graph TD
    A[Input Data]
    A1["desc-motion_bold"]
    A2["desc-preproc_bold"]
    A3["desc-brain_T1w"]
    A4["desc-preproc_T1w"]
    A5["desc-reorient_T1w"]

    A --> A1
    A --> A2
    A --> A3
    A --> A4
    A --> A5

    B[Run 3dAutomask]
    A1 -->|bold| B
    B --> B1["Initial BOLD Mask"]

    C[Extract 8th Volume as ROI]
    A1 -->|bold| C
    C --> C1["Func ROI"]

    D[Apply Initial Mask on ROI]
    C1 -->|roi_file| D
    B1 -->|mask_file| D
    D --> D1["Masked Func ROI"]

    E[Register ROI to Anatomical]
    D1 -->|in_file| E
    A3 -->|reference| E
    E --> E1["Func-to-Anat Transform"]

    F[Inverse Func-to-Anat Transform]
    E1 -->|out_matrix_file| F
    F --> F1["Inverse Transform"]

    G[Transform Anatomical Brain to Func Space]
    A3 -->|in_file| G
    C1 -->|reference| G
    F1 -->|in_matrix_file| G
    G --> G1["Anat Brain in Func Space"]

    H[Binarize and Dilate Anat Brain Mask]
    G1 -->|in_file| H
    H --> H1["Dilated Anat Brain Mask"]

    I[Binarize Detectable Func Signals]
    A2 -->|bold| I
    I --> I1["Binarized Func Signals"]

    J[Merge Masks]
    B1 -->|mask_file| J
    H1 -->|mask_file| J
    J --> J1["Merged Masks"]

    K[Take Intersection of Masks]
    J1 -->|operand_files| K
    I1 -->|in_file| K
    K --> K1["Intersected Mask"]

    L[Generate Example Func Brain]
    C1 -->|roi_file| L
    K1 -->|mask_file| L
    L --> L1["Masked Func Brain"]

    M[Generate Outputs]
    K1 -->|space-bold_desc-brain_mask| M
    L1 -->|desc-ref_bold| M

graph TD
    A[Input Data]
    A1["motion-basefile"]
    A2["desc-preproc_bold"]
    A3["FSL-AFNI-bold-ref"]
    A4["FSL-AFNI-brain-mask"]
    A5["FSL-AFNI-brain-probseg"]

    A --> A1
    A --> A2
    A --> A3
    A --> A4
    A --> A5

    B[Initialize Transforms with antsAI]
    A3 -->|fixed_image| B
    A4 -->|fixed_image_mask| B
    A1 -->|moving_image| B
    B --> B1["Affine Transform"]

    C[Set up Spatial Normalization]
    A3 -->|fixed_image| C
    A1 -->|moving_image| C
    B1 -->|initial_moving_transform| C
    C --> C1["Normalized Transform"]

    D[Map Brain Mask]
    A5 -->|input_image| D
    A1 -->|reference_image| D
    C1 -->|transforms| D
    D --> D1["Mapped Brain Mask"]

    E[Binarize Mask]
    D1 -->|in_file| E
    E --> E1["Binary Mask"]

    F[Dilate Pre-Mask]
    E1 -->|in_file| F
    F --> F1["Dilated Mask"]

    G[Fix Precision Errors]
    F1 -->|image| G
    G --> G1["Precision-Corrected Image"]

    H[Run N4BiasFieldCorrection]
    G1 -->|mask_image| H
    A1 -->|input_image| H
    H --> H1["Bias-Corrected Image"]

    I[Create Generous BET Mask]
    H1 -->|in_file| I
    I --> I1["BET Mask"]

    J[Dilate BET Mask]
    I1 -->|in_file| J
    J --> J1["Dilated BET Mask"]

    K[Apply BET Mask]
    I1 -->|in_file| K
    J1 -->|mask_file| K
    K --> K1["BET Masked Image"]

    L[Unifize for T2 Contrast]
    K1 -->|in_file| L
    L --> L1["Unifized Image"]

    M[Run 3dAutomask]
    L1 -->|in_file| M
    M --> M1["3dAutomask Output"]

    N[Take Intersection of Masks]
    I1 -->|in_file| N
    M1 -->|operand_file| N
    N --> N1["Final Mask"]

    O[Apply Final Mask]
    L1 -->|in_file| O
    N1 -->|mask_file| O
    O --> O1["Masked Brain"]

    P[Generate Outputs]
    N1 -->|space-bold_desc-brain_mask| P
    O1 -->|desc-ref_bold| P

graph TD

    A[space-bold_desc-brain_mask]
    B[desc-motion_bold]
    C[Unifize workflow]
    D[coregistration_prep_fmriprep]

    A --> C
    B --> C
    C --desc-ref_bold --> D
    D --> E[sbref]