Implementation of soma and neurite density imaging (SANDI) in the accelerated microstructure imaging via convex optimization (AMICO) framework

[palombom]

Title:
Implementation of soma and neurite density imaging (SANDI) in the accelerated microstructure imaging via convex optimization (AMICO) framework

Project lead:
Marco Palombo (email: [email protected]; Twitter: @MarcoPalombo3)

Project collaborators:
Simona Schiavi (email: [email protected]; Twitter: @simonaschiavi24)
Alessandro Daducci (email: [email protected]; Twitter: @ADaducci)

Registered Brainhack Global 2020 Event:
Brainhack Atlantis The Atlantic Ocean - Micro2Macro

Project Description:

AIM

The aim of the project is to implement an algorithm for fast and robust fitting of complex microstructure imaging methods, such as the soma and neurite density imaging (SANDI), using the accelerated microstructure imaging via convex optimization (AMICO) framework.

What is SANDI?

SANDI (https://doi.org/10.1016/j.neuroimage.2020.116835) is a novel imaging technique based on diffusion MRI and biophysical modelling, designed to provide maps of MR indices of apparent soma density and size, as well as apparent neurite density. As such, SANDI is of interest for studies involving the characterization of brain cytoarchitectonics in a wide range of conditions: e.g., brain development, aging, plasticity, neuroinflammation, neurodegeneration, and more.

What is AMICO?

The AMICO framework (https://doi.org/10.1016/j.neuroimage.2014.10.026) offers the possibility to re-formulates virtually any microstructure imaging model as convenient linear systems which, then, can be efficiently solved using very fast algorithms. To date, it has been successfully employed with other models, such as NODDI and ActiveAx. We will implement an AMICO version of SANDI building upon the code publicly available at https://github.com/daducci/AMICO

Why SANDI-AMICO

The fitting of the SANDI model originally proposed is based on machine learning regression, which provides ultra-fast model parameters estimation but requires the careful design of both the training strategy and the machine learning model.
The AMICO framework can overcome these issues and provide the scientific community with a more agnostic algorithm for the fast and robust estimation of SANDI indices.

Data to use:
We will use unpublished data collected at high field and high diffusion gradient strength on the mouse brain. Since it is unpublished, the data will be made available privately by the project leader.

Link to project repository/sources:
https://github.com/daducci/AMICO
Palombo, Marco, et al. "SANDI: a compartment-based model for non-invasive apparent soma and neurite imaging by diffusion MRI." NeuroImage (2020): 116835. (https://doi.org/10.1016/j.neuroimage.2020.116835)
Daducci, Alessandro, et al. "Accelerated microstructure imaging via convex optimization (AMICO) from diffusion MRI data." NeuroImage 105 (2015): 32-44. (https://doi.org/10.1016/j.neuroimage.2014.10.026)

Goals for Brainhack Global 2020:
Deliverable 1: stable version of SANDI-AMICO;
Deliverable 2: tested version of SANDI-AMICO on one suitable dataset;

Good first issues:

1. Implementing data and protocol loader: read NIFTI file; read b values and directions; check data consistency; separate data in shells and average across directions;
2. Implementing database generator: define functions to generate response functions to be used in the AMICO linear system according to the SANDI model and the Gaussian Phase Distribution approximation;
3. Implementing the optimizer: define the objective function, setup the optimizer, perform the voxelwise fitting;
4. Implementing the result writer: save the SANDI maps in NIFTI format, keeping the correct header file;
5. Test performances: generate known ground-truth conditions using analytical simulations and different noise characteristics (e.g. Gaussian, Gaussian + floor; Rician);
6. Write up an initial tutorial on the wiki page of the AMICO repository.

Skills:
Python programming;
Familiar with DWI data processing (e.g. NIFTI/DICOM format, diffusion-weighted MRI protocols etc.);
Basic understanding on inverse linear problems (least square method, common regularization techniques, etc.);

Tools/Software/Methods to Use:
Python 3, AMICO (pip install dmri-amico), Camino, visual studio code or spider or jupyter.

Communication channels:
https://mattermost.brainhack.org/brainhack/channels/micro2macro-sandi_in_amico

https://zoom.us/ (link will be posted in mattermost channel)

Project labels
#dMRI, #modelling, #AMICO, #SANDI, #Microstructure, #InVivoMicroscopy, #Neuro

• Type of project:
  #coding_methods #pipeline_development

• Project development status:
  #1_basic structure

• Topic of the projet:
  #diffusion #MR_methodologies

• Tools used in the project:
  #DIPY, #FSL, #Jupyter, #AMICO #Camino

• Tools skill level required to enter the project (more than one possible):
  #familiar

• Programming language used in the project:
  #Python

• Modalities involved in the project (if any):
  #DWI, #MRI

• Git skills reuired to enter the project (more than one possible):
  #0_no_git_skills

Project Submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under ‘Additional project info’

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Project Submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under ‘Additional project info’

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[palombom]

Hi @Brainhack-Global/project-monitors: my project is ready!

[complexbrains]

Dear @palombom Welcome to the Brainhack Micro2Macro event! Thank you very much for proposing such an amazing project 🎉

Your issue looks almost ready! May I just ask from you to add an image to the issue please so we can create a project card for you as the others here and use it for the Twitter advertisement if you would like please? Once you add the image, I will make the project published and it will be ready for the view!

We look forward to hearing from you. Again welcome to the Brainhack family! 🤗