[Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

External Email - Use Caution Dear FreeSurfer support team, I am running into some issues regarding the mandatory SUBJECTS_DIR writing permissions when running the hippocampal and amygdala subfields segmentation functionality

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

Dear Eva, The subfield temporary directory is under SUBJECTS_DIR, not FREESURFER_HOME. So you only need SUBJECTS_DIR to be local. Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Heese, E. van (Eva) Date: Friday, De

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

External Email - Use Caution Hi again Juan Eugenio, Thanks for your quick response. I meant to reach out again in our other trail of emails too. Changing the permissions of just the SUBJECTS_DIR does not seem sufficient, because the imagedump permission error still pops up. With

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

Sorry, I missed that detail. I’m pretty sure that the code does not write any files on FREESURFER_HOME, which makes this issue super weird! I’m CCing Jackson and Rob, in case they have any other ideas (if not, I would recommend that you simply use the local copy of FS). C heers, /E -- Juan Euge

Re: [Freesurfer] SUBJECTS_DIR writing permissions to run hippocampal/amygdala subfields

Hey Eugenio and Eva, I took a look through the code, and segmentHA_T1.sh ultimately calls a compiled version of segmentSubjectT1_autoEstimateAlveusML.m. There are a few 'mv * imageDump.mgz' calls, that look like they update the imageDump.mgz file after a transform is applied, but like Eugenio me

[Freesurfer] question regarding echo spacing and epi factor in TRACULA

Hello there, When we were trying the TRACULA tutorial, we noticed a discrepancy between the downloaded script and the wiki page. The echo spacing is set as 0.000689998 in the script, but it is exemplified in ms on the wiki page. For the epifactor, it is set as 139000.96811584961115829321 in the