I have successfully run the distortion correction on the BOLD images. The error was that the bvals and bvecs matrices (bvals: 3×246 and bvecs: 1×246) had to have only a zero in the first column and different values to 0 in the rest. However, at this moment I have two important questions:
1- Will it have any effect on the image if there are values other than zero in the rest of the columns? I used the value 1000. I think that this will not be a problem because b=0 will be used as the reference image. That’s right?
2. I would like to do the fMRI analysis in SPM12. In which preprocessing step should I include the EPI distortion correction with brainsuite? Maybe after realignment for motion correction? Pleas any insight about this would be very appreciated. This would be my pipeline
– Slice timing
– Realign: Estimate and Reslice
– Coregister: Estimate
– Dartel: create templates
– Dartel: Normalise to MNI structural scans.
– Dartel: Normalise to MNI functional scans.