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 > * > Here is the LICENSE file: > FreeSurfer Software License Agreement ("Agreement") > Version 1.0 (February 2011) > > This Agreement covers contributions to and downloads from the > FreeSurfer project ("FreeSurfer") maintained by The General Hospital > Corporation, Boston MA, USA ("MGH"). Part A of this Agreement applies to > contributions of software and/or data to FreeSurfer (including making > revisions of or additions to code and/or data already in FreeSurfer). Part > B of this Agreement applies to downloads of software and/or data from > FreeSurfer. Part C of this Agreement applies to all transactions with > FreeSurfer. If you distribute Software (as defined below) downloaded from > FreeSurfer, all of the paragraphs of Part B of this Agreement must be > included with and apply to such Software. > > Your contribution of software and/or data to FreeSurfer (including prior > to the date of the first publication of this Agreement, each a > "Contribution") and/or downloading, copying, modifying, displaying, > distributing or use of any software and/or data from FreeSurfer > (collectively, the "Software") constitutes acceptance of all of the > terms and conditions of this Agreement. If you do not agree to such > terms and conditions, you have no right to contribute your > Contribution, or to download, copy, modify, display, distribute or use > the Software. > > PART A. CONTRIBUTION AGREEMENT - License to MGH with Right to Sublicense > ("Contribution Agreement"). > > 1. As used in this Contribution Agreement, "you" means the individual > contributing the Contribution to FreeSurfer and the institution or > entity which employs or is otherwise affiliated with such > individual in connection with such Contribution. > > 2. This Contribution Agreement applies to all Contributions made to > FreeSurfer, including without limitation Contributions made prior to > the date of first publication of this Agreement. 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This Agreement shall supercede and > replace any license terms that you may have agreed to previously with > respect to FreeSurfer. > > * > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
