Hi Steve,
Thank you for your reply.
I ran the first avwmerge command starting with 2 subjects and adding 1 subject at a time subsequently.
I found that including a particular subject caused the avwmerge command to fail (segmentation fault).
I reprocessed the data, and the 3rd-level processing went ok, so the problem was probably due to corrupted mask.
-Yoshiko
> The problem starts at the first long avwmerge command - could you try
> running that command by hand to see if it works (if it's hard to
> paste such a long command successfully into the terminal then copy
> report.log, delete everything else except that command then run that
> file as a script.
>
> It may be that for some reason one of the second-level masks has
> gotten deleted or corrupted on your filesystem.
>
> Cheers, Steve.
>
>
>
>
> On 14 Mar 2007, at 01:54, Yoshiko Yamada wrote:
>
> > Dear List,
> >
> > I'm having a problem processing data from multiple subjects. On the
> > 2nd level analysis where
> > multiple runs of each subject were processed went fine. However,
> > on the 3rd level where multiple
> > subjects are processed, I got the following error message in the
> > terminal window:
> >
> > couldn't open "tmpreport.html": no such file or directory
> > while executing
> > "open tmpreport.html r "
> > (procedure "feat5:report_insert_stop" line 4)
> > invoked from within
> > "feat5:report_insert_stop poststatspics"
> > (procedure "feat5:poststats" line 348)
> > invoked from within
> > "feat5:poststats 0 [ expr $fmri(level) - 1 ]"
> > (procedure "feat5:proc" line 1362)
> > invoked from within
> > "feat5:proc [ file rootname [ lindex $argv 0 ] ]"
> > (file "/usr/local/fsl/bin/feat" line 16)
> >
> > In the report.log (1st one in the attachment), I saw the following
> > error:
> >
> > /usr/local/fsl/bin/avwmaths mask -Tmin mask
> > ** ERROR: nifti_image_read(mask): can't open header file
> > ** ERROR: nifti_image_open(mask): bad header info
> > Error: failed to open file mask
> > Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
> >
> > It seemed that the mask.nii.gz was not created by the avwmerge
> > command just before the
> > avwmaths command, so I tried running the avwmerge command by itself
> > in the terminal and got
> > “segmentation fault.”
> >
> > Is it this “segmentation fault” that is failing the 3rd level
> > analysis? What does it mean? From
> > reading some of the earlier postings, I understand that
> > segmentation fault occurs when you try to
> > convert large 3d data to 4d, but the masks that the above avwmerge
> > command is trying to
> > concatinate are pretty small (~21KB). I also checked the dimensions
> > of the masks, and they are all
> > the same.
> >
> > I’d appreciate any help you could give me!
> >
> > (I tried to post the above message in reply to an earlier posting,
> > but it didn't seem to go through. I
> > apologize if you have read my earlier message.)
> >
> > -Yoshiko
> > <report.log>
> > <report.log>
>
>
> ------------------------------------------------------------------------
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ------------------------------------------------------------------------
> ---
>
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