External Email - Use Caution
Hello Haley, You could try bringing up a new terminal window and then do the following, $ cd $HOME$ bash… output deleted …$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1 The ls command below should show you the two .sh files needed to setup the environment. If you don’t see those two files listed, then something is likely wrong with the installation and you could try re-installing freesurfer (see download links at the end of this message).
$ ls -l $FREESURFER_HOME/*Surfer*.sh-rwxr-xr-x 1 root wheel 18223 Aug 11 2020 /Applications/freesurfer/7.1.1/FreeSurferEnv.sh* -rwxr-xr-x 1 root wheel 1350 Aug 11 2020 /Applications/freesurfer/7.1.1/SetUpFreeSurfer.sh* Check you can read both of those files with the head command, $ head -1 $FREESURFER_HOME/FreeSurferEnv.sh#!/bin/bash -p $ head -1 $FREESURFER_HOME/SetUpFreeSurfer.sh#!/bin/bash -p If you don’t see that output from the head command for the first line in each file, then there could be a permission error. In that case you could try manually setting the permissions with the chmod command,$ sudo chmod 755 $FREESURFER_HOME/FreeSurferEnv.sh$ sudo chmod 755 $FREESURFER_HOME/SetUpFreeSurfer.sh Then try the "head -1" command again to test reading the first line in each file.
If the above all worked, then try source’ing the SetUpFreeSurfer.sh file (which in turn runs the FreeSurferEnv.sh file that you reported could not be found),$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.1.1 FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects MNI_DIR /Applications/freesurfer/7..1.1/mni If you need to re-install 7.1.1 for MacOS, the link for that is here, https://secure-web.cisco.com/1bISb5L_RaO9qHLk_GCjwJOWorsxrzGoSJ2bpiqR2EwuBjA... If you don’t need to continue to work with the 7.1.1 release, you could try the newer 7.2.0 release. You can have both 7.1.1 and 7.2.0 installed and set FREESURFER_HOME to point to either one of them. The link for the 7.2.0 release for MacOS is,https://secure-web.cisco.com/1zRdDSXh-D1BWJw53Mbc6pYU1EIIskfcqIPD-acokQWeEX9... You need admin/root privileges to run the .pkg installer files.
- R. On Aug 17, 2021, at 17:41, Haley Park <hparkit@gmail.com> wrote: External Email - Use Caution Hello,I was able to run Freesurfer before but when I try to source it now with the codesource $FREESURFER_HOME/7.1.1/SetUpFreesurfer.shI get the message:/Applications/freesurfer/7..1.1/SetUpFreeSurfer.sh:source:42: no such file or directory: /Applications/freesurfer/FreeSurferEnv.shBut I do see that file in the directory in Finder.Any ideas?Thank you,Haley_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer