Re: [Freesurfer] Error Messages for Accessing Bin

[dgw]

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.
>> >>> /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.
>> >>> 

Re: [Freesurfer] Error Messages for Accessing Bin

[Timothy Le]

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.
>> /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.

Re: [Freesurfer] Error Messages for Accessing Bin

[Timothy Le]

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.
>> >>> /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.
>> >>> 

[Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

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 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.
>> 

Re: [Freesurfer] Error Messages for Accessing Bin

[dgw]

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 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 

Re: [Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

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 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.
> >>> 

[Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

> 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
> 

Re: [Freesurfer] Error Messages for Accessing Bin

[Bruce Fischl]

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)

Re: [Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

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 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.
>> 

[Freesurfer] Error Messages for Accessing Bin

[Timothy Quang-Tin Le]

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