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Hello Paulo,

I could be wrong, but I don’t see that freesurfer 4 contains or shipped with any ./lib directory with its own copies of needed libraries like libvtk*, libtcl*, etc.   On Ubuntu, those libraries are installed on the system under /usr/lib/x86_64-linux-gnu.   One way to find them is to add a path to search for libraries via the environment variable LD_LIBRARY_PATH, e.g.,

$ export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH

But even after trying that, it looks like the freesurfer4 binaries cannot find the older versions of the libraries it expects in that system location for libs on Ubuntu 18, e.g.,  libtiff is version 5 but freesurfer4 expects version 3;  on Ubuntu 18 libtcl* is version 8.6 but freesurfer4 expects version 8.4, and so forth for libvtk*, libpango*, and other libs.

Another issue (which I did not look at) is that even if the same library revisions that  freesurfer4 expects are installed on Ubuntu 18, the older symbol references compiled into freesurfer4 libraries may no longer exist in the newer Ubuntu 18 versions of those libraries.   If you look at the web page with some freesurfer5 download info,

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3

- the entry for the Xubuntu12 VM I take to mean that freesurfer 5.3 ran on Ubuntu 12.  That was back in 2013, and freesurfer 4 is older than that.

So I might expect freesurfer4 to run on Ubuntu 12 or maybe 13, but I would not expect those binaries  to run some 6 iterations (and 6 years) later on Ubuntu 18.

- R.


On Nov 21, 2019, at 08:49, Baptista, Paulo <paulo_baptista@brown.edu> wrote:

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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
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,
  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:

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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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