CIFTI-indices of Volumetric Post-Analysis

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amirhussein.a

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Jul 3, 2021, 8:01:40 AM7/3/21
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Dear HCP users/experts,

Is there a way to identify corresponding CIFTI-indices of a FreeSurfer post-processed data from HCP-YA?

I am interested in the functional properties (both task and rest fMRI) of hypothalamic nuclei and they've been delineated by analyzing T1w/{$Subject}/nu.mgz using FreeSurfer's hypothalamic segmentation. Is there a way to identify what are the cifti-indices of each nucleus's voxels? Some sort of volume to volume mapping?

Bests,
Amir

Glasser, Matthew

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Jul 3, 2021, 8:17:47 AM7/3/21
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Someone asked me about the hypothalamus in fMRI recently.  It did not seem that there was much BOLD variance there (perhaps hypothalamic blood flow does not vary much). 

 

If the question is about subparcellating the CIFTI ventral diencephalon structure, yes that should be possible.  You would create a cifti label using the wb_command -cifti-create-label command using the output of wb_command -volume-label-import on your hypothalamic segmentation volume as the label volume and https://github.com/Washington-University/HCPpipelines/blob/master/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz as the structure label volume. 

 

Matt.

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amirhussein.a

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Jul 9, 2021, 4:33:07 AM7/9/21
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Interesting!

Thanks! I'll give it a try.

Bests,
Amir
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