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 $FREESURFER_HOME/subjects/sample-001.mgz .
and then,
mri_convert sample-001.mgz sample-001.nii.gz
On 05/21/2017 08:36 AM, Fekonja wrote:
> Hi FreeSurfer Developers,
>
> I’ve just installed FreeSurfer on my MacBook Pro and experience several Problems.
>
> 1. If I generate a .profile file with the command to source FS as soon as I open the Terminal, nothing happens.
> If I source FS manually it works (e.g. the extract below).
>
> 2. If I open Freeview, it crashes as soon as I try to load anything.
>
> 3. The command to target the subject sample „sample-001.mgz“ works, but the command to convert it doesn’t – e.g. extracted Terminal-Log below.
>
> I’ve searched the list and found some similar errors, but unfortunately I couldn’t find working solutions.
> My Security & Privacy settings allow to open apps downloaded from anywhere.
>
> 1)FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c / freesurfer-i386-apple-darwin11.4.2-stable6-20170119
> 2)Platform: MacOS Sierra 10.12.5
> 3)uname -a:Darwin Luciuss-MacBook-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
> 4)recon-all.log: see below
>
> Last login: Sun May 21 14:04:09 on ttys001
> Luciuss-MacBook-Pro:~ luciusfekonja$ 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
> Freesurfer@nmr.mgh.harvard.edu
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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