I am sorry, I just realized my email makes no sense.

I was following one of FreeSurfers webpages on how to use mideface program. It worked fine except one detail. The tutorial uses the argument "--facemask facemask.mgz", when I run the line it did not generate the facemask.mgz file. I tracked the problem to line 310 in mideface script, It should just be removed. It resets the facemask variable to the default setting despite it being handled in the parse_arg section of the script.

On Fri, Aug 9, 2024 at 2:49 PM Aaron Tanenbaum <aaron.b.tanenbaum@gmail.com> wrote:

I have been writing scripts with the mideface program. Her the exact line of code i am using.

mideface --i $Anatfolder/${mprs[0]}_T1w.nii.gz --odir $defacefolder --o $defacefolder/bids/${mprs[0]}_desc-defaced_T1w.nii.gz --pics --facemask facemask.mgz

I am using FreeSurfer 7.4 on Ubuntu 20.04 and 22.04

I noticed that it will not honor the --facemask flag. I found the exact issue is on line 310 of where it set the facemask variable. I am fine with the standard name, I was just following instructions on one of your tutorial. I just want to point this out.