name: ABCD_Recon
nodes:
# NODDI with WM parameters
-   action: fit_noddi
    input: qsirecon
    name: fit_noddi_wm
    parameters:
        dIso: 0.003
        dPar: 0.0017
        isExvivo: false
    qsirecon_suffix: wmNODDI
    software: AMICO
# NODDI with GM parameters
-   action: fit_noddi
    input: qsirecon
    name: fit_noddi_gm
    parameters:
        dIso: 0.003
        dPar: 0.0011
        isExvivo: false
    qsirecon_suffix: gmNODDI
    software: AMICO
# DIPY diffusion kurtosis modeling
-   action: DKI_reconstruction
    input: qsirecon
    name: dipy_dki
    parameters:
        write_fibgz: false
        write_mif: false
    qsirecon_suffix: DIPYDKI
    software: Dipy
# TORTOISE MAPMRI w/ small b-val tensor fit
-   action: estimate
    input: qsirecon
    name: tortoise_dtmapmri
    parameters:
        big_delta: null
        estimate_mapmri:
            map_order: 4
        estimate_tensor:
            bval_cutoff: 1200
            write_cs: true
        estimate_tensor_separately: true
        small_delta: null
    qsirecon_suffix: TORTOISE_model-MAPMRI
    software: TORTOISE
# Fit the GQI model to the data
-   action: reconstruction
    input: qsirecon
    name: dsistudio_gqi
    parameters:
        method: gqi
    qsirecon_suffix: DSIStudioGQI
    software: DSI Studio
# Get 3D images of DSI Studio's scalar maps
-   action: export
    input: dsistudio_gqi
    name: gqi_scalars
    qsirecon_suffix: DSIStudioGQI
    software: DSI Studio
 # Perform the registration using the GQI-based QA+ISO
-   action: autotrack_registration
    input: dsistudio_gqi
    name: autotrack_gqi_registration
    # qsirecon_suffix: Don't include here - the map.gz is saved in autotrack
    software: DSI Studio
# Do MSMT on all shells
-   action: csd
    software: MRTrix3
    input: qsirecon
    name: msmt_csd
    parameters:
        fod:
            algorithm: msmt_csd
            max_sh:
            - 8
            - 8
            - 8
        mtnormalize: true
        response:
            algorithm: dhollander
    qsirecon_suffix: MSMTAutoTrack
# Merge the FOD fib file and the map file
-   action: fod_fib_merge
    name: create_fod_fib_msmt
    # to include the fib file AND the map file
    input: autotrack_gqi_registration
    csd_input: msmt_csd
    # outputs include the FOD fib file and the map file is passed through
    qsirecon_suffix: MSMTAutoTrack
    parameters:
        model: msmt
# Execute AutoTrack
-   action: autotrack
    input: create_fod_fib_msmt
    name: autotrack_fod_msmt
    parameters:
        tolerance: 22,26,30
        track_id: Association,Projection,Commissure,Cerebellum
        track_voxel_ratio: 2.0
        yield_rate: 1.0e-06
        model: msmt
    qsirecon_suffix: MSMTAutoTrack
    software: DSI Studio
# Map scalars to bundles
-   action: bundle_map
    input: autotrack_fod_msmt
    name: bundle_means
    scalars_from:
    - fit_noddi_wm
    - dipy_dki
    - tortoise_dtmapmri
    - gqi_scalars
    software: qsirecon
# Map scalars to MNI
-   action: template_map
    input: qsirecon
    name: template_map
    parameters:
        interpolation: NearestNeighbor
    scalars_from:
    - fit_noddi_wm
    - fit_noddi_gm
    - dipy_dki
    - tortoise_dtmapmri
    - gqi_scalars
    software: qsirecon