[RESOLVED] HCP fMRIVolume pipeline, granular control of images to process

I am processing a legacy MRI data set that includes resting and stimulus-evoked BOLD runs. Unfortunately the rest and stim BOLD sequences have different resolutions and different echo spacing time (and different GRE field maps, respectively). So I believe that I need to run the rest BOLD runs separately from the stim BOLD runs, so each can be assigned their respective echo spacing time. However, all BOLD runs are numbered sequentially after the “setup_hcp” step - see screenshot of the “unprocessed” folder.

Thus I believe they would all be processed together. How can I do so using the “HCP fMRIVolume pipeline” command? Thank you.

The command has the --bolds parameter to filter bolds. You can use the contents of you batchfile to find a filtering that fits your use case. For example, --bolds=2,3 will process BOLDS 2 and 3, --bolds="rest" will process BOLDS that are tagged as rest inside the batch file, etc.

See hcp_fmri_volume — QuNex documentation and HCP fMRIVolume pipeline — QuNex documentation for additional details.

Exactly what I needed, thank you.