HI Kelli
It sounds like you started running at some point but didn't get very far? Try
something like:
mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234
recon-all -subjid 1234 -i 1234.nii -autorecon1
and see if that works (then you can probably delete the saved.1234 dir if you
want)
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Kelli Ann Nini
Sent: Saturday, November 7, 2020 5:28 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon1 command
External Email - Use Caution
Greetings, esteemed Surfers! I have a .nii file that I am trying to run through
recon1 and I'm not sure I have my commands correct. At first I typed this
command line and received this error: recon-all -subjid 1234 -i 1234.nii
-autorecon1
ERROR: You are trying to re-run an existing subject with (possibly)
new input data (-i). If this is truly new input data, you should delete
the subject folder and re-run, or specify a different subject name.
If you are just continuing an analysis of an existing subject, then
omit all -i flags.
However, if I omit the -i flag, I receive this message: recon-all -subjid 1234
-autorecon1
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
INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020
Actual FREESURFER_HOME /usr/local/freesurfer
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12
17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' ->
'/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy'
#--------------------------------------------
#@# MotionCor Tue Nov 3 17:46:26 CST 2020
ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to
have a volume called 001.mgz in /home/blah/blah/blah/1234/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12
17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2556 exited with ERRORS at Tue Nov 3 17:46:26 CST 2020
For more details, see the log file
/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
It's also been approx 1 year since FS was run on our machines. Perhaps an
update is needed? Thank you so much!
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