Please provide the following:
* The version number of the HCP Pipeline Scripts you are using
* Go to your HCP Pipelines Scripts directory (e.g.
/home/vasudev/Documents/Pipelines-
master) and issue the command: cat version.txt and send the
output from that command
* The version of FreeSurfer you are using
* Issue the following command: cat ${FREESURFER_HOME}/build-
stamp.txt and send the output from that command
* You should source the environment script you are using when running
the HCP Pipeline Scripts to get the FREESURFER_HOME environment
variable set correctly prior to issuing the above command (e.g.
source *<my-env-script>*)
* The path to the installed version of mris_make_surfaces you are using
* Try issuing the command: which mris_make_surfaces
* Similar to the above, please make sure you have sourced the
environment set up script prior to issuing the which
mris_make_surfaces command
* The output from the following command:
* mris_make_surfaces --all-info
* Exact text of your invocation of the PreFreeSurferPipeline.sh script.
* The captured standard output (stdout) and standard error (stderr)
from your successful run of the PreFreeSurferPipeline.sh script.
* Exact text of your invocation of the FreeSurferPipeline.sh script.
* The captured standard output (stdout) and standard error (stderr)
from you run of the FreeSurferPipeline.sh script.
Tim
On Fri, Mar 18, 2016, at 06:06, Dev vasu wrote:
> Dear Sir,
>
> I am able to run PreFreesurferPipeline.sh completely but i am still
> incurring the same error message which states as :
>
> "/home/vasudev/Documents/Pipelines-
> master/FreeSurfer/scripts/FreeSurferHiresPial.sh: line 48: 24890
> Segmentation fault (core dumped) mris_make_surfaces -nsigma_above
> 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm wm.hires
> -mgz -sdir $SubjectDIR -orig white.deformed -nowhite -orig_white
> white.deformed -orig_pial pial -T2dura "$mridir"/T2w_hires.norm -T1
> T1w_hires.norm -output .T2 $SubjectID lh "
>
>
> Thanks
> Vasudev
>
> On 17 March 2016 at 18:45, Timothy B. Brown <[email protected]> wrote:
>> Vasudev,
>>
>> > I am incurring segmentation fault error after during the course of
>> > running Freesurferpipeline
>> >
>> > Following is the error
>> >
>> > /home/vasudev/Documents/Pipelines-
>> > master/FreeSurfer/scripts/FreeSurferHiresPial.sh: line 48: 24964
>> > Segmentation fault (core dumped) mris_make_surfaces -
>> > nsigma_above
>> > 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm
>> > wm.hires
>> > -mgz -sdir $SubjectDIR -orig white.deformed -nowhite -orig_white
>> > white.deformed -orig_pial pial -T2dura "$mridir"/T2w_hires.norm -T1
>> > T1w_hires.norm -output .T2 $SubjectID lh "
>> >
>> > I am even attaching the log files generated during segmentation
>> > process
>> > ,kindly let me know the reason for this error
>>
>> I was unable to see anything in the log files that you attached that
>> would help me understand why you are getting a segmentation fault.
>>
>> Have you previously been able to successfully run the
>> PreFreeSurferPipeline.sh script? Or are you still having the
>> problems with that mentioned in your previous messages?
>>
>> If you haven't yet successfully run the Pre-FreeSurfer Pipeline, then
>> I would suggest you get that to complete without problems before
>> trying to run the FreeSurfer pipeline.
>>
>> Regards,
>>
>> Tim
>>
>>
>> --
>> Timothy B. Brown
>> Business & Technology Application Analyst III
>> Pipeline Developer (Human Connectome Project)
>> tbbrown(at)wustl.edu
>> ________________________________________
>> The material in this message is private and may contain Protected
>> Healthcare Information (PHI).
>> If you are not the intended recipient, be advised that any
>> unauthorized use, disclosure, copying
>> or the taking of any action in reliance on the contents of this
>> information is strictly prohibited.
>> If you have received this email in error, please immediately notify
>> the sender via telephone or
>> return mail.
--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
________________________________________
The material in this message is private and may contain Protected Healthcare
Information (PHI).
If you are not the intended recipient, be advised that any unauthorized use,
disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited.
If you have received this email in error, please immediately notify the sender
via telephone or
return mail.
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