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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:

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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# 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
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