[Freesurfer] Error Messages for Accessing Bin
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-go
[Freesurfer] Error Messages for Accessing Bin
> 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.1.2.840.113
[Freesurfer] Error Message when Accessing Bin
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-g
Re: [Freesurfer] Error Messages for Accessing Bin
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 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 for
[Freesurfer] Error Messages for Accessing Bin
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 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 for
Re: [Freesurfer] Error Messages for Accessing Bin
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 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 > 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 > > > 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
[Freesurfer] Fwd: Error Messages for Accessing Bin
-- Forwarded message -- From: Timothy Le Date: Tue, Oct 6, 2015 at 10:33 AM Subject: Re: [Freesurfer] Error Messages for Accessing Bin To: dgw Cc: Freesurfer support list 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 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 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 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 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 >>> 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 >>>> >>>> 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. >>>>
[Freesurfer] editsFail
Hello, I am using free surfer version 5.0.0; how do I continue to edit the brain with the previous edits made if the brain was processed under applyEdits, but is now in editsFail? Does this mean that I have to redo the entire brain, or can I have it restored somehow? Thank you Timothy Le ___ 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.
