remove unneeded synthstrip flags

mri_synth_strip/mri_synth_strip

@@ -19,12 +19,9 @@ parser.add_argument('-o', '--output', required=True, help='Masked output image f
 parser.add_argument('-m', '--mask', help='Output mask filename.')
 parser.add_argument('-b', '--border', default=1, type=int, help='Mask border threshold. Default is 1.')
 parser.add_argument('--model', help='Alternative model file.')
-parser.add_argument('--uthresh', type=float, help='Intensity threshold to erase from input image.')
 parser.add_argument('-v', '--verbose', action='store_true', help='Verbose output for debugging.')
 parser.add_argument('-g', '--gpu', help='GPU ID. CPU is used by default.')
 parser.add_argument('--max-norm', action='store_true', help='Normalize by max intensity instead of 97th percentile.')
-parser.add_argument('--remove-neck', type=int,
-                    help='Remove bottom part of 2nd axis from listed locations to end.')
 args = parser.parse_args()
 
 os.environ['TF_CPP_MIN_LOG_LEVEL'] = '0' if args.verbose else '3'
@@ -109,15 +106,6 @@ with tf.device(device):
 # load input volume
 in_img = fs.Volume.read(args.input)
 
-# threshold input
-if args.uthresh is not None:
-    in_img.data[in_img.data > args.uthresh] = 0
-
-# remove y-axis voxels
-if args.remove_neck is not None:
-    print(f'Removing neck from {args.remove_neck} to bottom of image.')
-    in_img.data[:, args.remove_neck:, :] = 0
-
 # conform image and normalize
 conf_img = in_img.conform(shape=(256, 256, 256), voxsize=1.0, dtype='float32', interp_method='nearest')
 in_data = conf_img.data