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workshop-dataset/code/ref_diffusion_config.ini
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ref_diffusion_config.ini
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[Global]
modalities = []
process_type = diffusion
subject_session = ses-01
diffusion_imaging_model = DSI
dmri_bids_acq =
subjects = [u'sub-01', u'sub-02']
subject = sub-01
[diffusion_stage]
tracking_processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
tracking_processing_tool = MRtrix
dilation_kernel = Box
recon_processing_tool_editor = ['Dipy', 'Custom']
custom_track_file =
dtb_tracking_config.step_size = 1.0
dtb_tracking_config.angle = 60
dtb_tracking_config.imaging_model = DSI
dtb_tracking_config.seeds = 32
dtb_tracking_config.flip_input = []
dtk_tracking_config.angle_threshold = 60
dtk_tracking_config.imaging_model = DSI
dtk_tracking_config.mask1_threshold_auto = True
dtk_tracking_config.mask1_threshold = [0.0, 1.0]
dtk_tracking_config.mask1_input = DWI
dilate_rois = True
gibbs_recon_config.sh_order = 4
gibbs_recon_config.flip_table_axis = []
gibbs_recon_config.csa = True
gibbs_recon_config.reg_lambda = 0.006
gibbs_recon_config.b_vectors =
gibbs_recon_config.b_values =
gibbs_recon_config.recon_model = Tensor
processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
recon_processing_tool = Dipy
dipy_tracking_config.fa_thresh = 0.2
dipy_tracking_config.number_of_seeds = 1000
dipy_tracking_config.tracking_mode = Deterministic
dipy_tracking_config.use_act = False
dipy_tracking_config.max_angle = 25.0
dipy_tracking_config.sh_order = 8
dipy_tracking_config.curvature = 0.0
dipy_tracking_config.step_size = 0.5
dipy_tracking_config.fast_number_of_classes = 3
dipy_tracking_config.sd = True
dipy_tracking_config.imaging_model = DSI
diffusion_imaging_model_editor = ['DSI', 'DTI', 'HARDI']
fsl_recon_config.weight = 1.0
fsl_recon_config.fibres_per_voxel = 1
fsl_recon_config.flip_table_axis = []
fsl_recon_config.burn_period = 0
fsl_recon_config.sampling = 25
fsl_recon_config.b_vectors =
fsl_recon_config.b_values =
fsl_recon_config.jumps = 1250
mrtrix_tracking_config.min_length = 5.0
mrtrix_tracking_config.angle = 45.0
mrtrix_tracking_config.tracking_mode = Deterministic
mrtrix_tracking_config.use_act = True
mrtrix_tracking_config.cutoff_value = 0.05
mrtrix_tracking_config.backtrack = False
mrtrix_tracking_config.curvature = 0.0
mrtrix_tracking_config.crop_at_gmwmi = True
mrtrix_tracking_config.seed_from_gmwmi = True
mrtrix_tracking_config.step_size = 0.5
mrtrix_tracking_config.desired_number_of_tracks = 2000000
mrtrix_tracking_config.max_length = 200.0
mrtrix_tracking_config.sd = True
mrtrix_recon_config.recon_mode = Probabilistic
mrtrix_recon_config.imaging_model = DSI
mrtrix_recon_config.single_fib_thr = 0.7
mrtrix_recon_config.lmax_order = Auto
mrtrix_recon_config.normalize_to_b0 = False
mrtrix_recon_config.local_model_editor = {True: 'Constrained Spherical Deconvolution'}
mrtrix_recon_config.local_model = True
mrtrix_recon_config.flip_table_axis = []
diffusion_model_editor = ['Deterministic', 'Probabilistic']
dipy_recon_config.shore_radial_order = 6
dipy_recon_config.shore_constrain_e0 = True
dipy_recon_config.positivity_constraint = True
dipy_recon_config.tracking_processing_tool = MRtrix
dipy_recon_config.imaging_model = DSI
dipy_recon_config.small_delta = 0.02
dipy_recon_config.big_delta = 0.5
dipy_recon_config.lmax_order = Auto
dipy_recon_config.shore_lambdal = 1e-08
dipy_recon_config.shore_lambdan = 1e-08
dipy_recon_config.shore_tau = 0.0253302959106
dipy_recon_config.local_model_editor = {True: 'Constrained Spherical Deconvolution'}
dipy_recon_config.shore_zeta = 700
dipy_recon_config.local_model = True
dipy_recon_config.radial_order_values = [2, 4, 6, 8, 10, 12]
dipy_recon_config.single_fib_thr = 0.7
dipy_recon_config.recon_mode = Probabilistic
dipy_recon_config.flip_table_axis = ['x']
dipy_recon_config.radial_order = 8
dipy_recon_config.shore_positive_constraint = True
dipy_recon_config.mapmri = False
dipy_recon_config.laplacian_weighting = 0.05
dipy_recon_config.laplacian_regularization = True
diffusion_model = Deterministic
dtk_recon_config.apply_gradient_orientation_correction = True
dtk_recon_config.imaging_model = DSI
dtk_recon_config.number_of_b0_volumes = 1
dtk_recon_config.number_of_output_directions = 181
dtk_recon_config.compute_additional_maps = ['gFA', 'skewness', 'kurtosis', 'P0']
dtk_recon_config.recon_matrix_file = DSI_matrix_515x181.dat
dtk_recon_config.gradient_table_file = siemens_06
dtk_recon_config.number_of_directions = 6
dtk_recon_config.flip_table_axis = []
dtk_recon_config.custom_gradient_table =
dtk_recon_config.dsi_number_of_directions = 514
dtk_recon_config.multiple_high_b_values = False
dtk_recon_config.maximum_b_value = 1000
dtk_recon_config.gradient_table = /app/connectomemapper3/cmtklib/data/diffusion/gradient_tables/siemens_06.txt
dtk_recon_config.number_of_averages = 1
dilation_radius = 1
diffusion_imaging_model = DSI
camino_tracking_config.tracking_model = dt
camino_tracking_config.angle = 60.0
camino_tracking_config.imaging_model = DTI
camino_tracking_config.tracking_mode = Deterministic
camino_tracking_config.units = m^2/s
camino_tracking_config.cross_angle = 20.0
camino_tracking_config.snr = 20.0
camino_tracking_config.fallback_index = 1
camino_tracking_config.iterations = 50
camino_tracking_config.trace = 2.1e-09
camino_tracking_config.pdf = bingham
camino_tracking_config.inversion_index = 1
camino_recon_config.inversion = 1
camino_recon_config.gradient_table =
camino_recon_config.mixing_eq = False
camino_recon_config.fallback_model = dt
camino_recon_config.imaging_model = DTI
camino_recon_config.flip_table_axis = []
camino_recon_config.fallback_editor = {'ldt_wtd': 'Weighted linear', 'dt': 'Linear fit', 'nldt_pos': 'Non linear positive semi-definite', 'nldt': 'Unconstrained non linear'}
camino_recon_config.local_model = dt
camino_recon_config.local_model_editor = {'ldt_wtd': 'Weighted linear', 'dt': 'Linear fit', 'nldt_pos': 'Non linear positive semi-definite', 'nldt': 'Unconstrained non linear'}
camino_recon_config.snr = 10.0
camino_recon_config.fallback_index = 1
camino_recon_config.model_type = Single-Tensor
camino_recon_config.b_value = 1000
fsl_tracking_config.curvature_threshold = 0.2
fsl_tracking_config.number_of_steps = 2000
fsl_tracking_config.number_of_samples = 5000
fsl_tracking_config.distance_threshold = 0.0
gibbs_tracking_config.temp_end = 0.001
gibbs_tracking_config.fiber_length = 20.0
gibbs_tracking_config.particle_weight = 0.0003
gibbs_tracking_config.particle_length = 1.5
gibbs_tracking_config.curvature_threshold = 90.0
gibbs_tracking_config.particle_width = 0.5
gibbs_tracking_config.iterations = 100000000
gibbs_tracking_config.inexbalance = -2
gibbs_tracking_config.temp_start = 0.1
[preprocessing_stage]
eddy_current_and_motion_correction = True
description = description
denoising = False
total_readout = 0.0
end_vol = 0
start_vol = 0
eddy_correct_motion_correction = True
dipy_noise_model = Rician
max_str =
denoising_algo = MRtrix (MP-PCA)
bias_field_algo = ANTS N4
bias_field_correction = False
fast_use_priors = True
resampling = (1, 1, 1)
partial_volume_estimation = True
max_vol = 0
eddy_correction_algo = FSL eddy_correct
interpolation = interpolate
[connectome_stage]
circular_layout = False
probtrackx = False
output_types = ['gPickle']
compute_curvature = False
log_visualization = True
connectivity_metrics = ['Fiber number', 'Fiber length', 'Fiber density', 'Fiber proportion', 'Normalized fiber density', 'ADC', 'gFA']
subject = sub-01
[registration_stage]
ants_nonlinear_cost = CC
ants_nonlinear_update_field_variance = 3.0
flirt_args =
contrast_type = dti
ants_upper_quantile = 0.995
ants_nonlinear_total_field_variance = 0.0
registration_mode = ANTs
init = header
ants_interpolation = BSpline
ants_linear_sampling_perc = 0.25
apply_to_eroded_wm = True
ants_convergence_thresh = 1e-06
ants_multilab_interpolation_parameters = (5.0, 5.0)
ants_gauss_interpolation_parameters = (5.0, 5.0)
ants_convergence_winsize = 10
ants_bspline_interpolation_parameters = (5,)
apply_to_eroded_brain = False
uses_qform = True
apply_to_eroded_csf = True
ants_lower_quantile = 0.005
no_search = True
ants_linear_cost = MI
ants_linear_gradient_step = 0.1
pipeline = Diffusion
ants_perform_syn = True
ants_linear_sampling_strategy = Regular
dof = 6
diffusion_imaging_model =
fsl_cost = normmi
ants_nonlinear_gradient_step = 0.1
[Multi-processing]
number_of_cores = 1
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