Hi,
We are trying to use topup to correct for image distortions. We have acquired 2 runs of resting state fMRI data with different phase encondings (AP and PA). I use fslmerge to combine both images and when I run topup, I get a message saying "mismatch between imain and datain"
My datain file looks like this
0 -1 0 .06136
0 1 0 .06136
I calculated the total redout time as 1/BandwidthPerPixelPhaseEncode: 16.29700089. I have seen some threads where they multiple the readout time by 1000, but I still get the same message. I also saw some threads where they mentioned that the # of slices can affect topup. We have 72 slices so tried to remove one slice and still did not work.
This is our data parameters
effective echo spacing: 0.59ms
matrix size: 104 104 72
TR: 1550
TE: 37.8
voxel size 2*2*2mm
Our scanner is a Siemens PRISMA.
Thank you,
Omar
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