---------- Forwarded message ---------- From: Timothy Le tle7@stanford.edu Date: Tue, Oct 6, 2015 at 10:33 AM Subject: Re: [Freesurfer] Error Messages for Accessing Bin To: dgw dgwakeman@gmail.com Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hi, We have a 64 bit system. We chose to install 5.0 because we already have data processed in 5.0 and want to keep the data consistent. What would you advise us to do? Thank you Timothy
On Oct 6, 2015, at 7:47 AM, dgw dgwakeman@gmail.com wrote:
what operating system are you running? 64 bit or 32 bit? Why did you decide to install version 5.0 instead of the current stable
5.3?
hth d
On Mon, Oct 5, 2015 at 5:41 PM, Timothy Le tle7@stanford.edu wrote: Hi, From the following output, how should I proceed? Thank you very much Timothy Le
On Oct 2, 2015, at 11:55 AM, Timothy Quang-Tin Le tle7@stanford.edu
wrote:
Hi, Thank you very much for your response. The output of that command was:
tle7@sni-vcs-gotlib:~$ ls -l /home/tle7/freesurfer/bin/mri_convert -rwxrwx--x 1 tle7 stanford 1672136 Aug 15 2010 /home/tle7/freesurfer/bin/mri_convert tle7@sni-vcs-gotlib:~$
On Fri, Oct 2, 2015 at 10:39 AM, dgw dgwakeman@gmail.com wrote:
Timothy,
What is the output of this command:
ls -l /home/tle7/freesurfer/bin/mri_convert
?
hth d
On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le tle7@stanford.edu wrote:
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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