Code & Data

Here you will find the codes from different projects we've been working on.


On our shared Github account you can find the codes for different projects.

Yearly Summerschool

Here you'll find the materials for the yearly summerschool of the IMCN.



Nighres is a Python package for processing of high-resolution neuroimaging data. It developed out of CBS High-Res Brain Processing Tools and aims to make those tools easier to install, use and extend. Nighres now includes new functions from the IMCN imaging toolkit.


MIST (Multimodal Image Segmentation Tool) is a flexible tool for subcortical segmentation. It differs from FIRST in that it can use complementary information in different MRI modalities and is less reliant on manual segmentations.

CBS High-Res Brain Processing Tools

With 7 Tesla MRI, neuroscientists can investigate the structure of the human brain with enhanced resolution, currently up to 350µm isotropic in vivo. Quantitative MR contrasts and increased level of detail within tissues reveal many fine anatomical structures, but require efficient computational methods that handle various contrasts and scale well with data complexity.

The CBS High-Res Brain Processing Tools provide a fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400µm, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness.

The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

Atlasing of the basal ganglia

This atlas takes advantage of ultra-high resolution 7T MRI to provide unprecedented levels of detail on structures of the basal ganglia in-vivo. The ATAG atlas includes probability maps of the striatum, GPe, GPi, red nucleus, substantia nigra, subthalamic Nucleus(STh) and the PAG. The atlas has been created on 30 young (M:24.2), 14 middle-aged (M: 52.5), and 10 elderly (M: 69.6) participants.

Separately a STh atlas was created based on 13 young (M:24.38), 8 middle-aged (M:50.67), and 9 elderly participants (M:72.33).


This data set consists of 136 subjects of which the following neuroimage data is acquired:
  • MRI (3T):
    - T1 anatomical scan
    - DWI scan (two different types of scan paramaters)
    - Resting state fMRI
  • EEG (64 channels):
    - Resting state EEG

3T DWI test-retest reliability dataset

This data-set contains all 3T MRI data used in Boekel et al., (2017), in which we aimed to investigate the invivo test-retest reliability of several DTI derived measures.

34 healthy young subjects were scanned twice on the same day with a 3T MRI scanner in which the following data was acquired:
- T1 weighted whole brain scan (1mm isotropic).
- B0 weighted whole brain scan (2mm isotropic)
- Diffusion weighted whole brain scan (2mm isotropic, 32 directions, b-value=1000, 4 repetitions)

A subset of 15 subjects were also scanned a third session on the same day, as well as in a two-week follow-up session with the same MRI protocol.

Paper: The functional microscopic neuroanatomy
of the human subthalamic nucleus



data (Only processed data available due to size):

Paper: Caution in decision-making
under time pressure is mediated by timing ability


code & data: