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.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary. On Sun, May 21, 2017 at 10:36 PM, Fekonja <l.feko...@fekonja.ch> 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). > 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. > > 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 > 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. >
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