/PerfusionDSA

Primary LanguagePython

PerfusionDSA

This simple programs calculates perfusion parametric images including

  • Cerebral Blood Flow (CBF),
  • Cerebral Blood Volume (CBV),
  • Mean Transit Time (MTT), and
  • Time to max flow-scaled residue function (Tmax)

from a series of 2D+t images produced by cerebral X-ray angiography.

The program is adopted from perfusionDSA. The main function non_parametric_deconvolution.py is modified from non_parametric_deconvolution.

Dependencies

  • NumPy
  • Nibabel
  • Pydicom
  • Scipy
  • Matplotlib

Usage

For a Digital Subtraction Angiogram (DSA) series of shape [t, x, y] saved as a DICOM file ./dsa.dcm, an (optional) arterial input function (AIF) mask of shape [x, y, t] saved as a NIfTI file ./aif.nii, the following script saves the parametric images as NIfTI files CBF.nii, CBV.nii, MTT.nii, and Tmax.nii under the directory specified by --output or -o.

python perfusiondsa.py -d ./dsa.dcm -a ./aif.nii -o ./output

If an AIF mask is not specified by --aif or -a, the user will be prompted to draw a region of interest (ROI) from which the AIF will be obtained. Note: only the last ROI drawn will be recorded.

The --show_aif and --show_results flags can be used to plot the AIF and display the parametric maps, respectively.

To apply a Gaussian filter to the AIF and the DSA time series, use the option --prefilter or -f.