From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu>
Sent: Sunday, November 8, 2020 10:07 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon1 command

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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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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.

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 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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