Overview

This repository contains example scripts (templates) and documentation for psuedo-continuous ASL (pCASL) MRI data registration into the MNI-152 template using the Advanced Normalization Tools (ANTs) software package for normalizing pseudo-continuous arterial spin labelling (pCASL) and FSL.

ANTs Registration on ASL Data 🧠

What is MNI-152?🤔

In preparation for group analysis to identify trends and relationships between various brain properties across individuals, data must be aligned in a standard space to accurately compare results. Here, we focus on the MNI-152 template, a widely used standard in neuroimaging research.

The MNI152 brain template was constructed in 2001 by aligning the 3D brain MRI images of 152 young adults (86 males and 66 females) with a reference brain image. It has since become the standard template used in research as it covers the entire brain and has higher resolution (1, 2)

Why is Registration Important?🧐

MRI images from different participants are not naturally aligned > Not everyone has the same head shape or had the same head placement/orientation when the MRI scan was taken. Therefore, registration aligns all scans to the same template. This allows for:

✅ Better group analysis
✅ Accurate spatial comparisons
✅ Consistant anatomical references

Pipeline Overview: 4-Step Registration Process👩‍💻

1. Align pCASL to T1-weighted low-resolution image (T1LR)

• Goal: Aligning a pCASL image to an individual's anatomy.

2. Align T1LR to T1-weighted high-resolution image (T1HR)

• Goal: Improving anatomical accuracy and precision.

3. Align T1HR to MNI-152 Template

• Goal: Registering the structural image to MNI space.

4. Transform pCASL to MNI-152 Template (Apply Transforms)

• Goal: Applying all previous transforms successively to bring the original pCASL image into MNI space.

What's Needed?💡

• Terminal* (BASH [Unix Shell])

• FSL* (fslview or fsleyes) (install here: https://fsl.fmrib.ox.ac.uk/fsl/oldwiki/)

  module load FSL/5.0.9

  fslview

• MATLAB*

  module load matlab/R2020a

  matlab

*Note: For students in Dr. Gauthier's lab, ask Dr. Gauthier for more details, including access.

References:

1. Mandal PK, Mahajan R, Dinov ID. Structural brain atlases: design, rationale, and applications in normal and pathological cohorts. J Alzheimers Dis. DOI: 10.3233/JAD-2012-120412. URL: https://pmc.ncbi.nlm.nih.gov/articles/PMC4324755/. Accessed: April 6, 2025.
2. Giff A, Noren G, Magnotti J, Lopes AC, Batistuzzo MC, Hoexter M, Greenberg B, Marsland R, Miguel EC, Rasmussen S, McLaughlin N. Spatial normalization discrepancies between native and MNI152 brain template scans in gamma ventral capsulotomy patients. Psychiatry Res Neuroimaging. 2023 Mar;329:111595. doi: 10.1016/j.pscychresns.2023.111595. URL: https://pubmed.ncbi.nlm.nih.gov/36680842/. Accessed: April 6, 2025

Contributors 📝

Sanami, Safa. PhD in Physics, Quantitative Physiological Imaging Lab

Gresseau, Hendrale. BSc in Honours Physics, Concentration: Biophysics.