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
