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.
