I suspect that you may not be using fslview quite right - to view a time
series along with a stats map you need to start by loading in
filtered_func_data.hdr as the first thing you load into fslview, the
file->add a stats image to get a colour overlay, then highlight the
filtered_func_data in the lower-left-corner list, then turn on timeseries
display.
cheers.
On Thu, 26 Feb 2004, Jane Aspell wrote:
> thanks Mark
> I am running Linux (redhat 9) so i'll have a go with the slower flirt.
> the registrations were fine for the other subject for which i completed
> a higher level analysis. the runs were quite variable though - i could see that
> from eye, looking at the locations of the activations (but each run
> was only made up of 30 volumes). i seem to have a
> problem looking at time series though - for most functional files that
> i load into fsl view, when i click time series nothing appears - even for
> stats images from the higher level analysis. the only
> time i am able to see time series is when i load an orignial series_2.*.hdr
> and overlay a stats image onto to it. is this correct?
>
> thanks again
>
> jane
>
>
> In message <[log in to unmask]> FSL - FMRIB's Software Library <[log in to unmask]> writes:
> > Hi Jane,
> >
> > I'm afraid you are experiencing the effects of an intermittent
> > bug in flirt which we think is caused by the compilers we use,
> > which was unexpected. What machine are you running it on?
> > If it is linux (redhat 8 or 9) then a non-optimised version of
> > flirt, which is slower but doesn't crash, can be installed.
> > See:
> > http://www.fmrib.ox.ac.uk/fslfaq/#flirt_crash
> >
> > You might need to get your sysadmin to do this for you.
> >
> > If you are not running on linux/redhat 8 or 9 then let us know.
> >
> > As for the group analysis, this can happen if there is a lot of
> > variation between the runs. Does the data from different runs
> > appear significantly different in fslview (look at the timeseries)?
> > Also, if your registrations aren't working then you won't get
> > any good higher level results. Do all the registrations in the
> > registrations reports look good?
> >
> > If you can't see anything obviously wrong in the above, then let
> > us know and we can try to have a look at your data/design.
> >
> > All the best,
> > Mark
> >
> >
> >
> > Jane Aspell wrote:
> >
> > >Hi
> > >
> > >I'm new to FSL and am having a few problems. When I run a first level
> > >analysis using FEAT for one of my subjects something seems to go wrong with
> > >the co-registration of the high res image to the standard brain. In Feat
> > >watcher i get the following error:
> > >
> > >/usr/local/fsl/bin/convert_xfm -matonly -inverse -omat standard2highres.mat
> > >highres2standard.mat
> > >Could not open matrix file highres2standard.mat
> > >Cannot read input-matrix
> > >
> > >/usr/local/fsl/bin/slicer highres2standard standard -s 1 -x 0.35 sla -x 0.45
> > >slb -x 0.55 slc -x 0.65 sld -y 0.35 sle -y 0.45 slf -y 0.55 slg -y 0.65 slh
> > >-z 0.35 sli -z 0.45 slj -z 0.55 slk -z 0.65 sll ; /usr/local/fsl/bin/convert
> > >-colors 100 +append sla slb slc sld sle slf slg slh sli slj slk sll
> > >highres2standard.gif ; /bin/rm -f sla slb slc sld sle slf slg slh sli slj
> > >slk sll
> > >Cannot open volume highres2standard.hdr for reading!
> > >convertb: no delegate for this image format (sla).
> > >convertb: no delegate for this image format (slb).
> > >convertb: no delegate for this image format (slc).
> > >convertb: no delegate for this image format (sld).
> > >convertb: no delegate for this image format (sle).
> > >convertb: no delegate for this image format (slf).
> > >convertb: no delegate for this image format (slg).
> > >convertb: no delegate for this image format (slh).
> > >convertb: no delegate for this image format (sli).
> > >convertb: no delegate for this image format (slj).
> > >convertb: no delegate for this image format (slk).
> > >convertb: no delegate for this image format (sll).
> > >convertb: Missing an image file name.
> > >
> > >/bin/rm -f highres2standard.hdr highres2standard.img
> > >
> > >And I found that the highres2standard.mat transform is missing from the /reg
> > >directory in the relevant .feat directory.
> > >So i tried to create it with the command:
> > >flirt -in highres -ref standard -omat highres2standard.mat
> > >But that just returns 'Segmentation fault'
> > >
> > >I haven't had this problem with my other subject. Any ideas?
> > >
> > >My second problem is with higher level analysis. I ran successful first
> > >level analyses for the 5 series(runs) for a single subject and got good
> > >activations for my contrasts (z~6) but when i run the higher level analysis
> > >to put all the runs (which are simply repeats of the same conditions)
> > >together all the activation seems to disappear! I re-ran the higher level
> > >analysis with a lower z threshold (1.0) and was then able to see activations
> > >(z scores <3 could be seen). Is this the correct thing to do? I thought
> > >the activations would be more significant, not less, when I average all
> > >my runs together so I'm puzzled.
> > >
> > >Thanks very much for your help.
> > >
> > >Jane Aspell
> > >
> > >
> >
>
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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