The localization of traumatic brain injury (TBI) lesions directly correlates with motor disabilities and cognitive impairment. By unfolding magnetic resonance (MR) images of a lesioned rat cortex on a two-dimensional (2D) cytoarchitecture map of the cortex, it is possible to predict the severity of the resulting cognitive and behavioral impairment.
CortexMap is a web application to estimate the location of the lesion on mouse cerebral cortex caused by TBI induced by lateral fluid-percussion injury. The application unfolds user-determined TBI lesion measurements, e.g., from histologic sections to a reference template, and estimates the total lesion area, including the percentage of cortex damaged in different cytoarchitectural cortical regions.
For off-line use, CortexMap is also available as a command-line application.
The web application is available at www.cortexmap.org
Windows:
Download Node.js installer. Execute the installation wizard.
Linux/macOS:
Follow the official instructions
After Node.js has been installed, type:
npm install cortexmap-cli -g
| Parameter | Description |
|---|---|
| -m, --measurements | Path to the measurement file, comma separated list of measurement file paths, or path to a folder containing measurements. |
| -o, --output-path | Output folder for mappings and area measurements. Optional. |
| -t, --timepoints | Comma separated list of measurement timepoints as integeres Optional. |
| -b, --border-color | Lesion border color as RGBA quadruplet, e.g. 0,0,255,1. Optional. |
| -f, --fill-color | Lesion fill color as RGBA quadruplet, e.g. 0,0,255,1. Optional. |
| -w, --border-width | Lesion border width as an integer value between 1 and 20. Optional. |
| -s, --border-style | Lesion border style. Accepted values are “solid”, “dashed” or “dotted”. Optional. |
| -d, --dpi | Output image dpi. Optional. |
| -c, --cortexmap | Path to the cortex map template used in mapping. Optional. |
Mapping a single measurement:
cortexmap-cli -m ./measurements/001_day_1.csv -o ./mapping-results/
Mapping a time series of measurements:
cortexmap-cli -m ./measurements/001_day_1.csv,./measurements/001_day_7.csv,./measurements/001_day_14.csv \
-o ./mapping-results/
Mapping a time series of measurements, with blue fill color:
cortexmap-cli -m ./measurements/001_day_1.csv,./measurements/001_day_7.csv,./measurements/001_day_14.csv \
-f 255,0,0,1 \
-o ./mapping-results/