Download freeview from https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview and copy DMG to Applications
sudo xattr -r -d com.apple.quarantine /path/to/MyApp.app OR authorice in Settings-Privacy…
Post installation - add to zsh (~/.zshrc) or in older OSx to ~/.bash_profile
export FS_LICENSE=/Users/bkossowski/Praca/license.txt
export SUBJECTS_DIR=~/Praca
alias freeview=/Applications/Freeview.app/Contents/MacOS/freeview
Then restart system and run normally
export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh (put in ~/.bash_profile)
SUBJECTS_DIR=$PWD
SUBJECTS_DIR=pwd
echo $SUBJECTS_DIR
cp -R $FREESURFER_HOME/subjects/fsaverage .
alias alias fsaseg='freeview -v mri/brainmask.mgz mri/aseg.mgz:colormap=lut:opacity=0.2 -f surf/lh.pial:edgecolor=red surf/rh.pial:edgecolor=red surf/lh.white:edgecolor=yellow surf/rh.white:edgecolor=yellow' alias fsbrainmask='freeview -v mri/brainmask.mgz -f surf/lh.pial:edgecolor=red surf/rh.pial:edgecolor=red surf/lh.white:edgecolor=yellow surf/rh.white:edgecolor=yellow' alias fswm='freeview -v mri/wm.mgz mri/brainmask.mgz -f surf/lh.pial:edgecolor=red surf/rh.pial:edgecolor=red surf/lh.white:edgecolor=yellow surf/rh.white:edgecolor=yellow' alias fst1='freeview -v mri/T1.mgz'
alias fsaparc='freeview -v mri/orig.mgz mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f surf/lh.white:annot=aparc.annot'
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.thickness.dyslexia.10.glmdir/CON-DYS/cache.th13.abs.sig.cluster.mgh $SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=rh.thickness.dyslexia.10.glmdir/CON-DYS/cache.th13.abs.sig.cluster.mgh
asegstats2table --inputs */stats/aseg.stats --tablefile asegtable.csv aparcstats2table
tr '\r' '\n' < CannabsiStudy_Age_Audit.txt > CannabisStudy_Age_Audit.fsgd
mris_preproc --fsgd gender_age.fsgd \ --target fsaverage \ --hemi lh \ --meas thickness \ --out lh.gender_age.thickness.00.mgh
mris_preproc --fsgd dyslexia.fsgd --target fsaverage --hemi lh --meas thickness --out lh.dyslexia.thickness.00.mgh