ENH: Add DKT labeling

Already available through cortical_thickness but useful to have independently

bin/runAntsXNet.sh

@@ -33,6 +33,7 @@ Required args:
     One of: brain_extraction
             brain_segmentation
             cortical_thickness
+            desikan_killiany_tourville_labeling
             hippocampal_segmentation
             interactive
             /path/to/custom/script.py

scripts/antsxnet_desikan_killiany_tourville_labeling.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
+                                 prog="desikan_killiany_tourville_labeling", add_help=False, description='''
+Wrapper for DKT labeling in ANTsPyNet.
+
+For more details of the algorithm and available options, see
+
+https://github.com/ANTsX/ANTsPyNet/blob/master/antspynet/utilities/desikan_killiany_tourville_labeling.py
+
+If you use this in your research, please cite:
+
+Tustison, N.J., Cook, P.A., Holbrook, A.J. et al. The ANTsX ecosystem for quantitative biological
+and medical imaging. Sci Rep 11, 9068 (2021). https://doi.org/10.1038/s41598-021-87564-6
+''')
+required = parser.add_argument_group('Required arguments')
+required.add_argument("-a", "--head-image", help="Input T1w image", type=str, required=True)
+required.add_argument("-o", "--output-root", help="Full path to output including file prefix", type=str, required=True)
+optional = parser.add_argument_group('Optional arguments')
+optional.add_argument("-h", "--help", action="help", help="show this help message and exit")
+optional.add_argument("-t", "--threads", help="Number of threads in tensorflow operations. Use environment variable "
+                    "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS to control threading in ANTs calls", type=int, default=1
+                    )
+args = parser.parse_args()
+
+
+import ants
+import antspynet
+import tensorflow as tf
+
+output_dir = os.path.dirname(args.output_root)
+output_file_prefix = os.path.basename(args.output_root)
+
+if not os.path.exists(output_dir):
+    os.makedirs(output_dir)
+
+tf.keras.backend.clear_session()
+tf.config.threading.set_intra_op_parallelism_threads(args.threads)
+tf.config.threading.set_inter_op_parallelism_threads(args.threads)
+
+anat = ants.image_read(args.head_image)
+
+deep_dkt = antspynet.desikan_killiany_tourville_labeling(anat, verbose=True)
+ants.image_write(deep_dkt, args.output_root + "DKT.nii.gz")