| term | definition |
|---|---|
| fsleyes | Thes picture viewing tool from the fsl-package. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes |
| MNI | Montreal Neurological Institute. https://nist.mni.mcgill.ca/atlases/ |
| MRI | Magnetic Resonance Imaging |
| NeMo | Network Modification tool. https://github.com/kjamison/nemo |
| pipeline | A set of tools working together as chain links being dependent on one-another. Just a fancy term for "ordered collection" |
| registration | I this context, registration denotes to art of registrering to normal space. In this case to the MNI space. Think of it as normalising data. |
Normalisation pipeline
Preface
The book was intended as documentation on a suggested pipeline for normalising brain and lesion masks from chronic stroke T1 weighted imaging. To make it a bid more widely useful, the pipeline documented here will register T1 weighted images to either 1 or 2 mm MNI standard space and include a lesion mask in that process, if any is present.
The pipeline was comprised as part of my exchange stay at the Brain Behaviour Lab at UBC, Vancouver, Canada during August-October 2023. It is my hope that the notes and scripts may be of help to others, myself being a new learner to FSL and everything around it.
Motivation
The reason for creating this tool is to use 1mm MNI normalised (registration) lesion masks for the NeMo tool.
Most of the hard working scripts in this pipeline are based on the work by Dr. Dianne Patterson, PhD, which in turn is also based on others work. I have tried my best at modifying the original scripts as little as possible for clarity, and instead created a few new scripts to work as wrappers.
And then, the frustration. I found that documentation that is easy to understand is highly lacking in the field (or I just didn’t manage to find it). Also, the documentation on fsl-functions is difficult to always follow. As an example, this is the best overview of fslmaths -help. And please notice, that to get help for fslmathsor flirt, type the command followed by -help. If you want the same from fnirt, then type -h or --help as is the case for most other command-line programs.
I have tried to lower the bar to get started working on MRI registration. Feedback is very welcome on GitHub.
License
This documentation is shared under the AGPL-v3 license if nothing else is explicitly stated. The source can be found here and contributions are very welcome in the discussion section on Github, through issues or pull requests.