Hi. I am trying to use topup on some diffusion-weighted images of a rat spinal cord. The results are great except I am losing some of the slices! The original data has 12 slices (all including the spinal cord, no blank ones on either side), but after running topup only some of the slices in the middle have image in them, and a few on either end are blank. I want to compare different subjects and this is a problem because on each subject a different number of slices are preserved. I am trying to find a way to use topup on this data and preserve all 12 slices every time.
So far I have tried padding my images with "empty" slices on either end first (to give more space for error), but that doesn't work. I would like to see if there is a way to apply topup 2-dimensionally, on each slice separately. I used fslsplit but realized topup won't each slice individually because 1 is an odd number in the slice dimension. So I combined the slices into pairs of two adjacent and tried running topup on these, but all I get is an "Abort trap: 6"
Is there any way that I haven't thought of to get topup to preserve all 12 slices? Thank you.
|