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

2018-04-16 Thread Anna Daniels 
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  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
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Re: [Freesurfer] reruns recon-all -long after edits

2018-04-16 Thread Martin Reuter 
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  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 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
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] reruns recon-all -long after edits

2018-04-15 Thread Anna Daniels 
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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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.