Hi Muhammad

what kind of dicom files are those? From what scanner? Bruce

On Mon, 29 Jul 2013, Muhammad Naveed Iqbal Qureshi wrote:

Dear Community,

I got the following error every time I try to calculate the cortical thickness of my MRI data:

bmssa-desktop:~> recon-all -i /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm -subject sub02 -all -qcache &

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

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/bmssa/freesurfer/subjects Actual FREESURFER_HOME /home/bmssa/freesurfer Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /home/bmssa/freesurfer/subjects/sub02

mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz

mri_convert /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm /home/bmssa/freesurfer/subjects/sub02/mri/orig/001.mgz ERROR: cannot determine file type for /home/bmssa/freesurfer/subjects/CHR/CHR01_PJH/t1/1.3.12.2.1107.5.2.32.35413.2010042817343895747424.dcm Linux bmssa-desktop 3.5.0-36-generic #57~precise1-Ubuntu SMP Thu Jun 20 18:21:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub02 exited with ERRORS at Mon Jul 29 14:10:40 KST 2013

For more details, see the log file /home/bmssa/freesurfer/subjects/sub02/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Please guide me how to rectify this error. I have used the same command for another dataset and it was working perfectly fine.

Best Regards, Muhammad Naveed Iqbal Qureshi Ph.D. Candidate Bio-Medical Signal & System Analysis Laboratory Department of Medical System Engineering Gwangju Institute of Sciences and Technology 123, Cheomdangwagi-ro, Buk-gu, Gwangju, 500-712, Republic of Korea Tel           : +82-62-715-3266 Email       : mniqureshi@hotmail.com URL         : http://bmssa.gist.ac.kr P please don't print this e-mail unless you really need to