dipy_fit module

Wrapper that uses DIPY to fit DTI and DKI representations.

dipy_fit.fit_dki(dwi, blur=False)

Fit a DKI model to a DWI, applying a mask if provided.

Parameters:
  • dwi (DiffusionWeightedImage) – DWI data to fit to the model.
  • blur (bool, optional) – True if the image should be blurred before the model fit.
Returns:

dwifit – A fit from which parameter maps can be generated
Return type:

DiffusionKurtosisFit
dipy_fit.fit_dti(dwi)

Fit a DTI model to a DWI, applying a mask if provided.

Parameters:
  • dwi (DiffusionWeightedImage) – DWI data to fit to the model.
  • blur (bool, optional) – True if the image should be blurred before the model fit.
Returns:

dwifit – A fit from which parameter maps can be generated
Return type:

TensorFit
dipy_fit.main(nifti_path, bval_path, bvec_path, mask_path=None, blur=False, fa_path=None, md_path=None, ad_path=None, rd_path=None, mk_path=None, ak_path=None, rk_path=None)

Load and fit an image to a DKI model, then save its parameters.

This is meant to deal with the functionality of this module being called as a script.

Parameters:
  • nifti_path (str) – Path to the nifti DWI
  • bval_path (str) – Path to the .bval file
  • bvec_path (str) – Path to the .bvec file
  • mask_path (str, optional) – Path to the nifti mask, if one exists
  • fa_path (str, optional) – Path to which the fractional anisotropy image should be saved
  • md_path (str, optional) – Path to which the mean diffusivity image should be saved
  • ad_path (str, optional) – Path to which the axial diffusivity image should be saved
  • rd_path (str, optional) – Path to which the radial diffusivity image should be saved
  • mk_path (str, optional) – Path to which the mean kurtosis image should be saved
  • ak_path (str, optional) – Path to which the axial kurtosis image should be saved
  • rk_path (str, optional) – Path to which the radial kurtosis image should be saved
dipy_fit.save_dki_metric_imgs(dwi, dkifit, fa_path=None, md_path=None, ad_path=None, rd_path=None, mk_path=None, ak_path=None, rk_path=None)

Save DTI metric images as NIFTI files.

Parameters:
  • dwi (DiffusionWeightedImage) – The source image from which the DTI metrics are derived.
  • dkifit (DiffusionKurtosisFit) – The fit data from the DKI.
  • md_path, ad_path, rd_path (fa_path,) – The filepaths to which each DTI metric image should be saved.
  • ak_path, rk_path (mk_path,) – The filepaths to which each DKI metric image should be saved.
dipy_fit.save_dti_metric_imgs(dwi, dtifit, fa_path=None, md_path=None, ad_path=None, rd_path=None)

Save DTI metric images as NIFTI files.

Parameters:
  • dwi (DiffusionWeightedImage) – The source image from which the DTI metrics are derived.
  • dtifit (TensorFit) – The fit data from the DTI.
  • md_path, ad_path, rd_path (fa_path,) – The filepath to which each metric image should be saved.