This was taken from the previous message I had sent. Would really appreciate any advice!
The output file uAPPA looks good, but my last slice (slice 20) is actually slice 1 repeated. Is this because FSL starts counting from 0, and is there any way to correct this?
I then know I need to use applytopup (to test this I will use a magnitude image of 20 slices, 24 time steps).
applytopup --imain=M_20 --inindex=1
--datain=topup_param.txt --topup=my_topup_results --method=jac
--interp=spline --out=u_M20
This all looks fine but except slice 20 is now missing. At least here I know that the distortion correction is working.
I then want to use mcflirt for the motion correction (for both magnitude and phase). I will use the original phase encode blip image (AP) as the reference volume:
mcflirt -refvol AP.nii.gz -in mag.nii -out mag_mc.nii.gz -mats
However, when I open the .mat files, the transformations contain 16 numbers in each file going from MAT_0000 to MAT_0023.
I wonder whether the 16 came from? I thought there should be 20 transformations as there are 20 slices? Does the MAT volumes correspond to the number of time steps? How can I be sure that the motion correction has been applied to all 24 time steps?
I would then like to apply the motion correction transform to the associated phase images. Can you apply the previous .mat file to the phase image directly?
mcflirt -refvol AP.nii.gz -in phase.nii.gz -out phase_mc.nii.gz -init mag_mc.nii.gz.mat
I don't think this is right; I am not sure what to put for the -init command or even if that is needed.
Many thanks,
Cheers
Lucy
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