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 x 0.4 mm x 2.0 mm or similar
  • oblique coronal slices perpendicular to the main hippocampus axis
  • covers the length of the hippocampus
• T1-weighted MRI:
  • voxel size 1.0 mm x 1.0 mm x 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+)

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
   • Images in the figure on the right 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 by 384 by 25 like on the right)
     • If this is not the case, you will need to use the convert3d -swapdim command to reorient the images