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settings.yaml
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# MANUAL SETTINGS
# See documentation for details on all these options.
# ========================================================================================
# WORKFLOWS
# ========================================================================================
# Startup folder
start_folder:
# anon, reg, main
workflow_mode: main
# se, steam
sequence_type: se
# ========================================================================================
# DEBUGGING
# ========================================================================================
# True, False
debug: True
# True, False
registration_extra_debug: False
# ========================================================================================
# IMAGE REGISTRATION
# ========================================================================================
# none, quick_rigid, elastix_rigid, elastix_affine, elastix_non_rigid
# elastix_groupwise (not working well at the moment)
registration: elastix_non_rigid
# fast, slow
registration_speed: fast
# best, groupwise
registration_reference_method: best
# ========================================================================================
# TENSOR FITTING
# ========================================================================================
# LS, WLS, NLLS, RESTORE
tensor_fit_method: NLLS
# ========================================================================================
# IMAGE REMOVAL
# ========================================================================================
# True, False
remove_outliers_manually: True
# True, False
remove_outliers_manually_pre: True
# True, False
# NOT WORKING WELL AT THE MOMENT
remove_outliers_with_ai: False
# ========================================================================================
# MISC
# ========================================================================================
# (STEAM only) float in msec
assumed_rr_interval: 1000
# (STEAM only) float in msec
calculated_real_b0: 29
# remove slices when reading data
remove_slices: []
# print series description
print_series_description: False
#registration mask scale for circle radius > 0, 1 for a circle diameter = image width
registration_mask_scale: 1.0
# remove b-values in this list
remove_b_values: []
# MD scale in plots
md_scale: [0, 2]
# ========================================================================================
# ex-vivo (in development)
# ========================================================================================
# process ex-vivo data
ex_vivo: False
# ========================================================================================
# AI MODELS (EXPERIMENTAL)
# ========================================================================================
# SEGMENTATION (STEAM only)
# ========================================================================================
# True, False
u_net_segmentation: False
# int [1, 5]
n_ensemble: 5
# ========================================================================================
# TENSOR DENOISING
# ========================================================================================
# True, False
uformer_denoise: False
# int: 1, 3, or 5
uformer_breatholds: 5