Freesurfer
- Volumetric analysis of our MRI images are completed using Freesurfer, a software package that allows users to process, visualize, and measure brain imaging data.
- RAs in the MILab use FS to auto-segment the T1-wieghted MRIs to obtain brain structure volumes, cortical thickness, and other measurements. We do this for patients with diseases such as ALD, MPS, CMV (infant Freesurfer), as well as healthy controls.
- "Woofsurfer" is a processing pipeline we created specifically for the auto-segmentation of canine brains.
- A paper from our lab that utilized FS: Attention and corpus callosum volumes in individuals with mucopolysaccharidosis type i
ITK-SNAP
- ITK-SNAP is a software application used for auto- and manual segmentation of brain structures in MRI images.
- We used ITK-SNAP to obtain lesion masks and volumes of brain structures which Freesurfer is unable to accurately identify when processing MR images.
FSL
Retina Imaging Toolbox
- Developed for automated dynamic or static retina image analysis.
- The RIT can be found on Github
Brains2
- Brains2 an image processing package with manual and automated features for visualizing and measuring different brain regions and structures.
- We utilized this package paired with a drawing tablet for tracing specific brain structures such as brain stem, cingulate cortex, cerebellum, hippocampi - especially in canine and murine animal models for MPS MRI studies.
- A paper from our lab that utilized Brains2: In-vivo cortical thickness estimation from high-resolution T1w MRI scans in healthy and mucopolysaccharidosis affected dogs
Programming languages
- For the processing and analysis of MR images and data, this lab heavily utilizes programming languages Python and Matlab.