Dear Sir,
Following are the outputs
1. vasudev@vasudev-OptiPlex-780:~/Documents/Pipelines-master$ cat
version.txt
Development after v3.13.2
2.vasudev@vasudev-OptiPlex-780:~/Documents/Pipelines-master$ cat
${FREESURFER_HOME}/build-stamp.txt
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
3. Environmental script for sourcing FREESURFER_HOME :
export FREESURFER_HOME=/usr/local/freesurfer
${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
4.Path for mris_make_surfaces
vasudev@vasudev-OptiPlex-780:~/Documents/Pipelines-master$ which
mris_make_surfaces
/usr/local/freesurfer/bin/mris_make_surfaces
5. Output from mris_make_surfaces --all-info
vasudev@vasudev-OptiPlex-780:~/Documents/Pipelines-master$
mris_make_surfaces --all-info
ProgramName: mris_make_surfaces ProgramArguments: --all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-16:20:13-GMT
BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v
1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: vasudev Machine:
vasudev-OptiPlex-780 Platform: Linux PlatformVersion: 3.19.0-25-generic
CompilerName: GCC CompilerVersion: 40400
6. Invocation of PreFreeSurferPipeline.sh :
vasudev@vasudev-OptiPlex-780
:~/Documents/Pipelines-master/PreFreeSurfer$/./PreFreeSurferPipeline.sh
7. The result after the successful run of PreFreeSurferPipeline.sh
" Running FAST segmentation
FLIRT pre-alignment
Running BBR
0.120524 0.999997 0.002582 -0.000243 0.000000 -0.002583 0.999993 -0.002809
0.000000 0.000235 0.002810 0.999996 0.000000 0.269985 -0.265698 0.479317
1.000000
START: T2w2T1Reg
Do 17. Mär 22:50:30 CET 2016 - PreFreeSurferPipeline.sh - Performing Bias
Field Correction
Do 17. Mär 22:50:30 CET 2016 - PreFreeSurferPipeline.sh - mkdir -p
/media/vasudev/Daten/HCP_Subject/mgh_1010/T1w/BiasFieldCorrection_sqrtT1wXT1w
START: BiasFieldCorrection
0.222666
0.976528
.8651950
END: BiasFieldCorrection
Do 17. Mär 22:53:25 CET 2016 - PreFreeSurferPipeline.sh - Performing Atlas
Registration to MNI152 (FLIRT and FNIRT)
START: AtlasRegistration to MNI152
END: AtlasRegistration to MNI152
Do 17. Mär 23:09:01 CET 2016 - PreFreeSurferPipeline.sh - Completed "
8.Invocation of FreeSurferPipeline.sh script :
vasudev@vasudev-OptiPlex-780
:~/Documents/Pipelines-master/PreFreeSurfer$/./FreeSurferPipeline.sh
9. The result after the successful run of FreeSurferPipeline.sh script
"setting MIN_GRAY_AT_WHITE_BORDER to 88.8 (was 70)
setting MAX_BORDER_WHITE to 122.1 (was 105)
setting MIN_BORDER_WHITE to 110.0 (was 85)
setting MAX_CSF to 67.7 (was 40)
setting MAX_GRAY to 97.9 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 99.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 46.5 (was 40)
mean inside = 98.9, mean outside = 96.3
reading initial white vertex positions from white.deformed...
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
reading volume
/media/vasudev/Daten/HCP_Subject/mgh_1010/mri/aseg.hires.mgz...
reading white vertex positions from white.deformed...
inhibiting deformation at non-cortical midline structures...
reading initial pial vertex positions from pial...
repositioning cortical surface to gray/csf boundary.
repositioning pial surface locations using
/media/vasudev/Daten/HCP_Subject/mgh_1010/mri/T2w_hires.norm.mgz
/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 "
I have mentioned the captured outputs after each successful run of
pipelines please kindly review them.
Thanks
Vasudev
On 18 March 2016 at 17:03, Timothy B. Brown <[email protected]> wrote:
> 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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