You can create a mask of the ROI using mri_annotation2label using the --seg output. Then create a mask with mri_binarize --i seg.nii.gz --match MATCHVAL --o mask.nii.gz where MATCHVAL is the ID of your ROI from $FREESURFER_HOME/FreeSurferColorLUT.txt You can then use the fslmeants command below. The one problem that might occur is that FS uses an extention to nifti that allows it to represent surface-based data. FSL might not be able to read this. If so, we can find a work-around

On 12/8/19 1:03 AM, DeCross, Stephanie N. wrote:

Hi,

How can I extract functional data (percent contrast) from an aparc ROI on the surface on a vertex-wise basis (i.e. not one value averaged across the whole ROI, but one value per vertex inside the ROI for a given contrast)? Funcroi-config/funcroi-sess/funcroi-table-sess seem to only provide values averaged across the whole ROI.

In other analysis pipelines, for a voxel-wise extraction it looks like I would use $ fslmeants -i <input 4D nii> -o <output.txt> -m <3D mask nii> --showall but I’m not sure how to do this on the surface.

Thank you, Stephanie DeCross

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