Question about ICAFIX / MSMAll setup for multi-day rfMRI data with TMS
李佳艺
We have an experimental design involving multi-day fMRI acquisition with TMS intervention. On Day 1, we collected rfMRI_day1_AP and tfMRI_day1_AP. On Day 3, we collected fMRI both before and after TMS. Before TMS: rfMRI_day3_bfTMS_AP, tfMRI_day3_bfTMS_AP, tfMRI_day3_bfTMS_PA. After TMS: rfMRI_day3_aftTMS_AP, tfMRI_day3_aftTMS_AP, tfMRI_day3_aftTMS_PA
Because TMS may alter resting-state functional connectivity, my plan is to run MSMAll using only rfMRI_day1_AP and rfMRI_day3_bfTMS_AP. In our current batch.sh configurations, the scripts are set as follow:
ConcatNames="rtfMRI_all"
In MSMAllPipelineBatch.sh:
In DeDriftAndResamplePipelineBatch.sh:
From the documentation and discussions I saw, it’s generally recommended to use all fMRI runs for a subject together in a single MRFIX group during ICAFIX. My questions are:
2. Should I separate the Day 1 and Day 3 sessions and process them independently be more appropriate?
Thank you very much for your help.
Glasser, Matthew
I always lean towards just combining everything for MR+FIX unless you have so much data that things become unmanageable (huge numbers of components, slow processing, etc.). For MSMAll, the tradeoff you are balancing is CNR for functional networks (and MSM’s sensitivity to overfit random noise) vs any potential effect on functional connectivity in the partial domain across the MSMAll sICA d=40 networks. Probably the effect of TMS is going to be pretty minor in the grant scheme of things and we successfully run MSMAll on task fMRI data when we don’t have resting state fMRI data.
Matt.
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