From c8dcf14d7925694c780e6c463890ea81a65b44d3 Mon Sep 17 00:00:00 2001 From: Usman Akinyemi Date: Tue, 11 Jun 2024 09:45:09 -0400 Subject: [PATCH] Updated the README.md file and also fixed issue with the nifti_wrapper.py by making the algorithm_args optional to prevent it from overiding algorithm --- Docker/README.md | 4 ++-- WrapImage/nifti_wrapper.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Docker/README.md b/Docker/README.md index 5d77553..32f5305 100644 --- a/Docker/README.md +++ b/Docker/README.md @@ -52,8 +52,8 @@ Before running the Docker container, here are the available options for the `Doc ```sh sudo docker run -it --rm --name TF2.4_IVIM-MRI_CodeCollection \ -v ~/TF2.4_IVIM-MRI_CodeCollection:/usr/src/app \ - -v ~/TF2.4_IVIM-MRI_CodeCollection:/usr/app/output \ - tf2.4_ivim-mri_codecollection brain.nii.gz brain.bvec brain.bval + -v ~/TF2.4_IVIM-MRI_CodeCollection:/usr/app/output \ + tf2.4_ivim-mri_codecollection Downloads/brain.nii.gz Downloads/brain.bvec Downloads/brain.bval \ ``` Replace `brain.nii.gz`, `brain.bvec`, and `brain.bval` with the actual file names you want to use. diff --git a/WrapImage/nifti_wrapper.py b/WrapImage/nifti_wrapper.py index a0d65af..5eae67e 100644 --- a/WrapImage/nifti_wrapper.py +++ b/WrapImage/nifti_wrapper.py @@ -84,7 +84,7 @@ def loop_over_first_n_minus_1_dimensions(arr): parser.add_argument("bval_file", type=str, help="Path to the b-value file.") parser.add_argument("--affine", type=float, nargs="+", help="Affine matrix for NIfTI image.") parser.add_argument("--algorithm", type=str, default="OJ_GU_seg", help="Select the algorithm to use.") - parser.add_argument("algorithm_args", nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.") + parser.add_argument("--algorithm_args", nargs=argparse.REMAINDER, help="Additional arguments for the algorithm.") args = parser.parse_args()