NeuroData's MR Graphs package, ndmg, run with different atlas

maryam.riazi · July 26, 2024, 9:11pm

Hi all,

I want to use ndmg on python for extracting structural connectivity from diffusion MRI and t1 images.
My reference on how to work with ndmg in python is:

github.com

neurodata/m2g/blob/deploy/docs/tutorials/Overview.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Ndmg Tutorial: Running Inside Python"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This tutorial provides a basic overview of how to run ndmg manually within Python. <br>\n",
    "We begin by checking for dependencies,\n",
    "then we set our input parameters,\n",
    "then we smiply run the pipeline.\n",
    "\n",
    "Running the pipeline is quite simple: call `ndmg_dwi_pipeline.ndmg_dwi_worker` with the correct arguments. <br>\n",
    "\n",

This file has been truncated. show original

and the source code of ndmg itself is on:

I need to run the ndmg_dwi_pipeline with my desired atlas which is not in the ndmg atlas list.

Has anyone had the experience of working with ndmg and help me with that?

Thanks!

Steven · July 26, 2024, 9:31pm

Hi @maryam.riazi,

That software looks outdated, you might be interested in MICAPIPE(GitHub - MICA-MNI/micapipe: micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below), QSIPrep (GitHub - PennLINC/qsiprep: Preprocessing and reconstruction of diffusion MRI), or TractoFlow (GitHub - scilus/tractoflow: TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity) instead.

Best,
Steven