Hi - the longer of the report.log files that you sent has all the
long commands interrupted with a "!" and a carriage return - is that
in the original log or a result of copying the file when you sent it
to the list? I suspect the latter but if the former then that would
indicate a problem.
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>
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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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