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
Hi Abdulqaw You need to specify an input T1-weighted volume, either explicitly with -i <volume file name/path to a single dicom file I a T1-weighted series>, or implicitly by converting the volume you want to process into mgz format and naming it 001.mgz and placing it in the orig sub directory. Cheers Bruce
On Dec 22, 2015, at 10:27 PM, abdulkawi alareefi alareefi abdulkawi3000@hotmail.com wrote:
Abdulqaw
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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abdulkawi alareefi alareefi -
Bruce Fischl -
Douglas Greve