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:
External Email - Use Caution
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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