LESYMAP

Lesion to Symptom Mapping (R toolbox)

Package details

Open Source Love
Version: 0.0.0.9221
Systems: Linux, Mac or Windows Linux Subsystem
Language: R (version 3.0 or above)
License: Apache License 2.0

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What does it do

Takes lesion maps and cognitive performance scores from patients with stroke, and maps the brain areas responsible for the cognitive deficit.

Install

The quickest way to install is:

if (! 'devtools' %in% installed.packages()) install.packages('devtools')
devtools::install_github('dorianps/LESYMAP')

This will install all the dependencies, including ANTsR (may take one hour on some computers). Here is the video of the installation process. If it doesn’t work, check out the more detailed installation instructions.

Docker container

If you use Docker, we have built a container with LESYMAP pre-installed (along with RStudio). We have also built scripts to start and stop the LESYMAP container easily (for Windows, Linux, Mac). See the instructions here and you should be good to go in minutes:
https://github.com/dorianps/docker
The history of the LESYMAP container builds is in DockerHub

Test the installation

Check these examples to make sure LESYMAP is working properly.

Use

library(LESYMAP)

# All functions have appropriate documentation. Start by typing
?lesymap

# run an example analyses using data provided with lesymap
example(lesymap)

22:14:19 Running LESYMAP 0.0.0.9210 
22:14:19 Checking a few things...
22:14:19 Loading behavioral data...131 scores found.
22:14:20 Filenames as input, checking lesion values on 1st image...
22:14:22 Searching voxels lesioned >= 10% subjects...326828 found
22:15:20 Computing unique patches...
22:15:58 Found 195102 patches in 326828 voxels - 1.7 times more voxels
22:15:58 Using existing lesion matrix... 131x195102
22:15:58 Running analysis: BMfast ...
22:16:02 Correcting p-values: fdr ...
22:16:02 Preparing images...
22:16:03 Logging call details...
22:16:03 Done! 1.7 mins 
Hit <Return> to see next plot:

Check out how this example looks on the screen.

Documentation

What is lesion to symptom mapping
Installing LESYMAP
Registering lesions in template space
Provided data
Understanding permutations
Fast lesion drawing in ITKsnap
All Videos
SCCAN questions
Known limitations
LESYMAP function reference

Note

Package under development, the behavior of some functions may change.