From jp at biospective.com  Mon Sep 25 17:07:54 2017
From: jp at biospective.com (Jean-Philippe Coutu)
Date: Mon, 25 Sep 2017 17:07:54 -0400
Subject: [MINC-users] pyminc and minc header
Message-ID: <CANHs=MfukQRgZGVFi1_oxUZEXp29zJAgSkkua_dG-VU0OyE05w@mail.gmail.com>

Dear MINC users,

I have been trying to find information on how to query arbitrary header
attributes of MINC files using pyminc. For instance, if I wanted the
acquisition:protocol attribute, is there a way for me to do so using
pyminc? I was able to find a way using h5py, but would prefer to do it
through pyminc if possible.

I have noticed the function libminc.miget_attr_values() is used to get the
minc history. I assume something similar could exist to fetch an arbitrary
header attribute (or all of them)?

Thank you,
Jean-Philippe

From bert at phalarope.com  Tue Sep 26 12:55:57 2017
From: bert at phalarope.com (Robert D. Vincent)
Date: Tue, 26 Sep 2017 12:55:57 -0400
Subject: [MINC-users] pyminc and minc header
In-Reply-To: <CANHs=MfukQRgZGVFi1_oxUZEXp29zJAgSkkua_dG-VU0OyE05w@mail.gmail.com>
References: <CANHs=MfukQRgZGVFi1_oxUZEXp29zJAgSkkua_dG-VU0OyE05w@mail.gmail.com>
Message-ID: <CAAd5DeSM-mn3ORUx4xzrZJEa0Pj2K9Cxb2PgdxaNaLTpgfP7yQ@mail.gmail.com>

Hi Jean-Philippe,

I am not a pyminc expert, but I would think that miget_attr_values() should
do the trick. I wrote a little demonstration program to check this and it
seems to work.

    -bert

On Mon, Sep 25, 2017 at 5:07 PM, Jean-Philippe Coutu <jp at biospective.com>
wrote:

> Dear MINC users,
>
> I have been trying to find information on how to query arbitrary header
> attributes of MINC files using pyminc. For instance, if I wanted the
> acquisition:protocol attribute, is there a way for me to do so using
> pyminc? I was able to find a way using h5py, but would prefer to do it
> through pyminc if possible.
>
> I have noticed the function libminc.miget_attr_values() is used to get the
> minc history. I assume something similar could exist to fetch an arbitrary
> header attribute (or all of them)?
>
> Thank you,
> Jean-Philippe
> _______________________________________________
> 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 Sep 27 11:42:57 2017
From: trisanna.sprung-much at mail.mcgill.ca (Trisanna Sprung-Much)
Date: Wed, 27 Sep 2017 11:42:57 -0400
Subject: [MINC-users] sulcal probability map
Message-ID: <CAG+ToRtdan+q=KuYL0qopKBiz751R1O+9_VBAquErQp-n+NeNw@mail.gmail.com>

Hi there

I have generated a SPAM of a sulcus of interest (across 40 subjects) and am
using Matlab to find the voxel with the greatest overlap. However, when I
open the map in DISPLAY and go to this voxel coordinate it is showing a
voxel that does not have max colour. You will notice, however that the
maximum % is the same across Matlab and DISPLAY. Please see the snapshots
attached.

*The function I am using has the following steps:*

niak_read_minc
and then [max_val,ind] = max(vol(:));
[x,y,z] = ind2sub(size(vol),ind);

I then multiple the coordinates by a matrix to go from voxel to world.

Why would Matlab and DISPLAY be giving me different results? Any help would
be greatly appreciated.

many thanks

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