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Hello Stephan, I’m assuming you’re running the freesurfer 6.0.0 release and used the Mac pkg file to install it on your Mac from,freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg You would need admin/root privileges to use the “Security and Privacy” tab from the System preferences window on the Mac to give the pkg file permission to install freesurfer as /Applications/freesurfer
I have just done this install on a machine running Catalina (Mac OS 10.15.2). Then I ran the commands below. Please try them and see if you get the same results. The first command I typed is “bash” to start a bash shell. % 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://support.apple.com/kb/HT208050. Mac:~>
Mac:~> export FREESURFER_HOME=/Applications/freesurfer Mac:~> source /Applications/freesurfer/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Mac:~> which mri_convert /Applications/freesurfer/bin/mri_convert Mac:~> file `which mri_convert` /Applications/freesurfer/bin/mri_convert: Bourne-Again shell script text executable, ASCII text Mac:~> which mri_convert.bin /Applications/freesurfer/bin/mri_convert.bin Mac:~> file `which mri_convert.bin` /Applications/freesurfer/bin/mri_convert.bin: Mach-O 64-bit executable x86_64 Mac:~> bash -x /Applications/freesurfer/bin/mri_convert --help + source /Applications/freesurfer/sources.sh +++ uname -s ++ '[' Darwin == Darwin ']' ++ source /Applications/freesurfer/SetUpFreeSurfer.sh +++ '[' -z /Applications/freesurfer ']' +++ '[' -z /Applications/freesurfer/subjects ']' +++ '[' -z /Applications/freesurfer/sessions ']' +++ source /Applications/freesurfer/FreeSurferEnv..sh ++++ VERSION='$Id: FreeSurferEnv.sh,v 1.61 2016/06/09 14:54:31 zkaufman Exp $' ++++ '[' 1 -gt 1 ']' +++++ uname -s ++++ os=Darwin ++++ export OS=Darwin ++++ OS=Darwin ++++ '[' -n '' ']' ++++ output=1 ++++ [[ -z synpro ]] ++++ [[ -z '' ]] ++++ output=0 ++++ '[' -z /Applications/freesurfer ']' ++++ '[' '!' -d /Applications/freesurfer ']' ++++ [[ 0 == 1 ]] ++++ '[' -z /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ']' ++++ '[' -z 0 ']' ++++ [[ -z /Applications/freesurfer/fsfast ]] ++++ [[ 0 != 0 ]] ++++ [[ -z /Applications/freesurfer/subjects ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/bin ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/lib ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ [[ -z /Applications/freesurfer/mni/data ]] ++++ [[ 0 != 0 ]] ++++ [[ -z '' ]] ++++ '[' -n '' ']' ++++ '[' -e /Applications/freesurfer/fsl ']' ++++ '[' -e /usr/pubsw/packages/fsl/current ']' ++++ '[' -e /usr/local/pubsw/packages/fsl/current ']' ++++ '[' -e /usr/local/fsl ']' ++++ export FREESURFER_HOME=/Applications/freesurfer ++++ FREESURFER_HOME=/Applications/freesurfer ++++ export LOCAL_DIR=/Applications/freesurfer/local ++++ LOCAL_DIR=/Applications/freesurfer/local ++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"' ++++ '[' '!' -d /Applications/freesurfer/fsfast ']' ++++ for d in '"$FSFAST_HOME"' '"$SUBJECTS_DIR"' ++++ '[' '!' -d /Applications/freesurfer/subjects ']' ++++ [[ -z nii.gz ]] ++++ [[ 0 != 0 ]] ++++ [[ 0 == 1 ]] ++++ [[ 0 == 1 ]] ++++ [[ -z '' ]] ++++ export FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast ++++ FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast ++++ SUF=/Users/synpro/matlab/startup.m ++++ '[' '!' -e /Users/synpro/matlab/startup.m ']' +++++ grep FSFAST_HOME /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp1=' 1' +++++ grep FMRI_ANALYSIS_DIR /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp2=' 0' +++++ grep FREESURFER_HOME /Users/synpro/matlab/startup.m +++++ wc -l ++++ tmp3=' 1' ++++ [[ 1 == 0 ]] ++++ [[ 0 == 1 ]] ++++ '[' -z '' ']' ++++ '[' -n /Applications/freesurfer/mni/bin ']' ++++ '[' '!' -d /Applications/freesurfer/mni/bin ']' ++++ '[' -n /Applications/freesurfer/mni/lib ']' ++++ '[' '!' -d /Applications/freesurfer/mni/lib ']' ++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' -z /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 '!=' /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.12.3 ']' ++++ '[' -z '' ']' ++++ '[' -n /Applications/freesurfer/mni/bin ']' ++++ PATH=/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ '[' -d /Applications/freesurfer/lib/misc/bin ']' ++++ '[' -d /Applications/freesurfer/lib/misc/lib ']' ++++ [[ 0 == 1 ]] ++++ '[' -d /Applications/freesurfer/bin/freeview.app ']' ++++ '[' -d /Applications/freesurfer/lib/gcc/lib ']' ++++ '[' -z '' ']' ++++ export DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gcc/lib ++++ DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gcc/lib ++++ '[' -n '' ']' ++++ [[ 0 == 1 ]] ++++ '[' -n '' ']' ++++ '[' -n '' ']' ++++ [[ 0 == 1 ]] ++++ '[' -d /Applications/freesurfer/tktools ']' ++++ PATH=/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ export PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ PATH=/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/synpro/bin ++++ export FIX_VERTEX_AREA= ++++ FIX_VERTEX_AREA= ++++ return 0 + mri_convert.bin --help mri_convert.bin --help Help
NAME mri_convert
SYNOPSIS mri_convert [options] <in volume> <out volume>
… rest of output deleted … On Apr 3, 2020, at 11:28, Stephan <stephan.wunderlich22@gmail.com> wrote: External Email - Use Caution Hi Freesurer team,I am trying to run mri_convert (and recon_all) with a Macbook Pro 2019 with Catalina.Running mri_convert always leads to the following error://Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert: line 3: //Users/neurolab/Desktop/Stephan/Programmes/freesurfer/bin/mri_convert.bin: cannot execute binary fileAll security changes haven't helped yet.Best,Stephan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer