revert config file
@@ -7,18 +7,9 @@ pixdim = (1.0, 1.0, 1.0)
axcodes=(A, R, S)
interp_order = 3
-[FLAIR]
-path_to_search
-filename_contains = T1
-filename_not_contains =
-spatial_window_size = (32, 32, 32)
-pixdim = (1.0, 1.0, 1.0)
-axcodes=(A, R, S)
-interp_order = 3
-
-[Lesion]
+[parcellation]
path_to_search = ./example_volumes/monomodal_parcellation
-filename_contains = Lesion
+filename_contains = Label
filename_not_contains =
spatial_window_size = (32, 32, 32)
pixdim = (1.0, 1.0, 1.0)
@@ -64,23 +55,19 @@ starting_iter = 0
save_every_n = 5
max_iter = 6
max_checkpoints = 20
-window_sampling = selective
-min_ratio_sampling = 0.00001
-compulsory_labels = (1)
-num_min_labels = 2
+window_sampling = uniform
[INFERENCE]
border = (5, 5, 5)
#inference_iter = 10
save_seg_dir = ./output/highres3dnet
output_interp_order = 0
-spatial_window_size = (64, 64, 64)
-
+spatial_window_size = (0, 0, 3)
############################ custom configuration sections
[SEGMENTATION]
-image = T1,FLAIR
-label = Lesion
+image = T1
+label = parcellation
output_prob = False
-num_classes = 2
+num_classes = 160
label_normalisation = True
