QSIPrep: what scan to mention in IntendedFor field of fieldmap to run SDC on HCP_ageing data?

1

Hi,

I am preprocessing the HCP-Ageing Data using QSIPrep.

The data has 4 diffusion scans with bvals and bvecs (with 98 directions, 99 directions and AP and PA Phase Encoding directions).
The fieldmaps are also 4 scans with 98 directions or 99 directions in AP and PA PE directions.

My question is:
What to mention in the IntendedFor field for each fieldmap when running it with qsiprep? I am confused if I am specifying the correct dwi scan for each fieldmap. Is using the reverse PE direction correct?

Should I do the following?

  1. dir98_AP fieldmap: Intended for dir98_PA_dwi.nii.gz

  2. dir98_PA fieldmap: Intended for dir98_AP_dwi.nii.gz

  3. dir99_AP fieldmap: Intended for dir99_PA_dwi.nii.gz

  4. dir99_PA fieldmap: Intended for dir99_AP_dwi.nii.gz

Any insight would be appreciated.
Awaiting your reply.
Thank you
Best,
Apoorva

2

Hi @apoorvakelkar,

You don’t need to use IntendedFor. QSIPrep always prefers to use reverse-phase-encoded images for SDC if possible. Since you have that information available, the fieldmaps will be ignored. As long as the image name within a pair have the same name (besides the dir-<> label) qsiprep will do the grouping automatically.

But in general, for your information, the IntendedFor field in the relevant fmap jsons should include a path, relative to the start of the subject folder, to the image you want to associated. E.g.,

"IntendedFor": "ses-x/dwi/sub-x_ses-x_dwi.nii.gz"

Best,
Steven

3

Hi @Steven

Thank you so much. I realized I hadn’t read the documentation well. I tested it out and it worked.

Thank you for the example of the path to put for the IntendedFor field. That makes sense to me.

Best,
Apoorva

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