enh: continuing deep overhaul of fieldmapless implementation

Salient points on this commit:

- There's no need for intensity inversion if MI is used as cost function
- Use of the T1w as reference (fixed) image increases reliability
- Giving more flexibility to ``restrict_deformation`` with 0.1 instead
  of 1 makes optimization faster leveraging a minimal increase of dofs
- To double-check things look good, use our internal transform object
  to generate the unwarped reference, and then generate the field, which
  should be fairly close to the one generated by ANTs.
- Addressed LPS orientation bug in the function node that extracts the
  nonzero component of distortion.
- Better registration parameters, with thanks to @yasseraleman for
  suggestions (in particular, the one about flexibilizing the gradient
  restriction above came from him).
- Use of laplacians in a multi-channel registration framework

Resolves: #186.

Author: oesteban

sdcflows/data/affine.json

@@ -1,24 +1,24 @@
 {
     "collapse_output_transforms": true,
-    "convergence_threshold": [ 1e-06, 1e-06 ],
-    "convergence_window_size": [ 50, 10 ],
+    "convergence_threshold": [ 1e-06, 1e-07 ],
+    "convergence_window_size": [ 10, 5 ],
     "dimension": 3,
     "initial_moving_transform_com": 1,
     "interpolation": "Linear",
     "metric": [ "Mattes", "Mattes" ],
     "metric_weight": [ 1.0, 1.0 ],
-    "number_of_iterations": [ [ 1000, 500, 0 ], [ 1000, 500, 250, 100 ] ],
+    "number_of_iterations": [ [ 1000, 0 ], [ 250, 100 ] ],
     "radius_or_number_of_bins": [ 32, 32 ],
-    "sampling_percentage": [ 1.0, 0.25 ],
+    "sampling_percentage": [ 1.0, 0.4 ],
     "sampling_strategy": [ "Regular", "Random" ],
-    "shrink_factors": [[ 8, 4, 1] , [ 8, 4, 2, 1 ]],
+    "shrink_factors": [[ 4, 1] , [ 2, 1 ]],
     "sigma_units": [ "mm", "vox" ],
-    "smoothing_sigmas": [ [ 8, 6, 0 ], [ 4, 2, 1, 0 ] ],
-    "transform_parameters": [ [ 10.0 ], [ 0.6 ] ],
+    "smoothing_sigmas": [ [ 6, 0 ], [ 2, 1 ] ],
+    "transform_parameters": [ [ 2.0 ], [ 1.0 ] ],
     "transforms": [ "Rigid", "Affine" ],
     "use_estimate_learning_rate_once": [ false, false ],
-    "use_histogram_matching": [ false, true ],
+    "use_histogram_matching": [ true, true ],
     "winsorize_lower_quantile": 0.001,
-    "winsorize_upper_quantile": 0.9999,
+    "winsorize_upper_quantile": 0.998,
     "write_composite_transform": false
 }

sdcflows/data/sd_syn.json

@@ -1,24 +1,24 @@
 {
     "collapse_output_transforms": true,
-    "convergence_threshold": [ 1e-06, 1e-06, 1e-08 ],
-    "convergence_window_size": [ 10, 5, 2 ],
+    "convergence_threshold": [ 1e-06, 1e-08 ],
+    "convergence_window_size": [ 5, 2 ],
     "dimension": 3,
     "interpolation": "Linear",
-    "metric": [ "Mattes", "Mattes", "CC" ],
-    "metric_weight": [ 1, 1, 1 ],
-    "number_of_iterations": [ [ 500, 500, 0 ], [ 20, 10, 0 ], [ 10 ] ],
+    "metric": [ ["Mattes", "Mattes"], ["Mattes", "Mattes"] ],
+    "metric_weight": [ [0.5, 0.5], [0.5, 0.5], [0.5, 0.5] ],
+    "number_of_iterations": [ [ 200, 100 ], [ 10 ] ],
     "output_transform_prefix": "fmap_syn",
-    "radius_or_number_of_bins": [ 32, 32, 5 ],
-    "sampling_percentage": [ 0.25, 0.40, 1.0 ],
-    "sampling_strategy": [ "Random", "Random", "Random" ],
-    "shrink_factors": [ [ 4, 2, 1 ], [ 2, 1, 1 ], [ 1 ] ],
-    "sigma_units": [ "mm", "mm", "vox" ],
-    "smoothing_sigmas": [ [ 8, 6, 0 ], [ 6, 2, 0 ], [ 0 ] ],
-    "transform_parameters": [ [ 0.5, 3.0, 3.0 ], [ 0.8, 2.8, 1.0 ], [ 0.8, 2.0, 1.0 ] ],
-    "transforms": [ "SyN", "SyN", "SyN" ],
-    "use_estimate_learning_rate_once": [ false, false, true ],
-    "use_histogram_matching": [ false, false, false ],
-    "winsorize_lower_quantile": 0.0001,
-    "winsorize_upper_quantile": 0.9999,
+    "radius_or_number_of_bins": [ [48, 48], [48, 48] ],
+    "sampling_percentage": [ [0.8, 0.8], [1.0, 1.0] ],
+    "sampling_strategy": [["Random", "Random"], [null, null] ],
+    "shrink_factors": [ [ 1, 1 ], [ 1 ] ],
+    "sigma_units": [ "vox", "vox" ],
+    "smoothing_sigmas": [ [ 2, 0 ], [ 0 ] ],
+    "transform_parameters": [ [ 0.8, 6.0, 3.0 ], [ 0.8, 2.0, 1.0 ] ],
+    "transforms": [ "SyN", "SyN" ],
+    "use_estimate_learning_rate_once": [ true, true ],
+    "use_histogram_matching": [ true, true ],
+    "winsorize_lower_quantile": 0.001,
+    "winsorize_upper_quantile": 0.998,
     "write_composite_transform": false
 }