5 Using the NeMo tool

Authors

Affiliations

Christina Rubino

This section will exists as documentation on how we have worked with the NeMo tool. Coding is very much inspired and copied from other sources. I will try to write sources and inspiration.

5.1 Package and upload

First step is to get the normalised lesion masks processed by the NeMo tool to get a “dis-connectome”.

The online instance of the tool offers to freely process lesion masks in batches of 10. You can use the bundled R-script to package lesion masks into compressed zip-batches of maximum 10.

Open the nemo_packing.R file and edit the variables in the first section, then run the script, from either RStudio or the command terminal window:
```
Rscript nemo-packing.R
```
Then head over to the NeMo processing website and upload the zip-files, one at a time with your desired settings and atlas for parcellation.

5.2 Glossary

term	definition
connectome	Term used to denote the collection of connections in the brain.
NeMo	Network Modification tool. https://github.com/kjamison/nemo