From 3e7f4e6bff32063a94cca589093f827656f4beb6 Mon Sep 17 00:00:00 2001 From: Andrew Hoopes Date: Fri, 24 Dec 2021 21:22:54 -0500 Subject: [PATCH] remove unneeded synthstrip flags --- mri_synth_strip/mri_synth_strip | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/mri_synth_strip/mri_synth_strip b/mri_synth_strip/mri_synth_strip index 2a70d6a8d5b..5b64a19d62b 100755 --- a/mri_synth_strip/mri_synth_strip +++ b/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