Hi,
I have files in AFNI format and would like to use FSL's flirt to automatically
coregister the functional and anatomical images. However, I don't seem to be
getting it to work...a couple of the anatomical views seem chopped (in fslview)
when I convert from AFNI to ANALYZE format (I have FSL set up to create the
ANALYZE format by default), and the alignment does not look right either.
Here is what I did
3dAFNItoANALYZE sampleAnat sub1.anat+orig.HEAD
3dAFNItoANALYZE sampleFcn sub2.%cs+orig.HEAD
and then I ran flirt:
flirt -in sampleFcn.hdr \
-ref sampleAnat.hdr \
-out check_temp.hdr \
-omat fcnl2anat.mat -dof 6
I've also tried using the GUI, stripping the anatomy so it's just brain, using
BET, and then running flirt through the GUI in case i've messed up some of the
parameters...but still unsuccessful....I checked by opening the output of BET
("sampleAnat_brain") in FSLView and File > Add > "check_temp.hdr"
What am I doing wrong?!
Thanks for any help!
g
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