It may also be that you are running out of disk space. If you're
confident neither of these are the case, could you run mcflirt on the data
manually using the -report flag and post the output to the mailing list?
regards
Peter
On Mon, 25 Mar 2002, Tim Behrens wrote:
> Hi there -
> The error
> Can't open /data/joha/nms_jn.feat/prefiltered_func_data_mcf.hdr
> while executing ....
>
> sounds like you may not have permission to write to the directory:
>
> /data/joha/nms_jn.feat/
>
> Have you checked the permissions on this directory?
>
>
> thanks
> Tim
>
>
> On Mon, 25 Mar 2002, Pasi Tuunanen wrote:
>
> > Hello,
> >
> > We have problems with aligning single-slice data which consist of R2-maps
> > from a visual study. Our flirt-version is 4.0. Since the data is parameter
> > maps, we wouldn't like to touch the pixel intensities. Intensities were set
> > to range of 100...1100.
> >
> > Mcflirt gave us an error:
> >
> > Started FEAT at Mon Mar 25 12:27:14 EET 2002 on keula89.uku.fi
> > Total original volumes = 70
> > Deleting 5 volume(s) - BE WARNED for future analysis!
> > /opt/fsl/bin/avwroi /data/joha/nms_jn
> > /data/joha/nms_jn.feat/prefiltered_func_data 5 65
> >
> > /opt/fsl/bin/avwroi /data/joha/nms_jn.feat/prefiltered_func_data
> > /data/joha/nms_jn.feat/example_func 32 1
> >
> > /opt/fsl/bin/mcflirt -in /data/joha/nms_jn.feat/prefiltered_func_data -out
> > /data/joha/nms_jn.feat/prefiltered_func_data_mcf -plots -refvol 32
> > Can't open /data/joha/nms_jn.feat/prefiltered_func_data_mcf.hdr
> > while executing
> > "exec sh -c $thecommand | grep THRESHOLD | awk {{ print $2 }} - "
> > (procedure "feat4:proc" line 223)
> > invoked from within
> > "feat4:proc [ file rootname [ lindex $argv 0 ] ]"
> > (file "/opt/fsl/bin/feat" line 17)
> > child killed: segmentation violation
> >
> > Basically the same error was produced when we tried modified stack of
> > NxMx3xseries (same slice three times as third dimension) instead of
> > NxMx1xseries.
> >
> > We also tried to use previously mentioned schedule files (3dof) for
> > alignment, but we got only background intensities as a result. High
> > resolution image is available from the same slice.
> >
> > Any ideas?
> >
> > Help appreciated,
> >
> > Pasi Tuunanen
> >
>
> --
> -------------------------------------------------------------------------------
> Tim Behrens
> Centre for Functional MRI of the Brain
> The John Radcliffe Hospital
> Headley Way Oxford OX3 9DU
> Oxford University
> Work 01865 222782
> Mobile 07980 884537
> -------------------------------------------------------------------------------
>
--
Peter R. Bannister
Analysis Group, FMRIB
Tel: +44 (0)1865 222782 Fax: 222717
http://www.fmrib.ox.ac.uk/~prb
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