[Freesurfer] re-running recon-all after aseg.presurf.mgz edits

External Email - Use Caution A few quick questions FS experts. I made manual edits on subcortical structures in outputs from FS6.0. Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using: recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3 Do the upd

[Freesurfer] Extracting cortical thickness values for each subject using labels

External Email - Use Caution Hi I have made custom labels to use as ROIs, I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files, So from the lh.thickness.fwhm0.fsaverage.mgh file,

Re: [Freesurfer] recon-all ends with error

External Email - Use Caution It looks like you started recon-all by copying in mri/orig/001.mgz. I saw multiple runs of recon-all that were run on top of each other. Can you try to restart clean by providing the input on the command line ‘recon-all -s -I -all’? Best, Yujing

Re: [Freesurfer] Longitudinal structural analysis in FreeSurfer ???

External Email - Use Caution Hi Bruce, Cool! Thank you so much. Best wishes, Hamied From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce R.,PHD Sent: Tuesday, June 27, 2023 8:29 PM To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal struct