Re: [Freesurfer] Installing Freesurfer

13 Oct 2020


      External Email - Use Caution
... Sorry, I should have said - if you expanded the tar archive under $HOME/Downloads, then
$ ls $HOME/Downloads/freesurfer
… would show you something like …
ASegStatsLUT.txt&nbsp;&nbsp;diffusion/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;FreeSurferEnv.sh&nbsp;&nbsp;mni@&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SetUpFreeSurfer.sh*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;subjects/average/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;docs/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fsafd/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;python/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;Simple_surface_labels2005.txt&nbsp;&nbsp;tkmeditParcColorsCMAbin/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;etc/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fsfast/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SegmentNoLUT.txt&nbsp; &nbsp; &nbsp;&nbsp;Simple_surface_labels2009.txt&nbsp;&nbsp;trctrain/build-stamp.txt&nbsp;&nbsp;&nbsp;FreeSurferColorLUT.txt&nbsp;&nbsp;lib/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sessions/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sources.csh*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;WMParcStatsLUT.txtDefectLUT.txt&nbsp;&nbsp; &nbsp;&nbsp;FreeSurferEnv.csh&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;matlab/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SetUpFreeSurfer.csh*&nbsp;&nbsp;sources..sh*
.... and then you would do
$ export FREESURER_HOME=$HOME/Downloads/freesurfer
… then the same as before ...
$ cat $FREESURFER_HOME/SetUpFreeSurfer.sh$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
- R.
On Oct 13, 2020, at 04:58, fsbuild &lt;fsbuild@contbay.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello Rio,I’m not sure why the paths you list include "$home/username”.Usually the absolute path listed by the environment variable HOME ends with the subdirectory named with your username. &nbsp;So your Downloads folder is usually referenced as $HOME/DownloadsIf you expanded the tar archive there, then the command,$ ls $HOME/Downloads… would show you something like ...ASegStatsLUT.txt&nbsp;&nbsp;diffusion/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;FreeSurferEnv.sh&nbsp;&nbsp;mni@&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SetUpFreeSurfer.sh*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;subjects/average/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;docs/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fsafd/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;python/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;Simple_surface_labels2005.txt&nbsp;&nbsp;tkmeditParcColorsCMAbin/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;etc/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fsfast/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SegmentNoLUT.txt&nbsp; &nbsp; &nbsp;&nbsp;Simple_surface_labels2009.txt&nbsp;&nbsp;trctrain/build-stamp.txt&nbsp;&nbsp;&nbsp;FreeSurferColorLUT.txt&nbsp;&nbsp;lib/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sessions/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sources.csh*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;WMParcStatsLUT.txtDefectLUT.txt&nbsp;&nbsp; &nbsp;&nbsp;FreeSurferEnv.csh&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;matlab/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SetUpFreeSurfer.csh*&nbsp;&nbsp;sources.sh*- and you would set FREESURFER_HOME as,$ export FREESURFER_HOME=$HOME/DownloadsIf you have permission to read the SetUpFreeSurfer.sh file, then you should see the file contents echoed to the terminal when you run,$ cat $FREESURFER_HOME/SetUpFreeSurfer.sh- and then it should work to do, e.g., in bash shell,$ source $FREESURFER_HOME/SetUpFreeSurfer.sh- R..On Oct 12, 2020, at 22:57, Rio Yamaguchi &lt;ryamaguchi..c@gmail.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear FreeSurfer team,I'm attempting to install freesurfer and am encountering a few problems.When I type in the command:$ source $FREESURFER_HOME/SetUpFreeSurfer.shIt comes back as saying:no such file or directory foundI have done the two previous commands as specified;$ export FREESURFER_HOME=$home/username/Downloads/freesurfer [which is the correct path to the freesurfer directory]$ export SUBJECTS_DIR=$FREESURFER_HOME/subjectsAlso, if I "ls" the files in $home/username/Downloads/freesurferthere is a file "SetUpFreeSurfer.sh" thus I am unsure why this error occurs.I've searched the list and whilst some similar errors have been reported. I could not resolve my issue. Does anyone have any thoughts on how to trouble-shoot this one?&nbsp;1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1..1.tar.gz2) Platform: Ubuntu 18.04&nbsp;Any help would be greatly appreciated.Thank you!Kind regards,Rio_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B______... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B

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Re: [Freesurfer] Installing Freesurfer