Recipes

How do I do X in DIPY? This page contains a collection of recipes that will help you quickly resolve common basic/advanced operation. If you have a question that is not answered here, please ask on the dipy discussions or even better, answer it yourself and contribute to the documentation!

How do I convert my tractograms?

We recommend to look at the tutorials Streamline File Formats

from dipy.io.streamline import load_tractogram, save_tractogram

# convert from fib to trk
my_fib_file_path = '/<my_folder>/<my_path>/my_tractogram.fib'
my_trk_file_path = '/<my_folder>/<my_path>/my_tractogram.trk'
my_trk = load_tractogram(my_fib_file_path, 'same')
save_tractogram(my_trk.streamlines, my_trk_file_path, 'same')

How do I convert my Spherical Harmonics from MRTRIX3 to DIPY?

*Available from DIPY 1.9.0+. See this thread for more information.

from dipy.reconst.shm import convert_sh_descoteaux_tournier
convert_sh_descoteaux_tournier(sh_coeffs)

How do I convert my tensors from FSL to DIPY or MRTRIX3 to DIPY?

*Available with DIPY 1.9.0+

from dipy.reconst.utils import convert_tensors
from dipy.io.image import load_nifti, save_nifti

data, affine, img = load_nifti('my_data.nii.gz', return_img=True)
# convert from FSL to DIPY
otensor = convert_tensors(data, 'fsl', 'dipy')
save_nifti(otensor, data, affine, image.header)
# convert from MRTRIX3 to DIPY
otensor = convert_tensors(data, 'mrtrix', 'dipy')
save_nifti(otensor, data, affine, image.header)