You have passed it the subject name as the registration file. You need to create a registration file (usually created with bbregister)
On 7/30/2020 2:50 PM, Erin Moe wrote:
External Email - Use Caution
Hi Doug, Thanks for the quick response. I've attached a text file of the terminal output after running vol2subfield with the --dubug option. Thanks! Erin
*From:* Erin Moe Erin.Moe@colorado.edu *Sent:* Tuesday, July 28, 2020 11:26 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Thalamic nuclei in FSL Hi 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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