On il-Ħamis, 22 ta Fra, 2018 12:41 , Glasser, Matthew wrote:
They are in ${StudyFolder}/${Subject}/MNINonLinear/xfms



From: < <>> 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-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 .


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
    me in the right direction?



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