons maintenant parti de la Fondation Mozilla, et en 2013 on a organis? pr?s de 100 ateliers pour plus de 3,500 personnes dans 12 pays. Vous pouvez en savoir plus ? http://software-carpentry.org.
> 
> On organise quatre ?v?nements s?par?s ? Montr?al:
> 
> * Un atelier en deux jours le 14-15 avril qui couvre le shell Unix, la programmation en Python, la gestion et contr?le de versions, et la gestion des donn?s: http://www.eventbrite.com/e/montreal-software-carpentry-bootcamp-registration-10151376039
> 
> * Un atelier similaire, durant les m?mes jours pour les biblioth?caires de recherche: http://www.eventbrite.com/e/software-skills-for-librarians-registration-10812972893
> 
> * Une classe de ma?tre en s?quen?age de prochaine g?n?ration le 14 avril: http://www.eventbrite.com/e/master-class-in-next-generation-sequencing-registration-10151618765
> 
> * Une classe d'un jour en R pour ceux qui savent d?j? programmer dans d'autres languages le 15 avril: http://www.eventbrite.com/e/r-for-programmers-registration-10319320365
> 
> Pour plus de d?tail, visitez http://pycon.blogspot.ca/2014/02/software-carpentry-at-pycon.html, et si vous ou vos coll?gues voudrez plus d'information, contactez nous ? admin at software-carpentry.org. (On sera ?galement ravi de parler de l'organisation d'autres ?v?nements en ?t? ou en automne s'il serait utile.)
> 
> Merci pour votre temps,
> Dr. Greg Wilson
> La Fondation Mozilla / Software Carpentry


----- End forwarded message -----