Hi,
Do you try to register the functional data to the whole brain? Maybe it
helps, if you zero parts of the brain that for sure are not present in
the functional data (fslmaths -roi option could help). Also, it might be
helpful, if you use masks selecting the part of your functional data
that does not show a strong intensity loss (flirt -inweight and
-refweight options). With a rigid body registration, this might work out
good enough. Make sure that the data is already oriented the same, so
you can use small search angles. Instead of using -nosearch, I set
-searchrx (/y and /z) to a small range.
Is the functional data already corrected for motion? If so, you might
try the average image (fslmaths -Tmean) instead of only the first
volume. corratio seems to give reasonable results for me.
This are just a few suggestions I can make based on my experience with
monkey surface coil data, so maybe this could help you. I guess zeroing
parts of the reference volume might help quiet a bit.
Good luck,
wolf
Marta Moraschi wrote:
> Dear all,
>
> I’m trying to register epi images of human visual cortex acquired with a surface coil ( ftp://lab-g1.phys.uniroma1.it/pub/surfcoil.nii.gz), thus suffering from large intensity variation and partial brain coverage, to T2 weighted images acquired with a volume coil. I've run FLIRT, but it didn't work very well.
> I’ve tried to use FAST before, in order to get the restored epi. I’ve tried to register the restored epi, using its bias field (previously max intensity normalised) as input weighting volume; I’ve mainly used 6 dof and normalised mutual information as cost function, but in point of fact I’ve tried every combination of DOF<6 and cost function. In any case the result was very far away from being good.
> As advised in the forum, I’ve also tried to use the Nudge Gui, thus i’ve found my initial alignment and then i’ve run FLIRT with the search set "Already virtually aligned (no search)" and also use a cost-function weighting volume (i've tried both the intensity normalised bias field and a mask set to 1 everywhere except in the areas where distortion and signal loss are evident, both were previously reported in the partial epi space with nudge). In particular I’ve used the suggested command line:
>
> flirt -in partial_brain -ref anatomical -dof 6 -nosearch -init nudge_matrix.mat -inweight partial_brain_weighting_volume -out partial2anat -omat partial2anat.mat
>
> However, running flirt I’ve noticed a worsening of the alignment i've reached before with the Nudge gui.
>
> I would appreciate any advice. Many thanks in advance.
>
> Marta
>
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