Merge pull request #161 from ANTsX/BEFOV

ENH:  Extend FOV

Author: ntustison

antspynet/utilities/brain_extraction.py

@@ -180,9 +180,9 @@ def brain_extraction(image,
             reorient_template_mask = ants.image_read(get_antsxnet_data("hcpyaTemplateBrainMask"))
             reorient_template = reorient_template * reorient_template_mask
             reorient_template = ants.resample_image(reorient_template, (1, 1, 1), use_voxels=False, interp_type=0)
-            reorient_template = pad_or_crop_image_to_size(reorient_template, (160, 176, 160))
+            reorient_template = pad_or_crop_image_to_size(reorient_template, (160, 192, 160))
             xfrm = ants.create_ants_transform(transform_type="Euler3DTransform",
-                center=np.asarray(ants.get_center_of_mass(reorient_template)), translation=(0, -10, -15))
+                center=np.asarray(ants.get_center_of_mass(reorient_template)), translation=(0, 0, 0))
             reorient_template = xfrm.apply_to_image(reorient_template)
         else:
             reorient_template = ants.image_read(get_antsxnet_data("S_template3"))

antspynet/utilities/get_pretrained_network.py

@@ -55,8 +55,8 @@ def switch_networks(argument):
             "brainExtractionInfantT1": "https://ndownloader.figshare.com/files/22968836",
             "brainExtractionInfantT2": "https://ndownloader.figshare.com/files/22968830",
             "brainExtractionBrainWeb20" : "https://figshare.com/ndownloader/files/50685390",
-            "brainExtractionT1Hemi" : "https://figshare.com/ndownloader/files/51341411",
-            "brainExtractionT1Lobes" : "https://figshare.com/ndownloader/files/51341408",
+            "brainExtractionT1Hemi" : "https://figshare.com/ndownloader/files/52184666",
+            "brainExtractionT1Lobes" : "https://figshare.com/ndownloader/files/52184660",
             "brainSegmentation": "https://ndownloader.figshare.com/files/13900010",
             "brainSegmentationPatchBased": "https://ndownloader.figshare.com/files/14249717",
             "bratsStage1": "https://figshare.com/ndownloader/files/42384756",