Hi Catherine, there is something wrong with that file or else the error msg would not be generated. Make sure it is world-readable. Make sure you did not download it to a windows machine first and then copy it (if so run dos2unix on it). Look inside it and make sure you can see plain text characters. doug
On 10/05/2012 10:04 AM, Nucleos P wrote: > Hi doug! > There is a license file and the script is set up to create the 001.mgz > files using mri_convert. So, I am confused as to why I am getting > these errors to begin with? > > Thanks for getting back to me, > Catherine > On Thu, Oct 4, 2012 at 4:51 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > 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 > <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"). 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None of the names, logos or trademarks of MGH or any of > > MGH's affiliates or any of the Contributors, or any funding > > agency, may be used to endorse or promote products produced in > > whole or in part by operation of the Software or derived from or > > based on the Software without specific prior written permission > > from the applicable party. > > > > 7. Any use, reproduction or distribution of the Software which > is not > > in accordance with this Software License shall automatically > revoke > > all rights granted to you under this Software License and render > > Paragraphs 1 and 2 of this Software License null and void. > > > > 8. This Software License does not grant any rights in or to any > > intellectual property owned by MGH or any Contributor except > > those rights expressly granted hereunder. > > > > PART C. MISCELLANEOUS > > > > This Agreement shall be governed by and construed in accordance with > > the laws of The Commonwealth of Massachusetts without regard to > > principles of conflicts of law. This Agreement shall supercede and > > replace any license terms that you may have agreed to previously > with > > respect to FreeSurfer. > > > > * > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
