download.file("https://raw.githubusercontent.com/kjamison/nemo/master/nemo_save_average_glassbrain.py", here::here("nemo_save_average_glassbrain.py"))
download.file("https://raw.githubusercontent.com/kjamison/nemo/master/nemo_save_average_graphbrain.py", here::here("nemo_save_average_graphbrain.py"))
download.file("https://raw.githubusercontent.com/kjamison/nemo/master/nemo_save_average_matrix_figure.py", here::here("nemo_save_average_matrix_figure.py"))1 Contents
The pipeline provides a set of handy tools listed below, which I will also go through:
Bash pipeline to process multiple subject folders to do cropping, bias correction and skull stripping before registering brain and possibly lesion mask to 1 or 2 mm MNI space (this is the primary content). The registration can be performed with fsl or ANTs.
A few other Bash-scripts to register brain and lesion mask after manual correction of brain mask (no, even using optiBET is not perfect), and to do other things.
A few R-scripts to organise files and to package lesion masks to supply to the NeMo tool in Chapter 5.
In a separate folder (
nemo/) I’ve included a few scripts to collect data from the NeMo-output and do basic visualisation based on the NeMo output data.Finally, three Python scripts from the NeMo-repository:
nemo_save_average_glassbrain.py,nemo_save_average_graphbrain.pyandnemo_save_average_matrix_figure.py. These are used for data visualisation in the included pipeline use case example in Chapter 5. The NeMo-project project, however is shared without a license. The files can be downloaded from the NeMo-repository or directly with the following lines of code:
1.1 Glossary
| term | definition |
|---|---|
| ANTs | Advanced Normalization Tools. https://github.com/ANTsX/ANTs |
| Bash | Short version: The language of the terminal console in Windows, Linux and MacOS. |
| 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 | |
| NeMo | Network Modification tool. https://github.com/kjamison/nemo |
| optiBET | A four step optimization of the fsl BET tool from the Monti lab at UCLA. https://montilab.psych.ucla.edu/fmri-wiki/optibet/ |
| pipeline | A set of tools working together as chain links being dependent on one-another. Just a fancy term for "ordered collection" |
| Python | A snake, or in this case refers to the free and open source programming language Python. https://www.python.org/ |
| R | |
| regex | |
| registration |