Did you follow the instructions in the error message? doug
On 10/04/2012 04:46 PM, Nucleos P wrote:
I am currently using a Linux Workstation with Redhat. I recently installed Freesurfer on this computer. It works fine on the other computers... These are the errors I am getting: (The important points are in Bold)
proc_fs test_mgi MGI2 #############start: /usr/local/freesurfer/bin/proc_fs Thu Oct 4 16:31:57 EDT 2012 ################# #############start: recon-all Thu Oct 4 16:31:57 EDT 2012 ################ Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/MGI2 Actual FREESURFER_HOME /usr/local/freesurfer Linux goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/MGI2/test_mgi
- mri_convert
/usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562 /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562 /usr/local/freesurfer/subjects/MGI2/test_mgi/mri/orig/001.mgz *
ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /usr/local/freesurfer/subjects/scan_todo/test_mgi/raw/MR.1.3.12.2.1107.5.2.32.35216.2012050713483330738693562... #-------------------------------------------- #@# MotionCor Thu Oct 4 16:32:16 EDT 2012 *ERROR: no run data found in /usr/local/freesurfer/subjects/MGI2/test_mgi/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/MGI2/test_mgi/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 goodman 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s test_mgi exited with ERRORS at Thu Oct 4 16:32:16 EDT 2012
For more details, see the log file /usr/local/freesurfer/subjects/MGI2/test_mgi/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
#############end: Thu Oct 4 16:32:16 EDT 2012 ################# [prasad@goodman scan_todo]$
*The mri_convert is supposed to create the mri/orig/001.mgz file and works on the other workstations...
Here is the script in detail:
#!/bin/tcsh ####################################################### # Program: proc_fs # # Author: Dhruman Goradia # # Date: 09/19/2010 # # Description: Runs freesurfer preprocessing # ####################################################### set program = $0 echo "#############start: $program `date` #################" if ( $#argv != 2 ) then echo "${program}: Wrong no of arguments" echo "Usage: ${program} dicomdir fs_subdir" exit endif set dirdcm = "/usr/local/freesurfer/subjects/scan_todo" set fs_subid = $1 set study_id = $2 set file1 = `ls ${dirdcm}/${fs_subid}/raw | head -n 1` setenv SUBJECTS_DIR "/usr/local/freesurfer/subjects/${study_id}" echo "#############start: recon-all `date` ################" if ( -f ${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz) then recon-all -s $fs_subid -all else *#mkdir -p ${SUBJECTS_DIR}/${fs_subid}/mri/orig #mri_convert ${dirdcm}/${fs_subid}/raw/${file1} ${SUBJECTS_DIR}/${fs_subid}/mri/orig/001.mgz recon-all -i ${dirdcm}/${fs_subid}/raw/${file1} -s $fs_subid -all* endif echo "#############end: `date` #################" exit
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