Hi Steve,
I've attached the file. In the meantime, I've successfully compiled FSL for
my SUSE system, and the Feeds test suite now runs fine. Still, my own data
crashes the same way. I'm a bit confused why this happens, but I'll try to
setup a Redhat system and see if that helps. By the way, is FSL fine with
mulitprocessor systems, or could this be the culprit?
Thanks for your help
Johannes
> -----Ursprüngliche Nachricht-----
> Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]]Im
> Auftrag von Stephen Smith
> Gesendet: Dienstag, 27. Juli 2004 23:19
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] AW: [FSL] Feat trouble
>
>
> 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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