Dear FreeSurfer team,
using the longitudinal stream in v6.0.0, I edited the cross and base runs, but still had to edit the long runs for some subjects. If I understood the LongitudinalEdits Wiki correctly, the long can still be edited if necessary.
Rerunning the respective recon-all command with -autorecon2 -autorecon3 and the edited long run as input did not work. How do I rerun the long correctly while incorporating the edits made directly to the long?
Here you see how I called the procedure:
anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ ls -lisa total 20 8527874 4 drwxrwxr-x 5 anna anna 4096 Apr 15 21:18 . 8527873 4 drwxrwxr-x 34 anna anna 4096 Apr 15 12:18 .. 8544378 4 drwxrwxr-x 10 anna anna 4096 Mär 29 23:54 11904_base 8527875 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:02 11904_T1_fs_edit.long.11904_base_edit 8527888 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:29 11904_T2_fs_edit.long.11904_base_edit anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ start=`date +%s` anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ !recon recon-all -long 11904_T1_fs_edit.long.11904_base 11904_base -autorecon2 -autorecon3
Unmatched ". anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ end=`date +%s` anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ runtime=$((end-start)) anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ echo $runtime 10
As you can see, the process ends very quickly (10s) and only gives the error 'Unmatched ".' though I did not open any double quotes when calling the procedure.
Thanks a lot for your help!
Best, Anna