Can I apply QSIprep on HCP minimal processed dwi data?

As the title, can I apply QSIprep on HCP minimal processed dwi data to construct the structual connectome or I have to do this from unprepocessed dwi images?

If you’re satisfied with the HCP preprocessed image, then I suppose you can just feed those images into QSIRecon and skip QSIPrep, making sure to include the following commands:
[--recon-only] [--recon-spec RECON_SPEC] [--recon-input RECON_INPUT], where RECON_SPECs the style of reconstruction you want and RECON_INPUT is path to your processed DWI image folder in BIDS format (e.g. the usual output of QSIPrep).

This becomes more complicated if 1) These preprocessed images are not in a BIDS format (solution: rearrange them to BIDS) or 2) You want to re-preprocess them in QSIPrep (solution: you’re probably best off using the raw images).


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Yes. The BIDSify is a complicated work. Raw images seem more easier to be converted to BIDS format with hcp2bids. Thank you.

No problem, good luck!

If either of you would be interested in helping out, I am planning on adding an HCP ingress to the next QSIPrep release. I believe they include all the outputs we need for the reconstruction workflows, and we don’t even need to map the files to real BIDS, just to match the file names of QSIPrep outputs.


Yes. That is great. Many work have to do for converting the folder struture to BIDS. If we could ingress directily, it will be more efficiency and flawless. If you need any assistant, I will.