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
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 l.fekonja@fekonja.ch wrote:
Hi FreeSurfer Developers,
I’ve just installed FreeSurfer on my MacBook Pro and experience several Problems.
- 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).
If I open Freeview, it crashes as soon as I try to load anything.
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):
Motion Correction and Conform
NU (Non-Uniform intensity normalization)
Talairach transform computation
Intensity Normalization 1
Skull Strip
EM Register (linear volumetric registration)
CA Intensity Normalization
CA Non-linear Volumetric Registration
Remove neck
EM Register, with skull
CA Label (Aseg: Volumetric Labeling) and Statistics
Intensity Normalization 2 (start here for control points)
White matter segmentation
Edit WM With ASeg
Fill (start here for wm edits)
Tessellation (begins per-hemisphere operations)
Smooth1
Inflate1
QSphere
Automatic Topology Fixer
White Surfs (start here for brain edits for pial surf)
Smooth2
Inflate2
Spherical Mapping
Spherical Registration
Spherical Registration, Contralater hemisphere
Map average curvature to subject
Cortical Parcellation (Labeling)
Cortical Parcellation Statistics
Pial Surfs
WM/GM Contrast
Cortical Ribbon Mask
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Cheers,
*Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham.
Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney
*E* Kevin.aquino@nottingham.ac.uk, aquino@physics.usyd.edu.au | *W* https://kevinaquino.github.io http://www.physics.usyd.edu.au/~aquino/
----------------------------------------------
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On Sun, May 21, 2017 at 10:36 PM, Fekonja l.fekonja@fekonja.ch wrote:
Hi FreeSurfer Developers,
I’ve just installed FreeSurfer on my MacBook Pro and experience several Problems.
- 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).
Have you tried putting the commands into .bash_profile instead? as far as i know that is the standard practice for doing this in macos.
If I open Freeview, it crashes as soon as I try to load anything.
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 labelsStep-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 Freesurfer@nmr.mgh.harvard.edu 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
The reason the mri_convert command failed is because the 'cp' command before it failed. Please make sure you copy the '$FREESURFER_HOME/subjects/sample-001.mgz' file into what ever directory you are currently in before executing the 'mri_convert' command. This is done as follows:
cp $FREESURFER_HOME/subjects/sample-001.mgz .
and then,
mri_convert sample-001.mgz sample-001.nii.gz
On 05/21/2017 08:36 AM, Fekonja wrote:
Hi FreeSurfer Developers,
I’ve just installed FreeSurfer on my MacBook Pro and experience several Problems.
- If I generate a .profile file with the command to source FS as soon as I open the Terminal, nothing happens.
If I source FS manually it works (e.g. the extract below).
If I open Freeview, it crashes as soon as I try to load anything.
The command to target the subject sample „sample-001.mgz“ works, but the command to convert it doesn’t – e.g. extracted Terminal-Log below.
I’ve searched the list and found some similar errors, but unfortunately I couldn’t find working solutions. My Security & Privacy settings allow to open apps downloaded from anywhere.
1)FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c / freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2)Platform: MacOS Sierra 10.12.5 3)uname -a:Darwin Luciuss-MacBook-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 4)recon-all.log: see below
Last login: Sun May 21 14:04:09 on ttys001 Luciuss-MacBook-Pro:~ luciusfekonja$ 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 labelsStep-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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think you may have sent this reply to me by accident. I just want to make sure the person that actually asked the question gets the reply.
Thanks,
Valerie
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Tuesday, May 23, 2017 3:04:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mac mghread and freeview error
The reason the mri_convert command failed is because the 'cp' command before it failed. Please make sure you copy the '$FREESURFER_HOME/subjects/sample-001.mgz' file into what ever directory you are currently in before executing the 'mri_convert' command. This is done as follows:
cp $FREESURFER_HOME/subjects/sample-001.mgz .
and then,
mri_convert sample-001.mgz sample-001.nii.gz
On 05/21/2017 08:36 AM, Fekonja wrote:
Hi FreeSurfer Developers,
I’ve just installed FreeSurfer on my MacBook Pro and experience several Problems.
- If I generate a .profile file with the command to source FS as soon as I open the Terminal, nothing happens.
If I source FS manually it works (e.g. the extract below).
If I open Freeview, it crashes as soon as I try to load anything.
The command to target the subject sample „sample-001.mgz“ works, but the command to convert it doesn’t – e.g. extracted Terminal-Log below.
I’ve searched the list and found some similar errors, but unfortunately I couldn’t find working solutions. My Security & Privacy settings allow to open apps downloaded from anywhere.
1)FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c / freesurfer-i386-apple-darwin11.4.2-stable6-20170119 2)Platform: MacOS Sierra 10.12.5 3)uname -a:Darwin Luciuss-MacBook-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 4)recon-all.log: see below
Last login: Sun May 21 14:04:09 on ttys001 Luciuss-MacBook-Pro:~ luciusfekonja$ 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 labelsStep-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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Becker, Valerie -
Fekonja -
Kevin Aquino -
Ruopeng Wang -
Z K