Hello,

I have a dataset where reviewers recommended that we analyze the pre- scan and post- scan together. In short, we are using fMRI to see our resting state data.

As a result, the plan is to align each epi to the mean T1 and then proceed with analysis. Further, I have been using slomoco instead of 3dvolreg, and the developers recommend the two not be run together.

My pipeline is as follows:
1) Run Slomoco
2) Align epi2anat (mean anat)
3) Use the following afni_proc.py on the slomoc data

afni_proc.py -subj_id $subj                                           \
        -script proc.$subj -scr_overwrite                             \
        -blocks blur mask scale regress      \
        -copy_anat $anat_dir/anat_ns_mean+orig                          \
        -dsets                                                        \
            $epi_dir_pre/SLOMOCO5/${subj}pre+orig.HEAD  \
            $epi_dir_post/SLOMOCO5/${subj}post+orig.HEAD  \
        -blur_size 5.0                                                \
        -regress_stim_times                                           \
            $top_dir/LeftHand.txt                                 \
        -regress_stim_labels                                          \
            LH                                                       \
        -regress_basis 'BLOCK(45,1)'                                \
        -regress_make_ideal_sum sum_ideal.1D                          \
        -regress_est_blur_epits                                       \
        -regress_est_blur_errts

The code runs fine, except I'm left with a "grid mismatch error" of the 2 runs on the .scale data.

My solution was to 3dresample the post- epi to the pre- epi. I no longer received the error, but I'm not sure if this is the right plan of action. I have read on the forum that others have used 3drefit, but from my understanding this doesn't change the .BRIK file.

When I compare the stats between the two approaches (3dresample vs. not doing anything different) there are slight differences.

Can someone guide me to the right solution?

Thanks



Edited 3 time(s). Last edit at 02/19/2021 04:54PM by Dxc536.