External Email - Use Caution
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
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:
External Email - Use Caution
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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Asa Borzabadi Farahani -
Douglas N. Greve