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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://secure-web.cisco.com/1UQYixkLhTyJq63goY7Pg_eCT-9bgdiZTokEQSMnHq7lBQtH... 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://secure-web.cisco.com/1jEiXRrElXVtXwKhwmcYmBf1ASyXbJIhbTjDDo8znrKWXGez...
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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