They are in ${StudyFolder}/${Subject}/MNINonLinear/xfms



 on behalf of Claude Bajada 
Date: Thursday, February 22, 2018 at 2:50 AM
To: Timothy Coalson <<>>
Cc: "<>" 
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?



On il-─Žamis, 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 .


On Wed, Feb 21, 2018 at 3:24 AM, Claude Bajada 
<<>> 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?



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