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