Re: [Freesurfer] Welcome to the "Freesurfer" mailing list {Disarmed} - Freesurfer

5 Nov 2020


      External Email - Use Caution
Hello Nicholas,
Please check you setting for the environment variable FREESURFER_HOME. &nbsp;I used the Mac 7.1.1 release package from&nbsp;https://secure-web.cisco.com/1UkHJYwewl8qS85O_CWV-J5WUiafp7vGnbHtJ7jYex3q0G5... install freesurfer, so that means after installation FREESURFER_HOME is set as,
$&nbsp;export FREESURFER_HOME=/Applications/freesurfer/7.1.1
.... and the ls command outputs …
$&nbsp;ls $FREESURFER_HOMEASegStatsLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;SetUpFreeSurfer.sh*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;etc/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sources.csh*DefectLUT.txt*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;Simple_surface_labels2009.txt*&nbsp;fsafd/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sources.sh*FreeSurferColorLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp;&nbsp;WMParcStatsLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;fsfast/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;subjects/FreeSurferEnv.csh*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;average/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;lib/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;tkmeditParcColorsCMA*FreeSurferEnv.sh*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;bin/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;matlab/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;trctrain/Freeview.app/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;build-stamp.txt*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;mni/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;uninstall.sh*SegmentNoLUT.txt*&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;diffusion/&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;python/SetUpFreeSurfer.csh*&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;docs/&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;sessions/
… and shows the SetUpFreesurfer.sh script is there …
Once you have set FREESURFER_HOME and verify with the ls command that you can see the SetUpFreesurfer.sh script, then it should work to do,
$&nbsp;source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.1.1-20200726-8b40551 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME&nbsp;&nbsp;&nbsp;/Applications/freesurfer/7.1.1FSFAST_HOME&nbsp;&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR&nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.1.1/subjectsMNI_DIR&nbsp;&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;&nbsp;/Applications/freesurfer/7.1.1/mni
There are instructions at&nbsp;https://secure-web.cisco.com/1yfyz92Kb9rfbFcHszgMJR0t3oQo4dtacsW4yWoxKnJic0O... the section "Using the Mac Package Installer” about using the installer package.
- R.
On Nov 4, 2020, at 22:58, Nicholas BH NG (NUHS) &lt;nicholas_bh_ng@nuhs.edu.sg&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear Free SurferI followed the excellent video step by step instructions. At the last part of putting the code/ key into the terminal, I encountered the error message as below: no such file or directory. As such I think my set up was not complete.Kindly advice.Thank youNicholas&nbsp;Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directoryNicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directoryNicholass-MacBook-Pro:~ Nic$&nbsp;Begin forwarded message:From:&nbsp;&lt;freesurfer-request@nmr.mgh.harvard.edu&gt;Subject:&nbsp;Welcome to the "Freesurfer" mailing listDate:&nbsp;5 November 2020 at 11:56:45 AM SGTTo:&nbsp;&lt;nicholas_bh_ng@nuhs.edu.sg&gt;Email is from external source.&nbsp;Do not click on links or open files if unsure of sender..Welcome to the&nbsp;Freesurfer@nmr.mgh.harvard.edu&nbsp;mailing list!To post to this list, send your email to:&nbsp;freesurfer@nmr.mgh.harvard.eduGeneral information about the mailing list is at:&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;https://secure-web.cisco.com/1U1Az2RL5IBE60ro0LKNRX0VzCwNbYE3pMJyje23j47fWom... you ever want to unsubscribe or change your options (eg, switch toor from digest mode, change your password, etc.), visit yoursubscription page at:&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;https://secure-web.cisco.com/19HZrRkjfKoxZblZuo0R6GPVxEHVP2CQHZavVhBZBqM-SjM... can also make such adjustments via email by sending a message to:&nbsp;Freesurfer-request@nmr.mgh.harvard.eduwith the word `help' in the subject or body (don't include thequotes), and you will get back a message with instructions.You must know your password to change your options (including changingthe password, itself) or to unsubscribe. &nbsp;It is:&nbsp;3:5proverbsNormally, Mailman will remind you of your&nbsp;nmr.mgh.harvard..edu&nbsp;mailinglist passwords once every month, although you can disable this if youprefer. &nbsp;This reminder will also include instructions on how tounsubscribe or change your account options. &nbsp;There is also a button onyour options page that will email your current password to you.&lt;p&gt;&lt;/p&gt;&lt;image94f29b.PNG&gt;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;http://secure-web.cisco.com/1f9F22Nst6o56NQIQrR5eAr7N2En2k2SbYSUoiZkfrHbhSnF... Facebook&nbsp;|&nbsp;LinkedIn&nbsp;|&nbsp;VimeoImportant: This email and its attachments are confidential and may be privileged. If you are not the intended recipient, please notify the sender and delete it immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person without prior written permission. Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer