#  This software and supporting documentation are distributed by
#      Institut Federatif de Recherche 49
#      CEA/NeuroSpin, Batiment 145,
#      91191 Gif-sur-Yvette cedex
#      France
#
# This software is governed by the CeCILL license version 2 under
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# You can  use, modify and/or redistribute the software under the 
# terms of the CeCILL license version 2 as circulated by CEA, CNRS
# and INRIA at the following URL "http://www.cecill.info". 
#
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include( 'base' )
include( 'registration' )


diffusion_content = (
    '<subject>_raw_dw_diffusion', SetType( 'Raw DW Diffusion MR' ),
    '<subject>_dw_diffusion', SetType( 'Corrected DW Diffusion MR' ),
                              SetPriorityOffset( +1 ),
    '<subject>_t2_diffusion', SetType( 'Raw T2 Diffusion MR' ),
    '<subject>_acpc_dw_diffusion', SetType( 'AC/PC DW Diffusion MR' ),
    '<subject>_acpc_t2_diffusion', SetType( 'AC/PC T2 Diffusion MR' ),
    '<subject>_eacpc_dw_diffusion', SetType( 'Extended AC/PC DW Diffusion MR' ),
    '<subject>_eacpc_t2_diffusion', SetType( 'Extended AC/PC T2 Diffusion MR' ),
#    '<subject>_eacpc_t1_mri', SetType( 'Extended AC/PC T1 Anatomy MR' ),
    '<subject>_mask', SetType( 'Diffusion Mask' ),
    '<subject>_fixedDT', SetType( 'DTI Model' ),
#    '<subject>_interpolatedDT', SetType( 'Interpolated Diffusion Tensor' ),
#    '<subject>_multiDT', SetType( 'Multicompartimental Diffusion Tensor' ),
#    '<subject>_qspace', SetType( 'Q-space' ),
    '<subject>_error_mask', SetType( 'Error Mask' ),
    '<subject>_adc', SetType( 'Apparent Diffusion Coefficient' ),
    '<subject>_fa', SetType( 'Fractional Anisotropy' ),
    '<subject>_vr', SetType( 'Volume Ratio' ),
    '<subject>_stddev', SetType( 'Diffusion Standard Deviation' ),
    '<subject>_dwt2', SetType( 'Diffusion Weighted T2' ),
    '<subject>_maxev', SetType( 'Maximum Eigenvector' ),
    '<subject>_rgbev', SetType( 'RGB Eigenvector' ),
    '<subject>_qball', SetType( 'QBall Model'),
    '<subject>_alphaMap', SetType('Diffusion Anisotropy'),
    '<subject>_orientation', SetType('Orientation File'),
    '<subject>_density', SetType('Diffusion Density Map'),
    '<subject>_regions', SetType( 'Tracking regions' ),
    '<subject>_bundles', SetType( 'Fascicles bundles' ),
#    '<subject>_bundles', SetType( 'Fascicles graph' ),
    '<subject>_statistics', SetType( 'Bundles scalar features' ),
    '<subject>_*_raw_dw_diffusion', SetType( 'Raw DW Diffusion MR' ),
    '<subject>_*_dw_diffusion', SetType( 'Corrected DW Diffusion MR' ),
                                SetPriorityOffset( +1 ),
    '<subject>_*_t2_diffusion', SetType( 'Raw T2 Diffusion MR' ),
    '<subject>_*_acpc_dw_diffusion', SetType( 'AC/PC DW Diffusion MR' ),
    '<subject>_*_acpc_t2_diffusion', SetType( 'AC/PC T2 Diffusion MR' ),
    '<subject>_*_eacpc_dw_diffusion', SetType( 'Extended AC/PC DW Diffusion MR' ),
    '<subject>_*_eacpc_t2_diffusion', SetType( 'Extended AC/PC T2 Diffusion MR' ),
#    '<subject>_*_eacpc_t1_mri', SetType( 'Extended AC/PC T1 Anatomy MR' ),
    '<subject>_*_mask', SetType( 'Diffusion Mask' ),
    '<subject>_*_fixedDT', SetType( 'DTI Model' ),
#    '<subject>_*_interpolatedDT', SetType( 'Interpolated Diffusion Tensor' ),
#    '<subject>_*_multiDT', SetType( 'Multicompartimental Diffusion Tensor' ),
#    '<subject>_*_qspace', SetType( 'Q-space' ),
    '<subject>_*_error_mask', SetType( 'Error Mask' ),
    '<subject>_*_adc', SetType( 'Apparent Diffusion Coefficient' ),
    '<subject>_*_fa', SetType( 'Fractional Anisotropy' ),
    '<subject>_*_vr', SetType( 'Volume Ratio' ),
    '<subject>_*_stddev', SetType( 'Diffusion Standard Deviation' ),
    '<subject>_*_dwt2', SetType( 'Diffusion Weighted T2' ),
    '<subject>_*_maxev', SetType( 'Maximum Eigenvector' ),
    '<subject>_*_rgbev', SetType( 'RGB Eigenvector' ),
    '<subject>_*_qball', SetType( 'QBall Model'),
    '<subject>_*_alphaMap', SetType('Diffusion Anisotropy'),
    '<subject>_*_orientation', SetType('Orientation File'),

    '{tracking_session}', SetContent(
      '<subject>_<tracking_session>_regions', SetType( 'Tracking regions' ),
      '<subject>_<tracking_session>_bundles', SetType( 'Fascicles bundles' ),
#      '<subject>_<tracking_session>_bundles', SetType( 'Fascicles graph' ),
      '<subject>_<tracking_session>_density', SetType( 'Diffusion Density Map' ),            
      '<subject>_<tracking_session>_statistics', SetType( 'Bundles scalar features' ),
      '<subject>_<tracking_session>_*_regions', SetType( 'Tracking regions' ),
      '<subject>_<tracking_session>_*_bundles', SetType( 'Fascicles bundles' ),
#      '<subject>_<tracking_session>_*_bundles', SetType( 'Fascicles graph' ),
      '<subject>_<tracking_session>_*_density', SetType( 'Diffusion Density Map' ),
      '<subject>_<tracking_session>_*_statistics', SetType( 'Bundles scalar features' ),
    ),
)


insert( '{protocol}/{subject}',
  'diffusion',
    SetContent( '{acquisition}', apply( SetContent, diffusion_content ) ),
)


#----------------- Registration -------------------------

insertFirst( '{protocol}/{subject}/registration',
    'DiffT2-<subject>', SetType( 'Referential of Raw T2 Diffusion MR' ),
    'DiffT2-<subject>-<acquisition>', SetType( 'Referential of Raw T2 Diffusion MR' ),
    'ACPC-<subject>', SetType( 'AC/PC T2 Diffusion MR referential' ),
    'ACPC-<subject>-<acquisition>', SetType( 'AC/PC T2 Diffusion MR referential' ),
    'ExtACPC-DiffT2-<subject>', SetType( 'Extended AC/PC T2 Diffusion MR referential' ),
    'ExtACPC-DiffT2-<subject>-<acquisition>', SetType( 'Extended AC/PC T2 Diffusion MR referential' ),
    ## Transform T2 Diffusion MR to Talairach-AC/PC-Anatomist
    #'DiffT2-<subject>_TO_Talairach-ACPC', SetType( 'Transform T2 Diffusion MR to Talairach-AC/PC-Anatomist' ),
    #'DiffT2-<subject>-<acquisition>_TO_Talairach-ACPC', SetType( 'Transform T2 Diffusion MR to Talairach-AC/PC-Anatomist' ),
    # Intra subject: Transform Raw T1 MRI to T2 Diffusion MR
    'RawT1-<subject>-<acquisition>_TO_DiffT2', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ),
    'RawT1-<subject>_TO_DiffT2', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ),
    # Intra subject: Transform T2 Diffusion MR to Raw T1 MRI
    'DiffT2-<subject>-<acquisition>_TO_RawT1', SetType( 'Transform T2 Diffusion MR to Raw T1 MRI' ),
    'DiffT2-<subject>_TO_RawT1', SetType( 'Transform T2 Diffusion MR to Raw T1 MRI' ),
    # Intra subject: Transform T2 Diffusion MR to AC/PC
    'DiffT2-<subject>-<acquisition>_TO_ACPC', SetType( 'Transform T2 Diffusion MR to AC/PC T2 Diffusion MR' ),
    'DiffT2-<subject>_TO_ACPC', SetType( 'Transform T2 Diffusion MR to AC/PC T2 Diffusion MR' ),
    # Transform T2 Diffusion MR to Extended AC/PC T2 Diffusion MR
    'DiffT2-<subject>-<acquisition>_TO_ExtACPC-DiffT2', SetType( 'Transform T2 Diffusion MR to Extended AC/PC T2 Diffusion MR' ),
    'DiffT2-<subject>_TO_ExtACPC-DiffT2', SetType( 'Transform T2 Diffusion MR to Extended AC/PC T2 Diffusion MR' ),
    # Transform AC/PC to Extended AC/PC T2 Diffusion MR
    'ACPC-<subject>-<acquisition>_TO_ExtACPC-DiffT2', SetType( 'Transform AC/PC T2 Diffusion MR to Extended AC/PC T2 Diffusion MR' ),
    'ACPC-<subject>_TO_ExtACPC-DiffT2', SetType( 'Transform AC/PC T2 Diffusion MR to Extended AC/PC T2 Diffusion MR' ),
    # Transform Raw T1 MRI to T2 Diffusion MR
    'RawT1-<subject>-<acquisition>_TO_DiffT2', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ),
    'RawT1-<subject>_TO_DiffT2', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ),
    # Transform Raw T1 MRI to Extended AC/PC T2 Diffusion MR
    'RawT1-<subject>-<acquisition>_TO_ExtACPC-DiffT2', SetType( 'Transform Raw T1 MRI to Extended AC/PC T2 Diffusion MR' ),
    'RawT1-<subject>_TO_ExtACPC-DiffT2', SetType( 'Transform Raw T1 MRI to Extended AC/PC T2 Diffusion MR' ),
    # Transform Raw T1 MRI to AC/PC
    'RawT1-<subject>-<acquisition>_TO_ACPC', SetType( 'Transform Raw T1 MRI to AC/PC T2 Diffusion MR' ),
    'RawT1-<subject>_TO_ACPC', SetType( 'Transform Raw T1 MRI to AC/PC T2 Diffusion MR' ),
)


insertFirst( '{protocol}/registration',
    # Inter subject: Transform T2 Diffusion MR to T2 Diffusion MR
    #'DiffT2_{source.subject}-{source.acquisition}_TO_DiffT2-{dest.subject}-{dest.acquisition}', SetType( 'Transform T2 Diffusion MR to T2 Diffusion MR' ),
    #'DiffT2_{source.subject}_TO_{dest.subject}-{dest.acquisition}', SetType( 'Transform T2 Diffusion MR to T2 Diffusion MR' ), SetPriorityOffset( -1 ),
    #'DiffT2_{source.subject}-{source.acquisition}_TO_{dest.subject}', SetType( 'Transform T2 Diffusion MR to T2 Diffusion MR' ), SetPriorityOffset( -1 ),
    #'DiffT2_{source.subject}_TO_{dest.subject}', SetType( 'Transform T2 Diffusion MR to T2 Diffusion MR' ), SetPriorityOffset( -2 ),
    # Inter subject: Transform Raw T1 MRI to T2 Diffusion MR
    'RawT1-{source.subject}-{source.acquisition}_TO_DiffT2-{dest.subject}-{dest.acquisition}', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ),
    'RawT1-{source.subject}_TO_DiffT2-{dest.subject}-{dest.acquisition}', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ), SetPriorityOffset( -1 ),
    'RawT1-{source.subject}-{source.acquisition}_TO_DiffT2-{dest.subject}', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ), SetPriorityOffset( -1 ),
    'RawT1-{source.subject}_TO_DiffT2-{dest.subject}', SetType( 'Transform Raw T1 MRI to T2 Diffusion MR' ), SetPriorityOffset( -2 ),
    # Inter subject: Transform T2 Diffusion MR to Raw T1 MRI
    'DiffT2-{source.subject}-{source.acquisition}_TO_RawT1-{dest.subject}-{dest.acquisition}', SetType( 'Transform T2 Diffusion MR to Raw T1 MRI' ),
    'DiffT2-{source.subject}_TO_RawT1-{dest.subject}-{dest.acquisition}', SetType( 'Transform T2 Diffusion MR to Raw T1 MRI' ), SetPriorityOffset( -1 ),
    'DiffT2-{source.subject}-{source.acquisition}_TO_RawT1-{dest.subject}', SetType( 'Transform T2 Diffusion MR to Raw T1 MRI' ), SetPriorityOffset( -1 ),
    'DiffT2-{source.subject}_TO_RawT1-{dest.subject}', SetType( 'Transform T2 Diffusion MR to Raw T1 MRI' ), SetPriorityOffset( -2 ),
)