Thanks
On il-Ħamis, 22 ta Fra, 2018 12:41 , Glasser, Matthew wrote:
They are in ${StudyFolder}/${Subject}/MNINonLinear/xfms
Peace,
Matt.
From: <[email protected]
<mailto:[email protected]>> on behalf of Claude
Bajada <[email protected] <mailto:[email protected]>>
Date: Thursday, February 22, 2018 at 2:50 AM
To: Timothy Coalson <[email protected] <mailto:[email protected]>>
Cc: "[email protected]
<mailto:[email protected]>" <[email protected]
<mailto:[email protected]>>
Subject: Re: [HCP-Users] Extracting Thalamus Brainordinates
Thanks Tim and Ely,
This is helpful.
Tim, I think I prefer your second suggestion (using the standard cifti
MNINonLinear group definition). I need a one to one correspondence
between every point in the thalamus across individuals and to a
template thalamus. The reason (and perhaps I need to go into more
detail of what I hope to do) is that I would like to perform
tractography seeding from every voxel (independently) in the thalamus
and then be able to project any statistics that are derived from those
tracts back onto the thalamus itself. I would like the correspondence
from beforehand since I would like to do all the projections directly
onto the template thalamus in MNI space. I also do not really need
native voxels but only a centroid coordinate for each template voxel
in native space; since I use mrtrix for my tractography.
I am also looking for the subjects' atlas warpfields but cannot seem
to find them could you point me in the right direction/directory?
Cheers,
Claude
On il-Ħamis, 22 ta Fra, 2018 01:07 , Timothy Coalson wrote:
It may be better to use the individual subject's "native space"
definitions. The files in the T1w folder are in what we refer to as
native volume space (it is actually rigidly-aligned MNI space, but
rigid alignment preserves shape, so it can be used as if it were
distortion-corrected scanner coordinates, after the appropriate
resamplings). There are aparc*+aseg.nii.gz files in that folder,
which should be the freesurfer segmentation/parcellation for that
single subject, which contains a thalamus definition.
If you prefer to use our standard cifti MNINonLinear group thalamus
definition, and work that backwards through each subject's atlas
warpfield, you can get the entire ROI of left and right thalamus by
using -cifti-separate with -volume THALAMUS_LEFT <junk> -roi
<roi-output> (and similar with RIGHT) on any small full-brain cifti
file (91282 grayordinates for 3T data), for instance the template in
the Pipelines at
global/templates/91282_Greyordinates/91282_Greyordinates.dscalar.nii .
Tim
On Wed, Feb 21, 2018 at 3:24 AM, Claude Bajada
<[email protected] <mailto:[email protected]>> wrote:
Dear all,
I would like to perform tractography seeding from the thalamus.
So as to
ensure that I have correspondence between individuals, I would
like to
use the thalamus defined in terms of the brainordinates already
used in
each participant.
I cannot find a way to identify the brainordinates that define the
thalamus and extract their voxels / MNI coordinates. Can someone
point
me in the right direction?
Regards,
Claude
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