Merge branch 'master' of https://github.com/ANTsX/ANTsPyNet

README.md

@@ -138,9 +138,9 @@ The following is an overview of the available model architectures and pre-traine
 - [HyperMapp3r white matter hyperintensity segmentation](https://pubmed.ncbi.nlm.nih.gov/35088930/)
 - [Hypothalamus segmentation](https://pubmed.ncbi.nlm.nih.gov/32853816/)
 - [Claustrum segmentation](https://arxiv.org/abs/2008.03465)
-- [Deep Flash](https://www.medrxiv.org/content/10.1101/2023.01.17.23284693v4)
+- [Deep Flash](https://www.nature.com/articles/s41598-024-59440-6)
 - [Desikan-Killiany-Tourville cortical labeling](https://pubmed.ncbi.nlm.nih.gov/33907199/)
-- [Cerebellum segmentation, parcellation, and thickness](https://www.medrxiv.org/content/10.1101/2023.01.17.23284693v4)
+- [Cerebellum segmentation, parcellation, and thickness](https://www.nature.com/articles/s41598-024-59440-6)
 - MRI modality classification
 - Lung extraction
   - [Proton](https://pubmed.ncbi.nlm.nih.gov/34227163/)
@@ -160,7 +160,7 @@ The following is an overview of the available model architectures and pre-traine
 <details>
 <summary>Publications</summary>
 
-- Nicholas J. Tustison, Michael A. Yassa, Batool Rizvi, Philip A. Cook, Andrew J. Holbrook, Mithra Sathishkumar, Mia G. Tustison, James C. Gee, James R. Stone, and Brian B. Avants. ANTsX neuroimaging-derived structural phenotypes of UK Biobank. [(medrxiv)](https://www.medrxiv.org/content/10.1101/2023.01.17.23284693v4)
+- Nicholas J. Tustison, Michael A. Yassa, Batool Rizvi, Philip A. Cook, Andrew J. Holbrook, Mithra Sathishkumar, Mia G. Tustison, James C. Gee, James R. Stone, and Brian B. Avants. ANTsX neuroimaging-derived structural phenotypes of UK Biobank. _Scientific Reports_ 14, 8848 (2024). [(pubmed)](https://www.nature.com/articles/s41598-024-59440-6)
 
 - Nicholas J. Tustison, Talissa A. Altes, Kun Qing, Mu He, G. Wilson Miller, Brian B. Avants, Yun M. Shim, James C. Gee, John P. Mugler III, and Jaime F. Mata. Image- versus histogram-based considerations in semantic segmentation of pulmonary hyperpolarized gas images. _Magnetic Resonance in Medicine_, 86(5):2822-2836, Nov 2021. [(pubmed)](https://pubmed.ncbi.nlm.nih.gov/34227163/)
 

antspynet/utilities/cerebellum_morphology.py

@@ -15,8 +15,7 @@ def cerebellum_morphology(t1,
     Perform cerebellum segmentation using a modification of the set of
     MaGET cerebellum atlases --- https://www.cobralab.ca/cerebellum-lobules
 
-    Current citation:
-    https://www.medrxiv.org/content/10.1101/2023.01.17.23284693v4
+    https://www.nature.com/articles/s41598-024-59440-6
 
     The tissue labeling is as follows:
 

antspynet/utilities/deep_flash.py

@@ -19,8 +19,7 @@ def deep_flash(t1,
     Perform hippocampal/entorhinal segmentation in T1 and T1/T2 images using
     labels from Mike Yassa's lab---https://faculty.sites.uci.edu/myassa/
 
-    Current citation:
-    https://www.medrxiv.org/content/10.1101/2023.01.17.23284693v4
+    https://www.nature.com/articles/s41598-024-59440-6
 
     The labeling is as follows:
     Label 0 :  background

antspynet/utilities/histogram_warp_image_intensities.py

@@ -93,9 +93,10 @@ def histogram_warp_image_intensities(image,
     transform_domain_origin = 0
     transform_domain_spacing = (1.0 - transform_domain_origin) / (transform_domain_size - 1)
 
-    bspline_histogram_transform = ants.fit_bspline_object_to_scattered_data( scattered_data,
+    bspline_histogram_transform = ants.fit_bspline_object_to_scattered_data(scattered_data,
         parametric_data, [transform_domain_origin], [transform_domain_spacing], [transform_domain_size],
-        data_weights=weights)
+        data_weights=weights, is_parametric_dimension_closed=None, number_of_fitting_levels=4, 
+        mesh_size=1, spline_order=3)
 
     transform_domain = np.linspace(0, 1, transform_domain_size)