NeuroData's MR Graphs package, ndmg (pronounced "nutmeg"), is the successor of the MRCAP, MIGRAINE, and m2g pipelines. ndmg combines dMRI and sMRI data from a single subject to estimate a high-level connectome reliably and scalably.

Installing ndmg is very simple! We have a few dependencies which must be installed, but once that's taken care of you are ready to dive in!

ndmg relies on: FSL, DiPy, networkx, and nibabel, as well as numpy and scipy. You should install FSL through the instructions on their website. Then, you can install ndmg with the following command and it'll handle the rest:

pip install ndmg

We provide the ability to exercise our entire end to end pipeline in < 3 minutes on downsampled data. The connectome produced may not have neurological significance, but this test should ensure that all of the pieces of the code and driver script still execute and is a great interface check.

python ndmg/scripts/ndmg_pipeline.py tests/data/KKI2009_113_1_DTI_s4.nii tests/data/KKI2009_113_1_DTI_s4.bval tests/data/KKI2009_113_1_DTI_s4.bvec tests/data/KKI2009_113_1_MPRAGE_s4.nii tests/data/MNI152_T1_1mm_s4.nii.gz tests/data/MNI152_T1_1mm_brain_mask_s4.nii.gz tests/data/outputs tests/data/desikan_s4.nii.gz

Check out our full documentation on our website, or our function reference for more information about ndmg.

If you're having trouble, notice a bug, or want to contribute (such as a fix to the bug you may have just found) feel free to open a git issue or pull request. Enjoy!