Tools overview

Mint Labs provides advanced neuroimaging analytics tools including widely known open source & licensed tools as well as our proprietary algorithms.

Open Source

ANTs

ANTs (Advanced Normalization Tools) is used to compute high-dimensional mappings to capture the statistics of brain structure and function. It offers:
  • Image registration
  • Image segmentation
  • Morphological and mathematical operations
  • Structural MRI
  • Bias field correction
  • Thickness: DiReCT

MRtrix

"MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses." It is used on the platform for:
  • Diffusion processing
  • White matter tractography
  • Constrained spherical deconvolution

Mindboggle

Mindboggle is an open-source pipeline for brain morphometry . It takes in T1-weighted MRI data, makes use of the Freesurfer and ANTs morphometry tools and generates volume images and tabular information for further analysis.
  • tissue segmentation
  • cortical and subcortical parcellation
  • volumetry analysis and cortical thickness

LST

LST (Lesion Segmentation Tool) is an open source toolbox developed by a group of institutions, including the Technical University Munich and Ludwig Maxmilians University and Friedrich Schiller University. This tool is able to segment T2 hyper-intense lesions in FLAIR images. It was originally developed to automatically segment multiple sclerosis (MS) lesions,  but has also proven to be useful for other diseases, such as Alzheimer's disease.

FreeSurfer

FreeSurfer is "an open source software suite for processing and analyzing (human) brain MRI images". It is used on the platform for:
  • Cortical segmentation
  • Cortical reconstruction
 

Licensed tools

FSL

"FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data." The tools used on the platform are:
  • FLIRT
  • BET
  • FAST
  • SIENAX & SIENA
  • EDDY
  • FUGUE
  • MCFLIRT

Proprietary tools

Morphology

  • From high-resolution, 3D, T1-weighted, non-contrast-enhanced MRI scan, Morphology tool identifies and segments brain tissue (grey matter, white matter) and multiple brain structures (atlas based).
  • With no user intervention, it provides the cortical thickness volume along with a report (.csv) of the average and standard deviation of the thickness per different structure.
volumetry

Volumetry

  • From high-resolution, 3D, T1-weighted, non-contrast-enhanced MRI scan, Volumetry tool identifies and segments brain tissue (grey matter, white matter, deep brain structures) and multiple brain structures (atlas based).
  • With no user intervention, it provides an automatically labeled dataset, along with report (.csv) of the absolute volumes of the different tissues and different structures.
FA maps

FA maps

  • From diffusion MRI files (DWI), the tool estimates tensor field (DTI).
  • With no user intervention, it provides a DTI map (tensors), a fractional anisotropy map (FA map), and a FA map weighted by principal direction.
tractography

Tractography

  • From diffusion MRI files (DWI), either DTI or HARDI sequences, it automatically estimates tensor or ODF fields.
  • With no user intervention, the tool provides a 3D tractography map.
     
connectome

Advanced Structural Connectome

  • Combining 3D, T1-weighted, and diffusion MRI files (DWI), it computes an automated cortical parcellation with 3D tractography in order to get a network description of the wiring of the brain.
  • With no user intervention, the tool provides a connectome (matrix) with several connectivity measures (number fibres, average FA, average fiber length, ...)

 Contact us for your own processing ideas.

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