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sitk_tools

Command-line tools written in Python using the SimpleITK library.

Contributors

Tanner Sorensen
Signal Analysis and Interpretation Laboratory
University of Southern California

Contents

fuse.py

Fuse three orthogonal stacks of DICOM MR images in the sagittal, coronal, and axial orientation. If path_to_dicom_dirs is the path to a directory containing three subdirectories with sag, cor, and axial in their names (case-insensitive, requires only partial match), then the following illustrates how to call fuse.py from a Bash session:

./fuse.py path_to_dicom_dirs output_file.mha

The script outputs the following .mha files:

  • resampled_sag.mha, resampled_cor.mha, resampled_axial.mha: imaged obtained by resampling the sagittal, coronal, and axial DICOM image stacks to have isotropic spatial resolution (taken to be the in-plane spatial resoluton of the DICOM MR image stack). These files only contain information from a single image stack (i.e., no fusion).
  • super-resolution image obtained by fusing resampled_sag.mha, resampled_sag.mha, and resampled_sag.mha by taking the median; file name is set by user as second argument.

to_dcm.py

Convert image (e.g., .mha image) to a DICOM series. Example usage:

./to_dcm.py image.mha path_to_dicom_series