diff --git a/.gitignore b/.gitignore index a65d046..3c89fde 100644 --- a/.gitignore +++ b/.gitignore @@ -56,3 +56,6 @@ docs/_build/ # PyBuilder target/ + +# other +.idea/ \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..94a25f7 --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/README.md b/README.md index 8f3bb3a..eb4972b 100644 --- a/README.md +++ b/README.md @@ -1 +1,26 @@ -sweep_recon +# sweep-recon + +--- +## Introduction +Reconstruction code for respiration resolved SWEEP acquisitions. The code presented here is a builds upon the reconstructiion pipeline described in the paper below. If you find this code useful please acknowledge this paper (in press). + +>Jackson LH, Price AN, Hutter J et al. Respiration resolved imaging with continuous stable state 2D acquisition using linear frequency SWEEP. Magn Reson Med. 2019;00:1–15. + +An outline of the reconstruction pipeline is given in the figure below. For more details please refer to the paper given above. + +![](./data/figures/Figure_1_pipeline.png) + +## Example +``` +Usage: + sweeprecon -i path_to_nii + + Optional arguments: + --thickness :: thickness of acquisition slices in mm (default 4mm) + --nstates :: number of respiration states to receonstruct to (defualt 4) + --recon_thickness :: thickness of reconstructed slices in mm (default isotropic) + --redo :: flag to redo processing from scratch + --resort_only :: flag to stop processing after resort step + --crop :: factor to crop from either side of image for bodyarea mask (default 0.2) +``` + diff --git a/__main__.py b/__main__.py new file mode 100644 index 0000000..ec4f242 --- /dev/null +++ b/__main__.py @@ -0,0 +1,7 @@ +import sys + +from sweeprecon.applications.app_sweep_recon import main + +if __name__ == "__main__": + print('running __main__') + sys.exit(main()) diff --git a/data/figures/Figure_1_pipeline.png b/data/figures/Figure_1_pipeline.png new file mode 100644 index 0000000..f21a707 Binary files /dev/null and b/data/figures/Figure_1_pipeline.png differ diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..e69de29 diff --git a/sweeprecon/applications/__init__.py b/sweeprecon/applications/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/sweeprecon/applications/app_sweep_recon.py b/sweeprecon/applications/app_sweep_recon.py new file mode 100644 index 0000000..564a461 --- /dev/null +++ b/sweeprecon/applications/app_sweep_recon.py @@ -0,0 +1,4 @@ + + +def main(): + return diff --git a/sweeprecon/io/__init__.py b/sweeprecon/io/__init__.py new file mode 100644 index 0000000..e69de29