Hi, I tried the chmod command, but it did not work. How I check that I've downloaded the correct version? Thank you very much Timothy
On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you try chmod a+x on one of them and see if it can then be executed? e.g.:
chmod a+x /home/tle7/freesurfer/bin/mri_convert /home/tle7/freesurfer/bin/mri_convert
and see if you get an error. If not, you probably downloaded the wrong hardware version cheers Bruce
On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
Hello,When I run the command "sFSstart" on version 5.0.0, I am receiving the messages below. Would you please explain to me what the problem is? It seems like there is trouble accessing the bin. Thank you
-------- freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/tle7/freesurfer FSFAST_HOME /home/tle7/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/tle7/freesurfer/subjects MNI_DIR /home/tle7/freesurfer/mni tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2 studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter H 0 checking sid number 00152-DT2 1 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects Actual FREESURFER_HOME /home/tle7/freesurfer Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_curvature_stats: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mris_calc: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_robust_register: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_robust_template: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_and: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_or: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_fuse_segmentations: Exec format error. Binary file not executable. /home/tle7/freesurfer/bin/mri_segstats: Exec format error. Binary file not executable. -cw256 option is now persistent (remove with -clean-cw256) /home/tle7/freesurfer/subjects/00152-DT2_v5
mri_convert/home/tle7/freesurfer/subjects/practicemotherdaughter/rawdata/00152-DT2/MR. 1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm /home/tle7/freesurfer/subjects/00152-DT2_v5/mri/orig/001.mgz
/home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 00152-DT2_v5 exited with ERRORS at Mon Sep 28 10:43:57 PDT 2015
tle7@sni-vcs-gotlib:~$
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