[Freesurfer] outputs for recon-all of T1-weighted and intersubject registration

External Email - Use Caution Hi Freesurfer experts, If I just want to normalize, register, and segment the T1-weighted images to the GM, WM, and CSF tissues, can certain steps be skipped from recon-all, such as the inflation process? What is the output for the segmentation of GM,

[Freesurfer] TRACULA tutorial and processing questions

Dear FreeSurfer TRACULA experts, I am new to FreeSurfer and using TRACULA to process DTI data. From the mail-archive, I understand TRACULA mainly needs the aparc+aseg output from recon_all in order to run. Using the recon_all output information, I was able to complete the 3 steps in TRACULA, bu

[Freesurfer] Are inflated surfaces vertices transformed in Freeview?

External Email - Use Caution Hi Doug, Thank you for your help! Yes, I have followed the points using vertex indices but there were some that didn't match up. It could be because of the 1-based indexing. Where would I change this? I am using freesurfer_read_surface.m to read in the

[Freesurfer] SynthSR and Apple M1 Incompatability

Dear FreeSurfers, I have been trying to get SynthSR up and running and have come to the realisation there is a conflict with the current tools and the new apple chips (macOS Monterey, Apple M1 chip, 16GB). I have tried the workaround via this thread on the mailing list to no avail (https://www