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
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