---------- Forwarded message ---------- From: Timothy Le <t...@stanford.edu> Date: Tue, Oct 6, 2015 at 10:33 AM Subject: Re: [Freesurfer] Error Messages for Accessing Bin To: dgw <dgwake...@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 <dgwake...@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 <t...@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 <t...@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 <dgwake...@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 <t...@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 >>>> <fis...@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:~$ >>>>> >>>>> _______________________________________________ >>>>> 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. >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>
_______________________________________________ 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.
