Hello all,

I made edits to the brainmask and wm of a base image (in the longitudinal stream) and am getting stuck when trying to re-process recon-all. Specifically, I can't seem to get the -make flag to work. I think it is probably either a silly error on my part or perhaps -make isn't designed for base edits? The command and error output are below.

Thanks in advance,
Emily


This is the command I ran on an HPC:
recon-all -base template_${SGE_TASK_ID} -tp T1_$SGE_TASK_ID -tp T2_$SGE_TASK_ID -make all

This is the error message:
Running on compute-0-0.local
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
rm: cannot remove `/share/aeg58/Freesurfer/4047_both/template_4047/scripts/patchdir.txt': Permission denied
cp: cannot create regular file `/share/aeg58/Freesurfer/4047_both/template_4047/scripts/lastcall.build-stamp.txt': Permission denied
Subject 'template_4047': make all
recon-all -s /share/aeg58/Freesurfer/4047_both/template_4047 -nuintensitycor

ERROR: It appears that this subject ID is an existing
       base/template from longitudinal processing (-base):
       template_4047
       If you are trying to re-run a -base template you
       need to pass the -base and all -tp flags: 

       \' -base <templateid> -tp <tpNid> ... -all \'

       (Instead of -all you can pass other flags, such
       as -autorecon2 -autorecon3 to run only parts.)
make: *** [/share/aeg58/Freesurfer/4047_both/template_4047/mri/nu.mgz] Error 1