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For what its worth, I got a segfault at the same place in melodic’s processing recently.  

Peace,

Matt.

From: Qasim Bukhari <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Monday, June 23, 2014 at 8:12 AM
To: <[log in to unmask]>
Subject: Re: [FSL] melodic segmentation fault

Hi Mark,
Thanks for the quick response. It helps to understand the error but I still couldnt fix it. 
I have the permission to write on the directory, the script already creates some output files, and then it suddenly crashes.
I have attached melodicConcat, the files list and also the log file.


Qasim Bukhari

Research Assistant and Doctoral Candidate

Institute for Biomedical Engineering

ETH and University Zurich

Wolfgang-Pauli-Strasse 27, HIT E22

webpages: MR-page

http://www.biomed.ee.ethz.ch/people/sybukhar





Date: Mon, 23 Jun 2014 11:55:33 +0000
From: [log in to unmask]
Subject: Re: [FSL] melodic segmentation fault
To: [log in to unmask]

Hi,

A "segmentation fault" is a general computing error and doesn't have anything to do with segmentation of brain tissues or structures.  It just means that the program crashed (and there could be many reasons for this).

It seems that your problems arise from the script:
  melodicConcat.sh
yet I do not recognise this as an FSL script.  Is this your own script?

Given that the error message is:
   creating report page ... melodicConcat.sh: line 43: 34013 Segmentation fault: 11  melodic -i /Volumes/G-DRIVE_USB/Analysis_RS_Anesthesia2014/nifti/Resultxfm/files.txt -o $filenameICA'.ica' -v -a concat -d 70 --nobet --tr=1 --report --guireport=./report.html --Oall -v
then it might be an error in this script, or a problem with the inputs to melodic (so it would be necessary to see the result of the variable substitutions) or it could be a problem with quotas or permissions to write to the output directory (in particular the report page, specified as ./report.html).

Hopefully the above will help you track down the problem, but if you cannot then please give us some more details to work with.

All the best,
Mark



On 23 Jun 2014, at 10:24, Qasim Bukhari <[log in to unmask]> wrote:

Dear experts,
can someone please suggest something to the error I discussed below ?  It seems everything was working fine until the last moment it generated some error. I didnt want to do any segmentation but still the error generated is actually segmentation fault. It would be great if someone can shed some light over it

Thanks a lot

best,
Qasim




Qasim Bukhari
Research Assistant and Doctoral Candidate
Institute for Biomedical Engineering
ETH and University Zurich
Wolfgang-Pauli-Strasse 27, HIT E22
webpages: MR-page




From: [log in to unmask]
To: [log in to unmask]
Subject: melodic segmentation fault
Date: Fri, 20 Jun 2014 11:45:38 +0000

Dear FSL experts,
I m getting following error while running melodic
Running Mixture Modelling on Z-transformed IC maps ...
  IC map 1 ... 
   calculating mixture-model fit 
   saving probability map:    /Volumes/G-DRIVE_USB/Analysis_RS_Anesthesia2014/nifti/Resultxfm/Melodic_concat/ICA70components.ica/stats/probmap_1
   saving mixture model fit:  /Volumes/G-DRIVE_USB/Analysis_RS_Anesthesia2014/nifti/Resultxfm/Melodic_concat/ICA70components.ica/stats/MMstats_1
   re-scaling spatial maps ... 
   thresholding ... 
   alternative hypothesis test at p > 0.5
   saving thresholded Z-stats image:  /Volumes/G-DRIVE_USB/Analysis_RS_Anesthesia2014/nifti/Resultxfm/Melodic_concat/ICA70components.ica/stats/thresh_zstat1
   creating report page ... melodicConcat.sh: line 43: 34013 Segmentation fault: 11  melodic -i /Volumes/G-DRIVE_USB/Analysis_RS_Anesthesia2014/nifti/Resultxfm/files.txt -o $filenameICA'.ica' -v -a concat -d 70 --nobet --tr=1 --report --guireport=./report.html --Oall -v


I used this command

melodic -i /Volumes/G-DRIVE_USB/Analysis_RS_Anesthesia2014/nifti/Resultxfm/files.txt -o $filenameICA$'.ica' -v -a concat -d 70 --nobet --tr=1 --report --guireport=./report.html --Oall -v

Can somebody please put light in to it, why is it generating this error ??

Thanks a lot and best,
Qasim





Qasim Bukhari
Research Assistant and Doctoral Candidate
Institute for Biomedical Engineering
ETH and University Zurich
Wolfgang-Pauli-Strasse 27, HIT E22
webpages: MR-page