External Email - Use Caution
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.tanenb...@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.
>
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