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ASHS-PMC Atlas Requirements

You are viewing the documentation for classic ASHS

For new projects we recommend HyperASHS, which produces isotropic-resolution segmentations of the same structures and is available in the cloud through ITK-SNAP as well as locally.

MRI Requirements: ASHS-PMC Atlas

Overview

This page describes the MRI data requirements for using ASHS with the ASHS-PMC atlas. This atlas is used to automatically segment hippocampal subfields and extrahippocampal medial temporal lobe subregions ERC, BA35, BA36 and PHC.

This requires high-resolution T2-weighted MRI in which the layers of the hippocampus can be visually separated. A whole-brain T1-weighted MRI scan is also required to run ASHS.

MRI requirements

To use the ASHS-PMC atlas, your data must meet these specifications:

  • T2-weighted MRI:
    • voxel size 0.4 mm × 0.4 mm × 2.0 mm or similar
    • oblique coronal slices perpendicular to the main axis of the hippocampus
    • covers the length of the hippocampus
  • T1-weighted MRI:
    • voxel size 1.0 mm × 1.0 mm × 1.0 mm or similar
    • whole brain coverage, not skull stripped
  • T1 and T2-weighted MRI are roughly aligned in space

In addition, your subjects should be older adults (55+).

MRI scans for the ASHS-PMC atlas

MRI scans for the ASHS-PMC atlas.

Checking MRI requirements using ITK-SNAP

We recommend using ITK-SNAP 3.6.2 or later to examine the datasets as described below.

  1. Load the T2-weighted MRI as the "Main Image" in ITK-SNAP
    • From the menu select File->Open Main Image...
  2. Load the T1-weighted MRI as the "Additional Image"
    • File->Add Another Image...
  3. Make sure that the T1 and T2-weighted images are properly aligned
    • The images in the figure below are well aligned
    • If the images are not properly aligned, use the registration tool to perform rigid registration (align the T1-weighted MRI to the T2)
    • Save the resulting transformation in Convert3D format
  4. Make sure that the T2 image is correctly encoded
    • Examine image properties using Tools->Image Information...
    • Make sure that the x and y dimensions of the T2-weighted image are larger than the z dimension (e.g., 384 × 384 × 25 as in the figure below)
    • If this is not the case, use the convert3d -swapdim command to reorient the images

T2 and T1-weighted MRI side by side in ITK-SNAP

T2-weighted MRI and T1-weighted MRI side by side in ITK-SNAP. In this example the two modalities are well aligned.

ITK-SNAP image information dialog

The ITK-SNAP Image Information dialog, showing the dimensions of the T2-weighted image.

See the equivalent page for HyperASHS.