Getting Started

Here is a quick snippet showing how to calculate color FA also known as the DEC map. We use a Tensor model to reconstruct the datasets which are saved in a Nifti file along with the b-values and b-vectors which are saved as text files. Finally, we save our result as a Nifti file

fdwi = 'dwi.nii.gz'
fbval = 'dwi.bval'
fbvec = 'dwi.bvec'

from dipy.io.image import load_nifti, save_nifti
from dipy.io import read_bvals_bvecs
from dipy.core.gradients import gradient_table
from dipy.reconst.dti import TensorModel

data, affine = load_nifti(fdwi)
bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
gtab = gradient_table(bvals, bvecs)

tenmodel = TensorModel(gtab)
tenfit = tenmodel.fit(data)

save_nifti('colorfa.nii.gz', tenfit.color_fa, affine)

As an exercise, you can try to calculate color FA with your datasets. You will need to replace the filepaths fdwi, fbval and fbvec. Here is what a slice should look like.

Next Steps

You can learn more about how you to use DIPY with your datasets by reading the examples in our Examples.