Welcome to CORTPRO

🧠 CortPro (Cortical Profiler) is an open-source toolbox for generating and analysing intracortical microstructure profiles. It provides a flexible framework to profile cortical depth-dependent signals across imaging modalities and resolutions—from MRI to 3D histology.

🚀 With only two inputs—an anatomical MRI suitable for cortical surface reconstruction (e.g., T1w) and a microstructure-sensitive image (e.g., qT1, T1w/T2w, MT)—CortPro enables reproducible microstructural mapping within the cortex.

Note

Find out more in the paper, now published in Imaging Neuroscience: Intracortical microstructure profiling: A cross-modal method for indexing cortical lamination.

What CortPro does

  • Generation and characterisation of intracortical microstructure profiles

  • Co-registration of microstructural images to cortical surfaces

  • Flexible sampling precision (user-defined number of cortical depths)

  • Versatile application across modalities (MRI, histology, etc.)

  • (Optional) Bias-corrected T1w/T2w images

  • (Optional) Cortical surface reconstruction

  • (Optional) Computation of intracortical SNR

Key outputs include:

  • MP.csv → intensity changes across cortical depths (rows = depths, columns = vertices)

  • MPmoments.csv → shape characterisation of profiles based on statistical moments (u0–u4)

Tips for Getting Started

  • Review the installation instructions to set up dependencies (essentially, Freesurfer + one container).

  • Check the general usage guide for command-line examples.

  • Explore the tutorials and examples.

  • Reach out if you have questions, suggestions, or want to contribute 🤙



Core developers