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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