Question regarding hcp_diffusion with asymmetric AP/PA acqusition

[Benjamin Bušelič]

Hi all,

I am a PhD student exploring analysis of diffusion images.
I am running the HCP diffusion pipeline on a dataset with an asymmetric AP/PA DWI acquisition design:
- AP direction: 3 b0 volumes only (used as field map reference for topup)
- PA direction: full multi-shell DWI dataset (~90 volumes, b=300/1000/2000)

The pipeline runs successfully through eddy:
- Pos_Neg.nii.gz: 187 volumes ✓
- eddy_unwarped_images.nii.gz: 187 volumes ✓

However, the final data.nii.gz contains only 6 volumes with bvals: 0 0 212 212 212 212. It appears that after eddy, the pipeline extracts only the AP volumes (3 b0 from session 1 + 3 b0 from session 2), discarding the full PA DWI dataset. As a result, dtifit produces physically impossible values (FA > 1, negative eigenvalues).

I have been advised that the parameter hcp_dwi_combinedata might be relevant here, but I am not sure how to configure it correctly for this acquisition design.

My questions:
1. Does the HCP diffusion pipeline support asymmetric AP/PA acquisitions where only one direction contains the full DWI dataset?
2. What are the correct HCP Pipelines parameters to handle this scenario (b0-only reference in AP, full DWI in PA)?
3. Specifically, how should hcp_dwi_combinedata be set in this case?

Any advice would be greatly appreciated!

Best regards,

Benjamin Bušelič

[Elam, Jennifer]

Hi Benjamin,

Please refer to this thread: 

https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/cVxMeR9wR70/m/BzE0mOVNBQAJ

Best,

Jenn

Jennifer Elam, Ph.D.
Project and Outreach Manager, Human Connectome Projects
Washington University School of Medicine
Departments of Neuroscience and Radiology
el...@wustl.edu
www.humanconnectome.org

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From: Benjamin Bušelič <benjamin...@gmail.com>
Sent: Thursday, July 16, 2026 4:03 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] Question regarding hcp_diffusion with asymmetric AP/PA acqusition

 

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