Re: [Freesurfer] Subregion Segmentation of thalamus for TRACULA

2022-07-29 Thread Makenna B McGill
External Email - Use Caution Hi Juan, Thank you for the response! I did rename the file to ThalamicNuclei.v12.T1.FSvoxelSpace.mgz as you suggested, however I run into the following error when running trac-all prep in v7.3: trac-all -prep -c /Volumes/schnyer/Makenna/DODADNI/BIDS/d

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

2022-07-29 Thread Douglas N. Greve
Can you send us a sample case? On 7/28/2022 8:58 PM, Miriam Taza wrote: Nothing strange about them. They’re T1w scans 1x1x1mm3 *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Thursd

Re: [Freesurfer] Problem with hypothalamus subunits?

2022-07-29 Thread Iglesias Gonzalez, Juan E.
It should be identical but if you want to rerun 1 or 2 subjects for peace of mind, you should totally do it. Or even rerun your whole dataset; the algorithms runs pretty fast anyway ;-) Juan Eugenio Iglesias http://www.jeiglesias.com On Jul 28, 2022, at 16:43, Zeng, Victor (BIDMC - Keshavan - P

Re: [Freesurfer] Subregion Segmentation of thalamus for TRACULA

2022-07-29 Thread Iglesias Gonzalez, Juan E.
Dear Makenna (and rest of users) Thanks for spotting this bug, and for bearing with us while we transition to the new, Matlab-free code. Renaming should be fine for now but we’ll certainly fix this on our end ASAP. Kind regards, Juan Eugenio Iglesias http://www.jeiglesias.com On Jul 28, 2022,