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
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