MANTiS neonate tissue segmentation
Preliminaries
MANTiS is designed to process brain extracted T2 weighted images that are in the same orientation as the template. Orientation in this case doesn’t imply that the new image and template should be registered - simply that the data ordering is the same. We use the fslswapdim tool to control data ordering.
All scans processed in a single batch must be in the same folder!
Brain extraction for the MANTiS validation studies were carried out using FSL BET. There is also a preliminary tool in MANTiS to perform brain extraction.
Finally, as with typical SPM segmentation, the origins of the image need to be roughly equivalent to the template. There is a tool in MANTiS to set the origin based on the centre of mass. This tool should also be applied to brain extracted images.
Getting started
MANTiS is an SPM toolbox and can be accessed as follows.
- Select mantis from the toolbox dropdown menu:
- Select the complete pipeline option to load the pipeline in the batch editor.
- Select scalped T2 structural scans from the batch editor file selection:
- Click the green run button, and wait. The results for each phase will be stored in two folders, named Phase1 and Phase2.
- The components from which the pipeline is constructed are available from the batch editor tools menu.
Brain Extraction
A preliminary tool: is available for brain extraction in T2 weighted images.
Setting image origin
SPM segmentation utilises the image origin from the nifti files if it is set on the assumption that is positioned similarly to the origin of standard space. Strange results can occur if this isn’t the case. A tool for setting image origin: based on the centre of mass of the brain is available. It should be applied to brain extracted images.
Preprocessing pipeline
A pipeline performing brain extraction and origin setting can be constructed in the batch editor as per the image below:
Make sure that the input volumes for the “Origin to COM” tool are set using the Dependency button and select Simple watershed scalping: scalped structurals from the options.
Check the output images for successful scalping, then feed into MANTiS tissue classification.
Changing templates
The template image used by mantis is specified in a defaults file: mantis/cg_mantis_defaults.m A custom template can be used by changing the mantis.opts.tpm and mantis.opts.tpm2 variables in this file to reference your own template. The components of the custom template must match those in the original (at least for gray, white and csf tissue classes), and changes will affect all toolbox users. Use multiple copies of the toolbox to simultaneously test different templates.