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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