High-Resolution Atlas Registration Failure (Bleeding) with FNIRT/MRtrix on HCP-style Data

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Dear MRtrix Community and Experts,

I am running a structural connectome pipeline (CSD/ACT/SIFT2) on HCP-preprocessed data (1.5mm T1w) and am facing persistent, critical issues with the non-linear registration quality when mapping the DKT308 atlas to the individual subject space.

My goal is to obtain a highly accurate parcellation (DKT308_parc.mif) that perfectly aligns with the gray matter (GM) surface, as required for ACT.

1. Pipeline Details

  • DWI/T1 Data: HCP-style preprocessed, T1w resolution is 1.5mm.

  • Target Atlas: DKT308 (a volume atlas, correctly in MNI space).

  • MRtrix Core: 5ttgen fsl, dwi2fod msmt_csd, tckgen, tcksift2, tck2connectome.

  • Registration Tools: FSL’s flirt and fnirt.

2. The Critical Problem (Diagnosis: Over-Regularisation)

Despite extensive tuning, the final transformed atlas (DKT308_parc.mif) consistently exhibits significant bleeding (invasion) into the white matter (WM) in high-curvature sulcal regions.

I diagnosed this as over-regularization in the FNIRT process (the algorithm prioritizes smoothness over anatomical accuracy).

3. Steps Taken to Resolve (All Failed to Fix)

I have attempted the highest precision settings possible within the volume-based FNIRT framework:

  1. Low Regularization: Modified the T1_2_MNI152_2mm.cnf to drastically lower the \\lambda schedule (e.g., final values from 30 to 5) and increased iterations (e.g., miter to 20). Result: Bleeding was only marginally reduced.

  2. MNI Target Resolution: Tested mapping the 1.5mm T1 to both 2mm MNI and 1mm MNI templates. Result: Precision remained poor due to inherent volume-warping limitations.

  3. Registration Input: Used the full (un-brain-extracted) T1w image for FLIRT/FNIRT input (--in) while using the brain mask (--inmask) for constraint. Result: Improved initial alignment, but did not fix GM/WM boundary bleeding

Visual Evidence

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(Please insert the image showing the atlas bleeding into the white matter here)

5. Request for Expert Advice

Given that volume-based FNIRT seems inadequate for this high-precision task, I am considering moving to a surface-based approach.

My questions for the community are:

  1. Tool Recommendation: What is the most robust and recommended non-FSL method to generate a high-quality, non-linear warp field that accurately maps a volume atlas (like DKT) onto the individual’s GM/WM interface for ACT? (e.g., Is ANTs/SyN a better volume-based solution, or is the effort better spent elsewhere?)

  2. Surface Solution: Since HCP data is usually processed with FreeSurfer, is the consensus that I must abandon volume-based registration for the atlas and instead use mri_surf2surf (FreeSurfer) combined with mri_aparc2aseg to create the final, accurate volume atlas (DKT308_parc.mif)?

Thank you in advance for any insights on how to proceed with the highest quality registration for ACT.

Best regards,

RuiWang