AutoReorient

Back to hMRI home page

Auto-Reorient

The reorientation of the images towards the MNI space is a standard step in neuroimage processing. It increases the consistency in individual head positions prior to normalisation, and often is a prerequisite for successful segmentation. The Unified Segmentation (Ashburner and Friston 2005) process is indeed rather sensitive to the initial orientation of the image. Auto-reorient provides you with a simple tool for reorientation of all images prior to any further processing including multiparameter map calculation.

Reorientation is based on rigid-body coregistration of a reference image to the MNI space (i.e. mainly set the AC location and correct for head rotation) and application of the coregistration matrix to all images acquired during the same session (specified as "other images"). The code makes use of spm affreg and templates available in SPM12.

The user must provide one reference image and a template for coregistration, and a series of other images that need to keep in alignment with the reference image (typically, all the images acquired during a given imaging session). The reference image is the one that will be coregistered to the template. It must have as good a signal-to-noise ratio (SNR) and a white matter/grey matter contrast-to-noise ratio (CNR) as possible to ensure a robust and reliable coregistration. The template can be chosen e.g. amongst SPM canonical templates (from the SPM/canonical directory) or any other user-defined template (e.g. atypical population-driven template), provided it is already oriented according to MNI. It is mandatory that the contrast of the reference image is close to the template image.

The following list is provided as guidelines:

SOURCE IMAGE > RECOMMENDED TEMPLATE    
First T1w echo > SPM/canonical/avg152T1.nii    
First PDw echo > SPM/canonical/avg152PD.nii    
First MTw echo > SPM/canonical/avg152PD.nii     

If no specific output directory is selected, then the original orientation of the images will be overwritten. If an output directory is selected then the images are copied to the output directory in a AutoReorient folder before being reoriented, therefore leaving the original data untouched. Furthermore, AutoReorient folder contains the file AutoReorient_output.json which can be read into a Matlab struct with the following fields:

- files  : the list (cell array of strings) of reoriented images listed in the same order as the input (ref, then other).
- M      : the rigid-body transformation matrix
- invM   : the rigid-body transformation matrix inverted

that is to say the transformation applied to the images (and its inverse) can be recovered if needed.

The reoriented images can be collected as dependencies for further processing, either all at once (Dependencies > Grouped) or as individual output images (Dependencies > Individual) which is more convenient to connect the Auto-reorient module to the next Create hMRI maps module.