Hi - from your original error message, it looks like the FEAT script is
unable to read the file "prefiltered_func_data_mcf_abs_mean.rms" in the mc
subdirectory. Could you send in this file for us to look at?
Cheers.
On Wed, 21 Jul 2004, Johannes Klein wrote:
> Hi Mark,
> sorry, the mc dirlist is:
> pollux /daten/draid/usr/oweber/RAWDATA/feat_skip+.feat/mc --> ls -l total
> 288
> -rw-r--r-- 1 johannes ecat 4453 Jul 15 18:43
> prefiltered_func_data_mcf.par
> -rw-r--r-- 1 johannes ecat 565 Jul 15 18:43
> prefiltered_func_data_mcf_abs.rms
> -rw-r--r-- 1 johannes ecat 9 Jul 15 18:43
> prefiltered_func_data_mcf_abs_mean.rms
> -rw-r--r-- 1 johannes ecat 587 Jul 15 18:43
> prefiltered_func_data_mcf_rel.rms
> -rw-r--r-- 1 johannes ecat 10 Jul 15 18:43
> prefiltered_func_data_mcf_rel_mean.rms
> -rw-r--r-- 1 johannes ecat 54031 Jul 15 18:43 rot.gif
> -rw-r--r-- 1 johannes ecat 54031 Jul 15 18:43 trans.gif
> I'm running on a 4 processor Xeon running Suse 8.2, 1GB Ram, 1GB Swap,
> Kernel 2.4.20. I've installed the precompiled version for Redhat, which runs
> fine otherwise (I only needed to change the tixwish link). So far, FSL ran
> smoothly, but I hadn't been using Feat. I've run the FEEDS suite and it
> fails with an error message which I've attached.
> So, I guess I should take another machine and install Redhat? Or has anyone
> had success running on Suse, which I'm more familiar with?
> Thanks
> Johannes
>
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: FSL - FMRIB's Software Library
> > [mailto:[log in to unmask]] Im Auftrag von Mark Jenkinson
> > Gesendet: Dienstag, 20. Juli 2004 18:15
> > An: [log in to unmask]
> > Betreff: Re: [FSL] AW: [FSL] Feat trouble
> >
> >
> > Hi,
> >
> > I was hoping for the ls -l of the mc directory, but if you
> > say they look
> > fine
> > then I'm not sure what it might be.
> > Can you please let us know:
> > # What platform are you running FSL on (CPU type, OS type &
> > version, how
> > much RAM, Swap space etc. is available on your system)?
> > # How did you install FSL (from binaries or compiled from
> > source)? # Does the software run on the FEEDS example data?
> >
> > Also, if you tar up the feat directory and put it on a
> > website (or ftp)
> > we can
> > download it and have a look at it.
> >
> > All the best,
> > Mark
> >
> >
> > Johannes Klein wrote:
> >
> > >Hi Mark,
> > >thanks for your answer!
> > >I've had a look at the data, and the mcflirt output exists and looks
> > >fine upon inspection with fslview. The ls -l output is
> > attached. There
> > >are no SPM files around, I've created new directories for
> > the data. Any
> > >suggestions what I might do to shed some light onto this would be
> > >highly appreciated ... It was all so much easier in Würzburg
> > ;) Thanks
> > >Johannes
> > >
> > >
> > >
> > >>-----Ursprüngliche Nachricht-----
> > >>Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im
> > >>Auftrag von Mark Jenkinson
> > >>Gesendet: Montag, 19. Juli 2004 17:10
> > >>An: [log in to unmask]
> > >>Betreff: Re: [FSL] Feat trouble
> > >>
> > >>
> > >>Hi,
> > >>
> > >>The report.log has some very strange entries in it after
> > the commands:
> > >>
> > >>/bin/mkdir mc ; /bin/mv -f prefiltered_func_data_mcf.par
> > >>prefiltered_func_data_mcf_abs.rms
> > >>prefiltered_func_data_mcf_abs_mean.rms
> > >>prefiltered_func_data_mcf_rel.rms
> > >>prefiltered_func_data_mcf_rel_mean.rms mc
> > >>
> > >>This probably means that something has gone wrong in the mcflirt run
> > >>which shows up when the motion plots are being generated. One
> > >>possibility is that mcflirt couldn't write to the right place so
> > >>that some output was not generated or that there were existing files
> > >>that were not overwritten (any SPM *.mat files that were in the
> > >>wrong place could cause a problem like this I guess). However, it
> > >>could be something unrelated to this as well.
> > >>
> > >>Could you check to see if the contents of your mc directory are
> > >>sensible and like other feat folders? If you are not sure then send
> > >>us a long listing (ls -l) of this subdirectory.
> > >>
> > >>All the best,
> > >> Mark
> > >>
> > >>
> > >>
> > >>Johannes Klein wrote:
> > >>
> > >>
> > >>
> > >>>Hi everyone,
> > >>>I'm trying to re-evaluate some old data with Feat for
> > >>>
> > >>>
> > >>comparison with
> > >>
> > >>
> > >>>the old SPM results, which is a simple ABAB style block
> > >>>
> > >>>
> > >>design. When I
> > >>
> > >>
> > >>>start the analysis, it runs for awhile and then the console
> > >>>
> > >>>
> > >>says: error
> > >>
> > >>
> > >>>reading "file4": I/O error
> > >>> while executing
> > >>>"gets $mcchannel line"
> > >>> (procedure "feat5:proc" line 598)
> > >>> invoked from within
> > >>>"feat5:proc [ file rootname [ lindex $argv 0 ] ]"
> > >>> (file "/usr/local/fsl/bin/feat" line 17)
> > >>>Processing stops. I've attached the report.log.
> > >>>I'm a bit lost here. Can anyone give me a hint what's wrong?
> > >>>
> > >>>
> > >>Thanks for
> > >>
> > >>
> > >>>your time Johannes
> > >>>
> > >>>
> > >>>
> > >>>
> > >
> > >
> > >
> >
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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