fsfast does not work with topup in this way. You can do a couple of things (1) do the preprocessing yourself and then turn it off for fsfast (2) create your own B0 map and put it in to sessid/fsd/b0dcmap.nii.gz and specify -b0dc in mkanalysis-sess
On 12/8/2022 9:50 AM, Asa Borzabadi Farahani wrote:
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Hi,
I have two basic questions.
1- I am currently having some AP fMRI runs and I have also acquired a single PA run to be able to do distortion correction, my original plan was to use FSL and apply topup to get the undistorted fMRI data. How can I fit it within the preproc-sess command? ( I suppose the motion correction and slice timing correction should be done before topup), could you please suggest me what is more appropriate to do?
2- In my study, for each subject I did 8 runs in a single data acquisition session. The runs that I have are 2 different types; The first type of runs ( 4 runs) have black background and the other 4 runs have the gray background. My ultimate goal is to compare these 2 conditions in a group and subject level. Do you suggest that in the functional folder, I create two sessions per subject and put the four runs with gray background in session 1 and the other four runs with the black background in session 2?
Thank you so much for your time and consideration.
Asa Farahani
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