It could not find any data. It is looking for something like $SUBJECTS_DIR/mine/mri/orig/001.mgz. Alternatively, you can run recon-all with -i and pass the input.

On 12/22/15 10:27 PM, abdulkawi alareefi alareefi wrote:

Hi Freesurfers,
I am currently learning how to use freesurfer to process the brain image and I acknowledge your great job. I contacting you regarding that I got an error after using recon-all command. By the way i am sill beginner in both linux and freesurer. Here is the log of the error
abdol@abdol-pc:~$ recon-all -s mine -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /home/abdol/Desktop/freesurfer/subjects
Actual FREESURFER_HOME /home/abdol/Desktop/freesurfer
-rw-rw-r-- 1 abdol abdol 100038 12月 22 10:59 /home/abdol/Desktop/freesurfer/subjects/mine/scripts/recon-all.log
Linux abdol-pc 3.13.0-73-generic #116-Ubuntu SMP Fri Dec 4 15:31:30 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
#--------------------------------------------
#@# MotionCor 2015年 12月 23日星期三 11:01:18 CST
ERROR: no run data found in /home/abdol/Desktop/freesurfer/subjects/mine/mri. Make sure to
have a volume called 001.mgz in /home/abdol/Desktop/freesurfer/subjects/mine/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 abdol-pc 3.13.0-73-generic #116-Ubuntu SMP Fri Dec 4 15:31:30 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s mine exited with ERRORS at 2015年 12月 23日星期三 11:01:18 CST

For more details, see the log file /home/abdol/Desktop/freesurfer/subjects/mine/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Regards
Abdulqawi Alarefi
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