hi experts,
a question about masking during estimation under SPM2...is there any
reason why the following should be happening? A subject whose brain normalizes fairly
reasonably to the EPI template, gets a portion of the frontal lobe lopped
off during estimation, as can be see in the mask produced by the
first-level analysis (I posted the output of 'check reg' online at
http://angora.snv.jussieu.fr/~chris/stuff/wierdmasking.tiff ....top left
EPI template; top right, smoothed normalized EPI image for this subject;
bottom left, mask.img created during estimation; bottom right, a con*
image). As you can see, although the smoothed normalized image is a good
match to the template, the most anterior bain gets masked out. Why is
this? I tried the following so far:
1) check realignment params (they are all OK, <1.5mm movement across 8
sessions), no bouncing around in the scanner.
2) check that there is not a misplaced volume (I extracted data from a
voxel falling within the missing part of the mask for each swavol* in each
run, and checked for zeros or NaNs...there were none. Nor were the values all the same. They
were all nice reasonably consisten values.
3) I tried to manually set an explicit mask corresponding to the EPI
template, by setting SPM.xM.VM=spm_vol('EPI.mnc') before analysis, vainly
hoping that SPM would let me choose what to mask out (it didn't...same old
problem).
4) I tried changing the bounding box to the EPI template default, which
seems to be a bit larger...this made no difference either.
Any ideas? many thanks....
Chris
Christopher Summerfield
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