Hi, There is some issue with running freeview as an application package on macOS. You can try running it as a command-line from Terminal:
/Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview Best, Ruopeng > On May 21, 2017, at 8:36 AM, Fekonja <[email protected]> wrote: > > Hi FreeSurfer Developers, > > I’ve just installed FreeSurfer on my MacBook Pro and experience several > Problems. > > 1. If I generate a .profile file with the command to source FS as soon as I > open the Terminal, nothing happens. > If I source FS manually it works (e.g. the extract below). > > 2. If I open Freeview, it crashes as soon as I try to load anything. > > 3. The command to target the subject sample „sample-001.mgz“ works, but the > command to convert it doesn’t – e.g. extracted Terminal-Log below. > > I’ve searched the list and found some similar errors, but unfortunately I > couldn’t find working solutions. > My Security & Privacy settings allow to open apps downloaded from anywhere. > > 1)FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c / > freesurfer-i386-apple-darwin11.4.2-stable6-20170119 > 2)Platform: MacOS Sierra 10.12.5 > 3)uname -a:Darwin Luciuss-MacBook-Pro.local 16.6.0 Darwin Kernel Version > 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 > x86_64 > 4)recon-all.log: see below > > Last login: Sun May 21 14:04:09 on ttys001 > Luciuss-MacBook-Pro:~ luciusfekonja$ export > FREESURFER_HOME=/Applications/freesurfer > Luciuss-MacBook-Pro:~ luciusfekonja$ source > $FREESURFER_HOME/SetUpFreeSurfer.sh > -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /Applications/fsl > Luciuss-MacBook-Pro:~ luciusfekonja$ cp > $FREESURFER_HOME/subjects/sample-001.mgz > usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file > cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... > target_directory > Luciuss-MacBook-Pro:~ luciusfekonja$ mri_convert sample-001.mgz > sample-001.nii.gz > mri_convert.bin sample-001.mgz sample-001.nii.gz > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from sample-001.mgz... > mghRead(/Users/luciusfekonja/sample-001.mgz, -1): could not open file > Luciuss-MacBook-Pro:~ luciusfekonja$ > Luciuss-MacBook-Pro:~ luciusfekonja$ recon-all > > USAGE: recon-all > > Required Arguments: > -subjid <subjid> > -<process directive> > > Fully-Automated Directive: > -all : performs all stages of cortical reconstruction > -autorecon-all : same as -all > > Manual-Intervention Workflow Directives: > -autorecon1 : process stages 1-5 (see below) > -autorecon2 : process stages 6-23 > after autorecon2, check white surfaces: > a. if wm edit was required, then run -autorecon2-wm > b. if control points added, then run -autorecon2-cp > c. proceed to run -autorecon3 > -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ > mri_seg) > -autorecon2-wm : process stages 15-23 > -autorecon2-inflate1 : 6-18 > -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon > -autorecon3 : process stages 24-34 > if edits made to correct pial, then run -autorecon-pial > -hemi ?h : just do lh or rh (default is to do both) > > Autorecon Processing Stages (see -autorecon# flags above): > 1. Motion Correction and Conform > 2. NU (Non-Uniform intensity normalization) > 3. Talairach transform computation > 4. Intensity Normalization 1 > 5. Skull Strip > > 6. EM Register (linear volumetric registration) > 7. CA Intensity Normalization > 8. CA Non-linear Volumetric Registration > 9. Remove neck > 10. EM Register, with skull > 11. CA Label (Aseg: Volumetric Labeling) and Statistics > > 12. Intensity Normalization 2 (start here for control points) > 13. White matter segmentation > 14. Edit WM With ASeg > 15. Fill (start here for wm edits) > 16. Tessellation (begins per-hemisphere operations) > 17. Smooth1 > 18. Inflate1 > 19. QSphere > 20. Automatic Topology Fixer > 21. White Surfs (start here for brain edits for pial surf) > 22. Smooth2 > 23. Inflate2 > > 24. Spherical Mapping > 25. Spherical Registration > 26. Spherical Registration, Contralater hemisphere > 27. Map average curvature to subject > 28. Cortical Parcellation (Labeling) > 29. Cortical Parcellation Statistics > 30. Pial Surfs > 31. WM/GM Contrast > 32. Cortical Ribbon Mask > 33. Cortical Parcellation mapped to ASeg > 34 Brodmann and exvio EC labels > > Step-wise Directives > See -help > > Expert Preferences > -pons-crs C R S : col, row, slice of seed point for pons, used in fill > -cc-crs C R S : col, row, slice of seed point for corpus callosum, used in > fill > -lh-crs C R S : col, row, slice of seed point for left hemisphere, used in > fill > -rh-crs C R S : col, row, slice of seed point for right hemisphere, used in > fill > -nofill : do not use the automatic subcort seg to fill > -watershed cmd : control skull stripping/watershed program > -wsless : decrease watershed threshold (leaves less skull, but can strip > more brain) > -wsmore : increase watershed threshold (leaves more skull, but can strip > less brain) > -wsatlas : use atlas when skull stripping > -no-wsatlas : do not use atlas when skull stripping > -no-wsgcaatlas : do not use GCA atlas when skull stripping > -wsthresh pct : explicity set watershed threshold > -wsseed C R S : identify an index (C, R, S) point in the skull > -norm3diters niters : number of 3d iterations for mri_normalize > -normmaxgrad maxgrad : max grad (-g) for mri_normalize. Default is 1. > -norm1-b N : in the _first_ usage of mri_normalize, use control > point with intensity N below target (default=10.0) > -norm2-b N : in the _second_ usage of mri_normalize, use control > point with intensity N below target (default=10.0) > -norm1-n N : in the _first_ usage of mri_normalize, do N number > of iterations > -norm2-n N : in the _second_ usage of mri_normalize, do N number > of iterations > -cm : conform volumes to the min voxel size > -no-fix-with-ga : do not use genetic algorithm when fixing topology > -fix-diag-only : topology fixer runs until ?h.defect_labels files > are created, then stops > -seg-wlo wlo : set wlo value for mri_segment and mris_make_surfaces > -seg-ghi ghi : set ghi value for mri_segment and mris_make_surfaces > -nothicken : pass '-thicken 0' to mri_segment > -no-ca-align-after : turn off -align-after with mri_ca_register > -no-ca-align : turn off -align with mri_ca_label > -deface : deface subject, written to orig_defaced.mgz > > -expert file : read-in expert options file > -xopts-use : use pre-existing expert options file > -xopts-clean : delete pre-existing expert options file > -xopts-overwrite : overwrite pre-existing expert options file > -termscript script : run script before exiting (multiple -termscript flags > possible) > This can be good for running custom post-processing after recon-all > The script must be in your path. The subjid is passed as the only argument > The current directory is changed to SUBJECTS_DIR before the script is run > The script should exit with 0 unless there is an error > > -mprage : assume scan parameters are MGH MP-RAGE protocol > -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol. > both mprage flags affect mri_normalize and mri_segment, > and assumes a darker gm. > -schwartzya3t-atlas : for tal reg, use special young adult 3T atlas > > -use-gpu : use GPU versions of mri_em_register, mri_ca_register, > mris_inflate and mris_sphere > > Notification Files (Optional) > -waitfor file : wait for file to appear before beginning > -notify file : create this file after finishing > > Status and Log files (Optional) > -log file : default is scripts/recon-all.log > -status file : default is scripts/recon-all-status.log > -noappend : start new log and status files instead of appending > -no-isrunning : do not check whether this subject is currently being > processed > > Segmentation of substructures of hippocampus and brainstem > -hippocampal-subfields-T1 : segmentation of hippocampal subfields using > input T1 scan > -hippocampal-subfields-T2 file ID : segmentation using an additional scan > (given by file); > ID is a user-defined identifier for the > analysis > -hippocampal-subfields-T1T2 file ID : segmentation using additional scan > (given by file) and input T1 > simultaneously; ID is a user-defined > identifier for the analysis > -brainstem-structures : segmentation of brainstem structures > > Other Arguments (Optional) > -sd subjectsdir : specify subjects dir (default env SUBJECTS_DIR) > -mail username : mail user when done > -umask umask : set unix file permission mask (default 002) > -grp groupid : check that current group is alpha groupid > -onlyversions : print version of each binary and exit > -debug : print out lots of info > -allowcoredump : set coredump limit to unlimited > -dontrun : do everything but execute each command > -version : print version of this script and exit > -help : voluminous bits of wisdom > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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