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Hello Paulo, What is the location of the freesurfer license file (?), i.e., I would make sure the freesurfer license file is under $FREESURFER_HOME and then see if you get different results running the command. Even with the license file though, I’m not sure all the Freesurfer 4 binaries will run on Ubuntu 18 - R. On Nov 19, 2019, at 15:26, Baptista, Paulo <paulo_baptista@brown.edu> wrote: External Email - Use Caution Hello FreeSurfer Developers,I am helping a researcher in my department run FreeSurfer on a new computer. They insist that it should run on FreeSurfer 4.5 because their old system ran that version. Is the following possible? We can run FreeSurfer 6.0 fine, but they say there are differences between the versions. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full 2) Platform: Ubuntu 18.04.1 LTS 3) uname -a: Linux clps-pb1 4.15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: n/a Segmentation Fault - see below(base) root@clps-pb1:/var/tmp# cd freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# lsASegStatsLUT.txt DefectLUT.txt FreeSurferEnv.sh mni Simple_surface_labels2009.txtAUTHORS diffusion fsafd SegmentNoLUT.txt subjectsaverage docs fsfast sessions tkmeditParcColorsCMAbin FreeSurferColorLUT.txt lib SetUpFreeSurfer.cshbuild-stamp.txt FreeSurferEnv.csh matlab SetUpFreeSurfer.sh(base) root@clps-pb1:/var/tmp/freesurfer4# export FREESURFER_HOME=/var/tmp/freesurfer4(base) root@clps-pb1:/var/tmp/freesurfer4# source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /var/tmp/freesurfer4FSFAST_HOME /var/tmp/freesurfer4/fsfastFSF_OUTPUT_FORMAT niiSUBJECTS_DIR /var/tmp/freesurfer4/subjectsMNI_DIR /var/tmp/freesurfer4/mni(base) root@clps-pb1:/var/tmp/freesurfer4# cd ..(base) root@clps-pb1:/var/tmp# cd f4bash: cd: f4: No such file or directory(base) root@clps-pb1:/var/tmp# mkdir f4(base) root@clps-pb1:/var/tmp# cd f4(base) root@clps-pb1:/var/tmp/f4# ls(base) root@clps-pb1:/var/tmp/f4# export SUBJECTS_DIR=/var/tmp/f4(base) root@clps-pb1:/var/tmp/f4# cp $FREESURFER_HOME/subjects/sample-001.mgz .(base) root@clps-pb1:/var/tmp/f4# ls -lrttotal 6136-rw-r--r-- 1 root root 6280209 Nov 19 15:13 sample-001.mgz(base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gzmri_convert sample-001.mgz sample-001.nii.gz$Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $reading from sample-001.mgz...Segmentation fault (core dumped)(base) root@clps-pb1:/var/tmp/f4#Thanks,Paulo_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hello--
Good morning. Thank you very much for your email.
Yes we have the license file. When we didn't have the license file, we would get an error about missing license file.
(base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls ASegStatsLUT.txt bin diffusion FreeSurferEnv.csh fsfast mni SetUpFreeSurfer.csh subjects AUTHORS build-stamp.txt docs FreeSurferEnv.sh lib SegmentNoLUT.txt SetUpFreeSurfer.sh tkmeditParcColorsCMA average DefectLUT.txt FreeSurferColorLUT.txt fsafd matlab sessions Simple_surface_labels2009.txt (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls -la .license -rw-r--r-- 1 root root 49 Nov 18 15:10 .license (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ cat .license pb@brown.edu 41878 *C8f07l/gczz6 FSdMgckdPeGoE (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$
(base) root@clps-pb1:/var/tmp/freesurfer4# mv .license license (base) root@clps-pb1:/var/tmp/freesurfer4# cd bin (base) root@clps-pb1:/var/tmp/freesurfer4/bin# export FREESURFER_HOME=/var/tmp/freesurfer4 (base) root@clps-pb1:/var/tmp/freesurfer4/bin# source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /var/tmp/freesurfer4 FSFAST_HOME /var/tmp/freesurfer4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /var/tmp/freesurfer4/subjects MNI_DIR /var/tmp/freesurfer4/mni (base) root@clps-pb1:/var/tmp/freesurfer4/bin# export SUBJECTS_DIR=/var/tmp/f4 (base) root@clps-pb1:/var/tmp/freesurfer4/bin# cd /var/tmp/f4 (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from sample-001.mgz... -------------------------------------------------------------------------- *ERROR: FreeSurfer license file /var/tmp/freesurfer4/.license not found.* 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. -------------------------------------------------------------------------- (base) root@clps-pb1:/var/tmp/f4#
*(base) root@clps-pb1:/var/tmp/f4# mv /var/tmp/freesurfer4/license /var/tmp/freesurfer4/.license* (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from sample-001.mgz... *Segmentation fault (core dumped)* (base) root@clps-pb1:/var/tmp/f4#
Ok, will you confirm Ubuntu 18 can not run Freesurfer 4?
Thanks,
Paulo
On Thu, Nov 21, 2019 at 1:14 AM fsbuild fsbuild@contbay.com wrote:
Hello Paulo,
What is the location of the freesurfer license file (?), i.e., I would make sure the freesurfer license file is under $FREESURFER_HOME and then see if you get different results running the command.
Even with the license file though, I’m not sure all the Freesurfer 4 binaries will run on Ubuntu 18
- R.
On Nov 19, 2019, at 15:26, Baptista, Paulo paulo_baptista@brown.edu wrote:
External Email - Use CautionHello FreeSurfer Developers,
I am helping a researcher in my department run FreeSurfer on a new computer.. They insist that it should run on FreeSurfer 4.5 because their old system ran that version. Is the following possible? We can run FreeSurfer 6.0 fine, but they say there are differences between the versions.
- FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0-full
- Platform: Ubuntu 18.04.1 LTS
- uname -a: Linux clps-pb1 4..15.0-64-generic #73-Ubuntu SMP Thu Sep 12 13:16:13 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
- recon-all.log: n/a Segmentation Fault - see below
(base) root@clps-pb1:/var/tmp# cd freesurfer4 (base) root@clps-pb1:/var/tmp/freesurfer4# ls ASegStatsLUT.txt DefectLUT.txt FreeSurferEnv.sh mni Simple_surface_labels2009.txt AUTHORS diffusion fsafd SegmentNoLUT.txt subjects average docs fsfast sessions tkmeditParcColorsCMA bin FreeSurferColorLUT.txt lib SetUpFreeSurfer.csh build-stamp.txt FreeSurferEnv.csh matlab SetUpFreeSurfer.sh (base) root@clps-pb1:/var/tmp/freesurfer4# export FREESURFER_HOME=/var/tmp/freesurfer4 (base) root@clps-pb1:/var/tmp/freesurfer4# source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /var/tmp/freesurfer4 FSFAST_HOME /var/tmp/freesurfer4/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /var/tmp/freesurfer4/subjects MNI_DIR /var/tmp/freesurfer4/mni (base) root@clps-pb1:/var/tmp/freesurfer4# cd .. (base) root@clps-pb1:/var/tmp# cd f4 bash: cd: f4: No such file or directory (base) root@clps-pb1:/var/tmp# mkdir f4 (base) root@clps-pb1:/var/tmp# cd f4 (base) root@clps-pb1:/var/tmp/f4# ls (base) root@clps-pb1:/var/tmp/f4# export SUBJECTS_DIR=/var/tmp/f4 (base) root@clps-pb1:/var/tmp/f4# cp $FREESURFER_HOME/subjects/sample-001.mgz . (base) root@clps-pb1:/var/tmp/f4# ls -lrt total 6136 -rw-r--r-- 1 root root 6280209 Nov 19 15:13 sample-001.mgz (base) root@clps-pb1:/var/tmp/f4# mri_convert sample-001.mgz sample-001.nii.gz mri_convert sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from sample-001.mgz... Segmentation fault (core dumped) (base) root@clps-pb1:/var/tmp/f4#
Thanks,
Paulo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Baptista, Paulo -
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