Hi - yes, FEAT cleans up the reg-standard directory (which saves a lot of
disk space but is a pain when trying to debug things like this!). Edit
fsl/tcl/feat.tcl and comment out the two lines with the
....featregapply...... -c
in them (make sure you look for the -c at the end) and then FEAT won't do
this cleanup.
Cheers, Steve.,
On Mon, 22 Mar 2004, Tyler Lesh wrote:
> Hi Steve,
>
> So I've actually monitored the analysis up to the point where it fails, and
> featregapply appears to be working correctly. It creates all of the
> requisite files in the reg_standard folder and I can view them. Also, it
> removed the reg_standard folders by itself (even though the avwmerge's
> failed). Therefore, every time I have tried to run the analysis, the
> reg_standard folder has already been removed.
>
> Thanks,
>
> Tyler
>
>
>
>
> On Sat, 20 Mar 2004 08:42:43 +0000, Stephen Smith <[log in to unmask]>
> wrote:
>
> >Hi - this all sounds reasonable. have you tried deleting all of the
> >.feat/reg_standard first-level subdirs before running the higher-level
> >analysis? If so, did the calls to featregapply from within the
> >higher-level run seem to work right?
> >
> >Cheers, Steve.
> >
> >
> >On Thu, 18 Mar 2004, Tyler Lesh wrote:
> >
> >> Hi,
> >>
> >> I've recently run into difficulty performing a 2nd level analysis.
> >>
> >> I have 14 subjects, with 3 sessions each. I ran the first level, creating
> >> feats for each session, registering to the standard template. The second
> >> and third levels completed without fail.
> >>
> >> However, I wanted to redo the analysis using an average brain composed of
> >> all of the subjects. I created the average brain according to the FSl
> >> tutorial and registered all of the first level feats to this average. (I
> >> achieved this by sed-ing the .fsf's and substituting the average brain
> for
> >> the supplied standard and only running registration.) The registrations
> >> look great and I have recently tried to perform a new 2nd level analysis
> on
> >> these average-registered feat directories.
> >>
> >> I keep getting this error:
> >>
> >> no files matched glob pattern "stats0/*hdr"
> >> while executing
> >> "glob stats0/*hdr "
> >> (procedure "feat5:proc" line 883)
> >> invoked from within
> >> "feat5:proc [ file rootname [ lindex $argv 0 ] ]"
> >> (file "/space/raid/fmri/fsl/bin/feat" line 17
> >>
> >> After viewing the log file, it appears that avwmerge does not
> successfully
> >> create the merged cope and varcope files and produces this line:
> >>
> >> /space/raid/fmri/fsl/bin/avwmaths cope1 -mas mask cope1
> >> Can't open cope1.hdr
> >>
> >> and
> >>
> >> /space/raid/fmri/fsl/bin/avwmaths varcope1 -mas mask varcope1
> >> Can't open varcope1.hdr
> >>
> >> etc.
> >>
> >> I apologize for the long post, but I have tried manually running
> >> featregapply and avwmerge on a single session and it was successful. I
> >> have reached the limits of my troubleshooting abilities and am trying to
> >> avoid rerunning all of the first level. If anyone has any
> recommendations,
> >> I would greatly appreciate it.
> >>
> >> Thanks so much,
> >>
> >> Tyler
> >>
> >
> > 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
>
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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