I'm not sure what is happening. Does cortex have label value that are just not in the LUT or are the values 0? Try adding --aseg aseg.presurf.hypos If you need more help,make sure to include the full terminal output
On 6/13/2022 4:49 PM, Benjamin Deck wrote:
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Hi Freesurfer experts,
I am attempting to turn my surface-based parcellation into a segmentation file using the following command:
mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask
However, when I load the resulting volume using my custom LUT the ROIs get labeled to the white matter and subcortical structures leaving the grey matter unlabeled.
When I examine the annotation files, they look appropriate and there isn't any overlap.
Do I need to include the subcortical structures in my custom LUT to avoid this from happening or is there a better solution?
Thank you!
-- *Benjamin L. Deck* /Doctoral Student/ /Applied Cognitive and Brain Sciences/ /Department of Psychological and Brain Sciences/ /Drexel University/
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