Lesion to Symptom Mapping (R toolbox)
Systems: Linux, Mac or Windows Linux Subsystem
Language: R (version 3.0 or above)
License: Apache License 2.0
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.
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.
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:
The history of the LESYMAP container builds is in DockerHub
Test the installation
Check these examples to make sure LESYMAP is working properly.
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.
What is lesion to symptom mapping
Registering lesions in template space
Fast lesion drawing in ITKsnap
LESYMAP function reference
Package under development, the behavior of some functions may change.