AFQ.models.dki

Module Contents

Functions

fit_dki(data_files, bval_files, bvec_files, mask=None, min_kurtosis=-1, max_kurtosis=3, out_dir=None, b0_threshold=50)

Fit the DKI model, save files with derived maps

predict(params_file, gtab, S0_file=None, out_dir=None)

Create a signal prediction from DKI params

AFQ.models.dki.fit_dki(data_files, bval_files, bvec_files, mask=None, min_kurtosis=- 1, max_kurtosis=3, out_dir=None, b0_threshold=50)[source]

Fit the DKI model, save files with derived maps

Parameters
data_filesstr or list

Files containing DWI data. If this is a str, that’s the full path to a single file. If it’s a list, each entry is a full path.

bval_filesstr or list

Equivalent to data_files.

bvec_filesstr or list

Equivalent to data_files.

maskndarray, optional

Binary mask, set to True or 1 in voxels to be processed. Default: Process all voxels.

min_kurtosisfloat, optional

The minimal plausible value of kurtosis. Default: -1.

max_kurtosisfloat, optional

The maximal plausible value of kurtosis. Default: 3.

out_dirstr, optional

A full path to a directory to store the maps that get computed. Default: maps get stored in the same directory as the last DWI file in data_files.

b0_thresholdfloat
Returns
file_pathsa dict with the derived maps that were computed and full-paths
to the files containing these maps.
AFQ.models.dki.predict(params_file, gtab, S0_file=None, out_dir=None)[source]

Create a signal prediction from DKI params

params_filestr

Full path to a file with parameters saved from a DKI fit

gtabGradientTable object

The gradient table to predict for

S0_filestr

Full path to a nifti file that contains S0 measurements to incorporate into the prediction. If the file contains 4D data, the volumes that contain the S0 data must be the same as the gtab.b0s_mask.