Merge pull request #7 from AlexVCaron/update/mrhardiflow

Sync with mrhardiflow
AlexVCaron · Aug 5, 2024 · 9442e80 · 9442e80
2 parents 0327bb1 + e6c4dcd
commit 9442e80
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Showing 24 changed files with 1,225 additions and 980 deletions.
diff --git a/.config/b0_to_template_affine_config.py b/.config/b0_to_template_affine_config.py
@@ -14,7 +14,7 @@
 
 c.AntsRegistration.log_level = 30
 
-c.AntsRegistration.init_with_ants_ai = True
+c.AntsRegistration.init_with_ants_ai = False
 
 c.AntsRegistration.base_config_file = ""
 
@@ -24,6 +24,10 @@
 # AntsConfiguration(mrHARDIConfigurable) configuration
 # -----------------------------------------------------------------------------
 
+c.AntsConfiguration.coarse_angular_split = 3
+
+c.AntsConfiguration.fine_angular_split = 4
+
 c.AntsConfiguration.accross_modalities = True
 
 c.AntsConfiguration.dimension = 3
@@ -39,20 +43,31 @@
 c.AntsConfiguration.match_histogram = False
 
 c.AntsConfiguration.passes = [{
-    "conv_eps": 1e-5,
+    "conv_eps": 1e-7,
     "conv_max_iter": [400, 200, 100, 50],
     "conv_win": 20,
-    "grad_step": 0.1,
+    "grad_step": 0.05,
     "klass": "mrHARDI.traits.ants.AntsRigid",
     "metrics": [
+        {
+            "target_index": 0,
+            "moving_index": 0,
+            "args": [
+                0.75,
+                128,
+                "Regular",
+                1.
+            ],
+            "klass": "mrHARDI.traits.ants.MetricMI"
+        },
         {
             "target_index": 0,
             "moving_index": 1,
             "args": [
-                1.,
-                64,
+                0.25,
+                128,
                 "Regular",
-                0.7,
+                1.,
                 True
             ],
             "klass": "mrHARDI.traits.ants.MetricMI"
@@ -71,20 +86,31 @@
         0
     ]
 }, {
-    "conv_eps": 1e-5,
+    "conv_eps": 1e-7,
     "conv_max_iter": [500, 300, 150, 75],
     "conv_win": 10,
-    "grad_step": 0.1,
+    "grad_step": 0.05,
     "klass": "mrHARDI.traits.ants.AntsAffine",
     "metrics": [
+        {
+            "target_index": 0,
+            "moving_index": 0,
+            "args": [
+                0.75,
+                128,
+                "Regular",
+                1.
+            ],
+            "klass": "mrHARDI.traits.ants.MetricMI"
+        },
         {
             "target_index": 0,
             "moving_index": 1,
             "args": [
-                1.,
-                64,
+                0.25,
+                128,
                 "Regular",
-                0.8,
+                1.,
                 True
             ],
             "klass": "mrHARDI.traits.ants.MetricMI"

diff --git a/.config/b0_to_template_syn_config.py b/.config/b0_to_template_syn_config.py
@@ -35,17 +35,17 @@
 c.AntsConfiguration.match_histogram = False
 
 c.AntsConfiguration.passes = [{
-    "conv_eps": 1e-5,
-    "conv_max_iter": [100, 50, 20, 10, 10],
+    "conv_eps": 1e-7,
+    "conv_max_iter": [200, 200, 140, 100, 40],
     "conv_win": 10,
-    "grad_step": 0.2,
+    "grad_step": 0.05,
     "var_penality": 3,
-    "var_total": 0,
+    "var_total": 3,
     "klass": "mrHARDI.traits.ants.AntsSyN",
     "metrics": [
         {
             "target_index": 0,
-            "moving_index": 1,
+            "moving_index": 0,
             "args": [
                 0.65,
                 64,
@@ -54,73 +54,43 @@
             ],
             "klass": "mrHARDI.traits.ants.MetricMI"
         },
-        {
-            "target_index": 0,
-            "moving_index": 2,
-            "args": [
-                0.35,
-                2,
-                "Regular",
-                1.
-            ],
-            "klass": "mrHARDI.traits.ants.MetricCC"
-        }
-    ],
-    "shrinks": [
-        12,
-        8,
-        4,
-        2,
-        1
-    ],
-    "smoothing": [
-        3.,
-        1.5,
-        1.,
-        0.5,
-        0
-    ]
-}, {
-    "conv_eps": 1e-5,
-    "conv_max_iter": [50, 20, 20],
-    "conv_win": 20,
-    "grad_step": 0.1,
-    "var_penality": 3,
-    "var_total": 0,
-    "klass": "mrHARDI.traits.ants.AntsSyN",
-    "metrics": [
         {
             "target_index": 0,
             "moving_index": 1,
             "args": [
-                0.65,
+                0.15,
                 64,
                 "Regular",
-                1.
+                1.,
+                True
             ],
             "klass": "mrHARDI.traits.ants.MetricMI"
         },
         {
             "target_index": 0,
             "moving_index": 2,
             "args": [
-                0.35,
-                2,
+                0.20,
+                4,
                 "Regular",
                 1.
             ],
             "klass": "mrHARDI.traits.ants.MetricCC"
         }
     ],
     "shrinks": [
-        8,
+        10,
+        6,
         4,
+        2,
         1
     ],
     "smoothing": [
-        1.5,
+        5.,
+        3.,
+        2.,
         1.,
-        0
+        0.
     ]
 }]
 

diff --git a/.config/dwi_n4_normalization_config.py b/.config/dwi_n4_normalization_config.py
@@ -23,21 +23,21 @@
 
 # -----------------------------------------------------------------------------
 # N4BiasCorrectionConfiguration(mrHARDIConfigurable) configuration
-c.N4BiasCorrectionConfiguration.bins = 150
+c.N4BiasCorrectionConfiguration.bins = 200
 
-c.N4BiasCorrectionConfiguration.filter_width = 0.075
+c.N4BiasCorrectionConfiguration.filter_width = 0.60
 
 c.N4BiasCorrectionConfiguration.spline_order = 3
 
-c.N4BiasCorrectionConfiguration.knot_distance = 64.0
+c.N4BiasCorrectionConfiguration.nvox_between_knots = 7.0
 
-c.N4BiasCorrectionConfiguration.iterations = [100, 100, 50, 30]
+c.N4BiasCorrectionConfiguration.iterations = [300, 300, 150, 75, 40]
 
 c.N4BiasCorrectionConfiguration.noise = 0.01
 
 c.N4BiasCorrectionConfiguration.rescale = True
 
-c.N4BiasCorrectionConfiguration.shrink = 2
+c.N4BiasCorrectionConfiguration.shrink = 4
 
 c.N4BiasCorrectionConfiguration.threshold = 1E-8
 

diff --git a/.config/dwi_n4_normalization_quick_config.py b/.config/dwi_n4_normalization_quick_config.py
@@ -25,11 +25,13 @@
 # N4BiasCorrectionConfiguration(mrHARDIConfigurable) configuration
 c.N4BiasCorrectionConfiguration.bins = 150
 
-c.N4BiasCorrectionConfiguration.filter_width = 0.075
+c.N4BiasCorrectionConfiguration.filter_width = 0.6
 
-c.N4BiasCorrectionConfiguration.knot_distance = 4.0
+c.N4BiasCorrectionConfiguration.spline_order = 3
 
-c.N4BiasCorrectionConfiguration.iterations = [300, 150, 75, 40]
+c.N4BiasCorrectionConfiguration.nvox_between_knots = 7.0
+
+c.N4BiasCorrectionConfiguration.iterations = [300, 300, 150, 75, 40]
 
 c.N4BiasCorrectionConfiguration.noise = 0.01
 

diff --git a/.config/prepare_topup_base_config.py b/.config/prepare_topup_base_config.py
@@ -28,74 +28,74 @@
 c.TopupConfiguration.klass = "mrHARDI.config.topup.TopupConfiguration"
 
 c.TopupConfiguration.passes = [{
-    "warp_resolution": 8.8,
-    "subsampling": 2,
-    "blur_fwhm": 3.5,
-    "n_iter": 100,
+    "warp_resolution": 25.1,
+    "subsampling": 4,
+    "blur_fwhm": 10,
+    "n_iter": 10,
     "estimate_motion": 1,
     "minimizer": 0,
     "w_reg": 5E-3
 }, {
-    "warp_resolution": 7.1,
-    "subsampling": 2,
-    "blur_fwhm": 2.6,
-    "n_iter": 100,
+    "warp_resolution": 20.3,
+    "subsampling": 4,
+    "blur_fwhm": 7.4,
+    "n_iter": 10,
     "estimate_motion": 1,
     "minimizer": 0,
     "w_reg": 1e-3
 }, {
-    "warp_resolution": 6.2,
-    "subsampling": 2,
-    "blur_fwhm": 1.8,
-    "n_iter": 100,
+    "warp_resolution": 17.7,
+    "subsampling": 4,
+    "blur_fwhm": 5.1,
+    "n_iter": 10,
     "estimate_motion": 1,
     "minimizer": 0,
     "w_reg": 1e-4
 }, {
-    "warp_resolution": 5.3,
-    "subsampling": 2,
-    "blur_fwhm": 1.3,
-    "n_iter": 100,
+    "warp_resolution": 15.1,
+    "subsampling": 4,
+    "blur_fwhm": 3.7,
+    "n_iter": 10,
     "estimate_motion": 1,
     "minimizer": 0,
     "w_reg": 1.5e-5
 }, {
-    "warp_resolution": 4.4,
+    "warp_resolution": 12.6,
     "subsampling": 2,
-    "blur_fwhm": 1.3,
-    "n_iter": 100,
+    "blur_fwhm": 3.7,
+    "n_iter": 15,
     "estimate_motion": 1,
     "minimizer": 0,
     "w_reg": 5e-6
 }, {
-    "warp_resolution": 2.7,
-    "subsampling": 1,
-    "blur_fwhm": 0.9,
-    "n_iter": 100,
+    "warp_resolution": 7.7,
+    "subsampling": 2,
+    "blur_fwhm": 2.6,
+    "n_iter": 15,
     "estimate_motion": 0,
     "minimizer": 1,
     "w_reg": 5e-7
 }, {
-    "warp_resolution": 1.7,
-    "subsampling": 1,
-    "blur_fwhm": 0.4,
-    "n_iter": 150,
+    "warp_resolution": 6.1,
+    "subsampling": 2,
+    "blur_fwhm": 1.1,
+    "n_iter": 20,
     "estimate_motion": 0,
     "minimizer": 1,
     "w_reg": 5e-8
 }, {
-    "warp_resolution": 1.7,
+    "warp_resolution": 6.1,
     "subsampling": 1,
     "blur_fwhm": 0.,
-    "n_iter": 200,
+    "n_iter": 20,
     "estimate_motion": 0,
     "minimizer": 1,
     "w_reg": 5e-10
 }, {
-    "warp_resolution": 1.5,
+    "warp_resolution": 6.1,
     "subsampling": 1,
     "blur_fwhm": 0.,
-    "n_iter": 400,
+    "n_iter": 40,
     "estimate_motion": 0,
     "minimizer": 1,
     "w_reg": 1e-11
@@ -105,7 +105,7 @@
 
 c.TopupConfiguration.reg_model = "bending_energy"
 
-c.TopupConfiguration.scale_intensities = False
+c.TopupConfiguration.scale_intensities = True
 
 c.TopupConfiguration.spl_order = "cubic"
 

diff --git a/.config/t1_n4_normalization_config.py b/.config/t1_n4_normalization_config.py
@@ -25,21 +25,21 @@
 # N4BiasCorrectionConfiguration(mrHARDIConfigurable) configuration
 c.N4BiasCorrectionConfiguration.bins = 200
 
-c.N4BiasCorrectionConfiguration.filter_width = 0.075
+c.N4BiasCorrectionConfiguration.filter_width = 0.60
 
 c.N4BiasCorrectionConfiguration.spline_order = 3
 
-c.N4BiasCorrectionConfiguration.knot_distance = 16.0
+c.N4BiasCorrectionConfiguration.nvox_between_knots = 14.0
 
-c.N4BiasCorrectionConfiguration.iterations = [80, 80, 40, 30]
+c.N4BiasCorrectionConfiguration.iterations = [300, 300, 150, 70]
 
 c.N4BiasCorrectionConfiguration.noise = 0.01
 
 c.N4BiasCorrectionConfiguration.rescale = True
 
-c.N4BiasCorrectionConfiguration.shrink = 2
+c.N4BiasCorrectionConfiguration.shrink = 4
 
-c.N4BiasCorrectionConfiguration.threshold = 1E-6
+c.N4BiasCorrectionConfiguration.threshold = 1E-8
 
 # Base traits configuration