All,
Using flirt, I am having somewhat unsatisfying alignment between
whole-brain EPI and T1w images. After alignment, It appears that the EPI
volume is always "pulled down" by a few millimeters. It happens to almost
all my data. I guess it is because of the signal dropout.
Here is the command I typically use.
flirt -in epi_dewarp_bet -ref T1w_bet -omat epi2t1.mat -out
epi_dewarp_bet_aligned
The EPI images have been corrected for distortion before running flirt.
I heard of a solution to mask the images or weighted the voxels when
computing the cost function. But not sure how to do it. Any thought or
solution is gratefully appreciated?
Zhongming Liu
NIH
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