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FSL  2004

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Subject:

Re: feeds failed

From:

Zrinka Bilusic <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 7 Jul 2004 14:06:28 -0700

Content-Type:

text/plain

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text/plain (143 lines)

Hello,
"melodic --help" did display the help info on melodic - so it did run.
However, I got "segmentation fault" error while running the feeds data
using melodic. The only thing I can find in the output folder in the
mask image, and that one seems fine (compared to the mask image in the
corresponding ica folder in results folder). So I am guessing that
something happened during compilation? (there were no errors reported).
any ideas? Thanks!!

here is the output from running melodic:

melodic -i feeds/data/fmri -v --report

Melodic Version 2.0

Melodic results will be in feeds/data/fmri.ica+

Reading data file feeds/data/fmri  ...  done
Create mask ...   Calling BET: /Users/nina/fsl_gcc_G5opt/bin/bet
/var/tmp/tmp.0.xCk5ot /var/tmp/tmp.0.xCk5ot_brain -m -f 0.4 > /dev/null
done
Excluding voxels with constant value
Data size : 180 x 16911
Removing mean image ... done
Estimating data covariance ... done
Perform variance-normalisation ... done
Removing mean time course ... done
Segmentation fault

On Jul 7, 2004, at 3:44 AM, Christian F. Beckmann wrote:

> Hi Zrinka,
>
> feeds is a very simple script which runs different parts of FSL. If
> melodic does not complete feeds this is quite likely to be due to
> compilation issues. First, you should try and see if the different
> binaries run at all (just type melodic --help).
> If the binaries are OK, run melodic on the feeds example fmri data set
>
> melodic -i /PATH_TO_FEEDS/data/fmri -v --report
>
> and see if that tells you more about what is going on.
> cheers
> christian
>
>
> On 30 Jun 2004, at 18:48, Zrinka Bilusic wrote:
>
>> Hello...
>>
>> I have just recompiled FSL again with the latest version of gcc (3.3)
>> using also the G5 optimization flags (suggested by apple and
>> applicable
>> only for gcc 3.3 I believe) and I ran feeds (I wanted to compare the
>> performance of the G5 optimized gcc vs IBM xlc). However, it failed
>> while testing Melodic (see below for the output). I checked the
>> compilation and it completed without any errors and almost no
>> warnings.
>> What does it exactly mean when feeds test fails? What should I be
>> looking for to fix this?
>>
>> Thanks!
>> zrinka
>>
>> FSL Evaluation and Example Data Suite v3.1
>>
>> start time = Tue Jun 29 15:09:14 PDT 2004
>> hostname = nina.local
>> os = Darwin nina.local 7.4.0 Darwin Kernel Version 7.4.0: Wed May 12
>> 16:58:24 PDT 2004; root:xnu/xnu-517.7.7.obj~7/RELEASE_PPC  Power
>> Macintosh powerpc
>>
>>
>> /bin/rm -rf /Users/nina/feeds/results /Users/nina/feeds/data/fmri+*
>>
>>
>> mkdir /Users/nina/feeds/results
>>
>>
>> Starting SUSAN at Tue Jun 29 15:09:14 PDT 2004
>> % error = 0.0
>>
>> Starting PRELUDE & FUGUE at Tue Jun 29 15:12:53 PDT 2004
>> % error = 0.0
>> % error = 0.0
>>
>> Starting SIENAX (including testing BET and FLIRT and FAST) at Tue Jun
>> 29 15:12:56 PDT 2004
>> checking error on BET:
>> % error = 0.0
>> checking error on FLIRT:
>> % error = 0.322037594668
>> checking error on FAST:
>> checking error on single-image binary segmentation:
>> % error = 0.345114163645
>> checking error on partial volume images:
>> % error = 0.393971552914
>> % error = 0.281726013818
>> % error = 0.264880778174
>> checking error on SIENAX volume outputs:
>> % error = 0.0351231718211
>> % error = 0.00218948572482
>> % error = 0.00546535143417
>> % error = 0.0313234567567
>> % error = 0.0367888081908
>>
>> Starting FEAT at Tue Jun 29 15:24:52 PDT 2004
>> checking error on filtered functional data:
>> % error = 0.179583640438
>> checking error on raw Z stat images:
>> % error = 0.311126636832
>> % error = 0.202559213588
>> % error = 0.303332786639
>> checking error on thresholded Z stat images:
>> % error = 0.388013690501
>> % error = 0.196759687433
>> % error = 0.335210397996
>> checking error on position of largest cluster of Talairached zfstat1:
>> % error = 0.04
>> % error = 0.28
>> % error = 0.184
>> % error = 0.032
>> % error = 0.14
>> % error = 0.028
>>
>> Starting MELODIC at Tue Jun 29 15:39:48 PDT 2004
>> % error = 6.66666666667
>> Warning - test failed!
>>
>> Warning - not all tests passed
>>
>> end time = Tue Jun 29 15:40:24 PDT 2004
>>
>>
> --
>  Christian F. Beckmann
>  Oxford University Centre for Functional
>  Magnetic Resonance Imaging of the Brain,
>  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>  Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
>  Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
>

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