From 444d2111b9d7141711c9c2c77fdbcade4e18ad12 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 14 May 2021 23:01:01 +0200
Subject: [PATCH 1/2] ENH: Fine-tune the registration parameters in coeff2epi
 workflow

---
 sdcflows/data/fmap-any_registration.json      | 20 +++++++++----------
 .../data/fmap-any_registration_testing.json   | 10 +++++-----
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/sdcflows/data/fmap-any_registration.json b/sdcflows/data/fmap-any_registration.json
index ef14cae47f..4713051f51 100644
--- a/sdcflows/data/fmap-any_registration.json
+++ b/sdcflows/data/fmap-any_registration.json
@@ -1,23 +1,23 @@
 {
     "collapse_output_transforms": true,
     "convergence_threshold": [ 1e-07, 1e-08 ],
-    "convergence_window_size": [ 200, 100 ],
+    "convergence_window_size": [ 5, 3 ],
     "dimension": 3,
-    "float": true,
+    "initial_moving_transform_com": 2,
     "interpolation": "LanczosWindowedSinc",
     "metric": [ "Mattes", "Mattes" ],
     "metric_weight": [ 1.0, 1.0 ],
-    "number_of_iterations": [ [ 500 ], [ 200 ] ],
-    "radius_or_number_of_bins": [ 64, 64 ],
-    "sampling_percentage": [ 0.5, 0.5 ],
+    "number_of_iterations": [ [ 50 ], [ 20 ] ],
+    "radius_or_number_of_bins": [ 32, 32 ],
+    "sampling_percentage": [ 0.25, 0.5 ],
     "sampling_strategy": [ "Random", "Random" ],
     "shrink_factors": [ [ 2 ], [ 1 ] ],
     "sigma_units": [ "mm", "mm" ],
     "smoothing_sigmas": [ [ 8.0 ], [ 2.0 ] ],
-    "transform_parameters": [ [ 0.05 ], [ 0.01 ] ],
-    "transforms": [ "Translation", "Rigid" ],
-    "use_estimate_learning_rate_once": [ true, true ],
+    "transform_parameters": [ [ 0.1 ], [ 0.1 ] ],
+    "transforms": [ "Rigid", "Rigid" ],
+    "use_estimate_learning_rate_once": [ true, false ],
     "use_histogram_matching": [ true, true ],
-    "winsorize_lower_quantile": 0.005,
-    "winsorize_upper_quantile": 0.998
+    "winsorize_lower_quantile": 0.001,
+    "winsorize_upper_quantile": 0.999
 }
\ No newline at end of file
diff --git a/sdcflows/data/fmap-any_registration_testing.json b/sdcflows/data/fmap-any_registration_testing.json
index 129993b34e..8da664c665 100644
--- a/sdcflows/data/fmap-any_registration_testing.json
+++ b/sdcflows/data/fmap-any_registration_testing.json
@@ -1,15 +1,15 @@
 {
     "collapse_output_transforms": true,
     "convergence_threshold": [ 1e-07, 1e-08 ],
-    "convergence_window_size": [ 20, 10 ],
+    "convergence_window_size": [ 5, 3 ],
     "dimension": 3,
-    "float": true,
+    "initial_moving_transform_com": 2,
     "interpolation": "LanczosWindowedSinc",
     "metric": [ "Mattes", "Mattes" ],
     "metric_weight": [ 1.0, 1.0 ],
-    "number_of_iterations": [ [ 500 ], [ 100 ] ],
-    "radius_or_number_of_bins": [ 64, 64 ],
-    "sampling_percentage": [ 1.0, 1.0 ],
+    "number_of_iterations": [ [ 50 ], [ 10 ] ],
+    "radius_or_number_of_bins": [ 32, 32 ],
+    "sampling_percentage": [ 0.25, 0.5 ],
     "sampling_strategy": [ "Regular", "Regular" ],
     "shrink_factors": [ [ 2 ], [ 1 ] ],
     "sigma_units": [ "mm", "mm" ],

From 9d8f6bdbd882473f658e093c5ecb46c3778eb1b7 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 14 May 2021 23:43:45 +0200
Subject: [PATCH 2/2] fix: pin nitransforms-20.0.0rc4 with fix for ANTs'
 ``.mat``

---
 min-requirements.txt | 2 ++
 requirements.txt     | 2 ++
 setup.cfg            | 1 +
 3 files changed, 5 insertions(+)

diff --git a/min-requirements.txt b/min-requirements.txt
index 93f44d952d..a4152603d8 100644
--- a/min-requirements.txt
+++ b/min-requirements.txt
@@ -2,8 +2,10 @@
 nibabel==3.0.1
 nipype==1.5.1
 niworkflows==1.4.0rc5
+nitransforms==20.0.0rc4
 numpy
 pybids==0.11.1
 scikit-image==0.18
+scipy==1.6.1
 svgutils!=0.3.2
 templateflow==0.6
diff --git a/requirements.txt b/requirements.txt
index 53a56d350c..ed07342958 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,8 +2,10 @@
 nibabel>=3.0.1
 nipype<2.0,>=1.5.1
 niworkflows>=1.4.0rc5
+nitransforms>=20.0.0rc4
 numpy
 pybids>=0.11.1
 scikit-image>=0.18
+scipy~=1.6.1
 svgutils!=0.3.2
 templateflow>=0.6
diff --git a/setup.cfg b/setup.cfg
index 111a4b7958..852811be82 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -31,6 +31,7 @@ install_requires =
     nibabel >=3.0.1
     nipype >=1.5.1,<2.0
     niworkflows >= 1.4.0rc5
+    nitransforms >= 20.0.0rc4
     numpy
     pybids >= 0.11.1
     scikit-image >= 0.18