Can you run it with --debug as the first option, capture the (large amount of) terminal output in a file, and send the file?
On 7/28/2020 1:26 PM, Erin Moe wrote:
External Email - Use CautionHi Freesurfer experts,
I ran segmentThalamicNuclei on my dataset and would like to use the segmentations on BOLD data in FSL using Featquery. I tried running vol2subfield but got an error: “set: Variable name must contain alphanumeric characters. I’ve tried a mired of other things to get the thalamic nuclei output into the mean_func.nii.gz space but haven’t had much success. What would you recommend I try?
Terminal input for vol2subfield (note the dashes are double, my email client automatically changes them to single dashes):
vol2subfield —i mean_func.nii.gz —reg $subject —$subject/mri/ThalamicNuclei.v12.T1.mgz —BOLD_thalamus.mgz
Thanks! Erin
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