Re: [Freesurfer] reruns recon-all -long after edits

Hi Martin,

thank you so much for the quick and helpful reply!

As I only edited the wm.mgz in the base, there was still some non-wm included there in the long and also some minor edits to the brainmask.mgz were necessary that I had probably overlooked in the cross.

To run this command recon-all -long 11904_T1_fs 11904_base -autorecon2 -autorecon3

do I only need to have 11904_T1_fs.long.11904_base (the edited long) and 11904_base in the subjects dir?

Or also the cross folder (11904_T1_fs)? I'm submitting the jobs from a HPC system where the upload is time-consuming.

Thanks again!

Best, Anna

---

Hi Anna, yes, long can still be edited, but usually this is not necessary. What kind of edits did you need to do in the long?

You would need to call with the long flag, and passing the cross and base name. So just like the regular processing of the -long step, only replace -all with -autorecon2 etc.

recon-all -long 11904_T1_fs 11904_base -autorecon2 -autorecon3

for this to work 11904_T1_fs.long.11904_base needs to contain your edits, so maybe backup the old long run and call it backup, then edit this one and run it. You cannot simply append the _edit or you will confuse the naming convention.

Best, Martin

On 15. Apr 2018, at 23:07, Anna Daniels anna.daniels@fu-berlin.de wrote:

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 M?r 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