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
>
>
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