Hi HCP gurus: I've been trying to adapt the HCP pipeline for use in our group, and having trouble with the tools for resting state processing. The pipeline's Example programs are super helpful for illustrating calls to the minimal preprocessing and the Task-fMRI tools. However the resting-fMRI tools are organized differently, with no example calling program provided. I wonder if I could get a few tips? I am using pipeline version v3.22.0-beta.2, and I have so far successfully run pipeline modules on HCP subjects as well as our own: PreFreesurferPipeline.sh FreesurferPipeline.sh PostFreesurferPipeline.sh GenericfMRIVolumeProcessingPipeline.sh GenericfMRISurfaceProcessingPipeline.sh ICA-FIX I know that after ICA-Fix I could continue with a group analysis using Dual Regression and FSLnets. But how to proceed if one wanted to do a seed-based analysis? I'm not sure I see the purpose of PostFix, ReApplyFix and RestingStateStats. They rely on compiled matlab code, so it is hard to figure out what they are actually doing. Regardless, I tried running RestingStateStats, but it triggered an error when it could not find a file apparently created by MSMSulc. (I assume this is because I ran earlier parts of the pipeline with RegName="FS"). When I tried to rerun PostFreesurferPipeline.sh with RegName="MSMSulc", it seems that our version of the pipeline does not include an MSM binary. I have searched the HCP website but don't see where this binary is available. Alternatively, if I download the available MSMAll, can it be used with pipeline version 3.22? Unfortunately with all of the excellent documentation on the HCP website, there is a dearth of *high-level* guidance on how to proceed with resting-state processing. I'd be grateful for any insights... Thanks, Christina Fales
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