Re: [Freesurfer] FreeSurfer Issue - Freesurfer

17 Feb 2022


      External Email - Use Caution
Hello Anna,
You could try the bash shell commands below … freeview should open an empty window.
Those commands are documented for the bash shell and also csh/tcsh shells on the help page, https://secure-web.cisco.com/1HXGi2MgGyKrnZsUEDporX-UQ3IrQRAR1UaZSL_m2PtlLk-...
- R.
%&nbsp;bash
The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1Tcz7fGutzZau6blDkstZVkR5nPiyXBdbX07yX4PuhMcNra...
you@Host-Mac:~&gt;&nbsp;export FREESURFER_HOME=/Applications/freesurfer/7.2.0
you@Host-Mac:~&gt;&nbsp;source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME&nbsp;&nbsp;&nbsp;/Applications/freesurfer/7.2.0FSFAST_HOME&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.2.0/subjectsMNI_DIR&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.2.0/mni
you@Host-Mac:~&gt;&nbsp;freeview
On Feb 17, 2022, at 18:44, Pusok, Anna &lt;anna.pusok@yale.edu&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi,Sorry but this did not fix the issues- could I ask you to help with Freesurfer? I tried to get it work many times, with no success and what you recommended also did not work.Thank you.From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of Tim Schäfer &lt;ts+ml@rcmd.org&gt;Sent:&nbsp;Thursday, February 17, 2022 2:10 PMTo:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Re: [Freesurfer] FreeSurfer Issue&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear Anna,You should use 'setenv' (for tcsh and related shells) or 'export' (for BASH) when defining environment variables, as listed here:&nbsp;&nbsp;&nbsp;&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-web...; setenv FREESURFER_HOME /Applications/freesurfer/7.2.0You should also source (instead of executing) the SetUpFreeSurfer.csh script:&nbsp;&nbsp;&nbsp; source $FREESURFER_HOME/SetUpFreeSurfer.cshBest,Tim&gt; On 02/17/2022 5:32 PM Pusok, Anna &lt;anna.pusok@yale.edu&gt; wrote:&gt;&nbsp;&gt;&nbsp;&nbsp;&gt; External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&gt;&nbsp;&gt; Hi there,&gt; I hope this email finds you well!&gt; I ran into some issues when I tried to use freesurfer. This is the error message I get in my terminal. Could you help me with this issue? If we could set up a Zoom meeting to discuss the issue, that would be helpful as well!&gt; Thank you,&gt; Anna&gt; _______________________________________________&gt; Freesurfer mailing list&gt;&nbsp;Freesurfer@nmr.mgh.harvard.edu&gt;&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-web.... Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer