CI: add diffusion config for testing FLIRT co-registration and tracto…

…gram filtering with MRtrix3 SIFT

.circleci/tests/configuration_files/ref_diffusion_config_5.ini

@@ -0,0 +1,142 @@
+[Global]
+process_type = diffusion
+diffusion_imaging_model = DTI
+subjects = ['sub-01']
+subject = sub-01
+subject_session = ses-01
+modalities = []
+dmri_bids_acq = DSI
+
+[preprocessing_stage]
+total_readout = 0.0
+description = description
+denoising = True
+denoising_algo = MRtrix (MP-PCA)
+dipy_noise_model = Rician
+bias_field_correction = True
+bias_field_algo = ANTS N4
+eddy_current_and_motion_correction = True
+eddy_correction_algo = FSL eddy_correct
+eddy_correct_motion_correction = True
+partial_volume_estimation = True
+fast_use_priors = True
+resampling = (1, 1, 1)
+interpolation = interpolate
+
+[registration_stage]
+pipeline = Diffusion
+registration_mode = FSL
+diffusion_imaging_model = 
+use_float_precision = False
+ants_interpolation = BSpline
+ants_bspline_interpolation_parameters = (3,)
+ants_gauss_interpolation_parameters = (5.0, 5.0)
+ants_multilab_interpolation_parameters = (5.0, 5.0)
+ants_lower_quantile = 0.005
+ants_upper_quantile = 0.995
+ants_convergence_thresh = 1e-06
+ants_convergence_winsize = 10
+ants_linear_gradient_step = 0.1
+ants_linear_cost = MI
+ants_linear_sampling_perc = 0.25
+ants_linear_sampling_strategy = Regular
+ants_perform_syn = True
+ants_nonlinear_gradient_step = 0.1
+ants_nonlinear_cost = CC
+ants_nonlinear_update_field_variance = 3.0
+ants_nonlinear_total_field_variance = 0.0
+flirt_args = 
+uses_qform = True
+dof = 6
+fsl_cost = normmi
+no_search = True
+init = header
+contrast_type = dti
+apply_to_eroded_wm = True
+apply_to_eroded_csf = True
+apply_to_eroded_brain = False
+
+[diffusion_stage]
+diffusion_imaging_model_editor = ['DSI', 'DTI', 'HARDI']
+diffusion_imaging_model = DSI
+dilate_rois = True
+dilation_kernel = Box
+dilation_radius = 1
+recon_processing_tool_editor = ['Dipy', 'Custom']
+tracking_processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
+processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
+recon_processing_tool = Dipy
+tracking_processing_tool = MRtrix
+custom_track_file = .
+dipy_recon_config.flip_table_axis = []
+dipy_recon_config.imaging_model = DSI
+dipy_recon_config.local_model_editor = {False: '1:Tensor', True: '2:Constrained Spherical Deconvolution'}
+dipy_recon_config.local_model = True
+dipy_recon_config.lmax_order = 2
+dipy_recon_config.single_fib_thr = 0.7
+dipy_recon_config.recon_mode = Probabilistic
+dipy_recon_config.mapmri = False
+dipy_recon_config.tracking_processing_tool = MRtrix
+dipy_recon_config.laplacian_regularization = False
+dipy_recon_config.laplacian_weighting = 0.05
+dipy_recon_config.positivity_constraint = True
+dipy_recon_config.radial_order = 4
+dipy_recon_config.small_delta = 0.02
+dipy_recon_config.big_delta = 0.5
+dipy_recon_config.radial_order_values = [2, 4, 6, 8, 10, 12]
+dipy_recon_config.shore_radial_order = 4
+dipy_recon_config.shore_zeta = 700
+dipy_recon_config.shore_lambda_n = 1e-08
+dipy_recon_config.shore_lambda_l = 1e-08
+dipy_recon_config.shore_tau = 0.0441759
+dipy_recon_config.shore_constrain_e0 = False
+dipy_recon_config.shore_positive_constraint = True
+mrtrix_recon_config.flip_table_axis = []
+mrtrix_recon_config.local_model_editor = {True: 'Constrained Spherical Deconvolution'}
+mrtrix_recon_config.local_model = True
+mrtrix_recon_config.lmax_order = 2
+mrtrix_recon_config.normalize_to_b0 = False
+mrtrix_recon_config.single_fib_thr = 0.7
+mrtrix_recon_config.recon_mode = Probabilistic
+mrtrix_recon_config.imaging_model = DSI
+dipy_tracking_config.imaging_model = DSI
+dipy_tracking_config.tracking_mode = Deterministic
+dipy_tracking_config.sd = True
+dipy_tracking_config.number_of_seeds = 1000
+dipy_tracking_config.seed_density = 1.0
+dipy_tracking_config.fa_thresh = 0.2
+dipy_tracking_config.step_size = 0.5
+dipy_tracking_config.max_angle = 25.0
+dipy_tracking_config.sh_order = 8
+dipy_tracking_config.use_act = False
+dipy_tracking_config.seed_from_gmwmi = False
+dipy_tracking_config.curvature = 0.0
+mrtrix_tracking_config.tracking_mode = Deterministic
+mrtrix_tracking_config.sd = True
+mrtrix_tracking_config.desired_number_of_tracks = 200000
+mrtrix_tracking_config.curvature = 0.0
+mrtrix_tracking_config.step_size = 0.5
+mrtrix_tracking_config.min_length = 5.0
+mrtrix_tracking_config.max_length = 200.0
+mrtrix_tracking_config.angle = 45.0
+mrtrix_tracking_config.cutoff_value = 0.05
+mrtrix_tracking_config.use_act = False
+mrtrix_tracking_config.seed_from_gmwmi = False
+mrtrix_tracking_config.crop_at_gmwmi = False
+mrtrix_tracking_config.backtrack = False
+mrtrix_tracking_config.sift = True
+diffusion_model_editor = ['Deterministic', 'Probabilistic']
+diffusion_model = Deterministic
+
+[connectome_stage]
+output_types = ['gPickle']
+connectivity_metrics = ['Fiber number', 'Fiber length', 'Fiber density', 'Fiber proportion', 'Normalized fiber density', 'ADC', 'gFA']
+probtrackx = False
+compute_curvature = False
+log_visualization = True
+circular_layout = False
+subject = 
+
+[Multi-processing]
+number_of_cores = 1
+