FREESURFER_HOME should point to the absolute/full path to the installation directory doug
On 7/10/13 10:00 PM, Stéphane Poulin wrote:
Hello Freesurfer experts
I have just installed Freesurfer and tried to run recon-all command.
I get these "command not found" errors.
Any idea?
Stephane
Last login: Wed Jul 10 21:42:55 on ttys001 [silicium:~] stephanep% cd /Volumes/Macintosh_HD_Donnees/Applications/ [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% setenv FREESURFER_HOME freesurfer [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME freesurfer FSFAST_HOME freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR freesurfer/subjects MNI_DIR freesurfer/mni [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% setenv SUBJECTS_DIR /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/ [silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep% recon-all -i /Volumes/Macintosh_HD_Donnees/Imaging/ADNI_2/002_S_4171/MPRAGE/2011-08-08_17_22_19.0/S118013/ADNI_002_S_4171_MR_MPRAGE_br_raw_20110809145237100_127_S118013_I249535.dcm -subjid 002_S_4171 Subject Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects Actual FREESURFER_HOME /Volumes/Macintosh_HD_Donnees/Applications/freesurfer Darwin silicium.crulrg.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 mri_motion_correct.fsl: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_make_uchar: Command not found. mri_normalize: Command not found. mri_watershed: Command not found. mri_gcut: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_and: Command not found. mri_or: Command not found. mri_fuse_segmentations: Command not found. mri_segstats: Command not found. cp: freesurfer/bin/recon-all: No such file or directory /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171 \n mri_convert /Volumes/Macintosh_HD_Donnees/Imaging/ADNI_2/002_S_4171/MPRAGE/2011-08-08_17_22_19.0/S118013/ADNI_002_S_4171_MR_MPRAGE_br_raw_20110809145237100_127_S118013_I249535.dcm /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171/mri/orig/001.mgz \n mri_convert: Command not found. Darwin silicium.crulrg.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
recon-all -s 002_S_4171 exited with ERRORS at Wed Jul 10 21:53:13 EDT 2013
For more details, see the log file /Volumes/Macintosh_HD_Donnees/Applications/freesurfer/subjects/002_S_4171/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[silicium:/Volumes/Macintosh_HD_Donnees/Applications] stephanep%
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