All our code is available at

Below you’ll find descriptions of some of our tools, as well as additional software resources that were developed by lab members over the years.

Resting-state processing pipelines

Pipelines for processing resting-state fMRI data using Nipype.

Connectivity visualization

We have developed a few tools for visualization of brain data.

Edge-bundling & connectivity glyphs

Joachim Böttger developed several software tools to facilitate the interactive visualization of high-dimensional connectivity data in three-dimensions:

Sebastian Eichelbaum developed the Directionality Indicator, which enables the visualization of directional information along the cortical surface.
Click the image to the right to see an example.

Measuring distance along the cortical surface

The surfdist Python package can be used to calculate the exact geodesic distance from nodes or regions-of-interest along the cortical surface.

  •  PDF |  Link |  Code | Margulies DS, Falkiewicz M, Huntenburg JM (2016) A cortical surface-based geodesic distance package for Python GigaScience 5(suppl_1): s13742–016-0147–0-q

Mind-wandering questionnaire

The New York Cognition Questionnaire (NYC-Q) is a questionnaire developed by Jonny Smallwood to characterize the content and form of mind-wandering.

  •  PDF |  Link | Gorgolewski KJ, Lurie D, Urchs S, Kipping JA, Craddock RC, Milham MP, Margulies DS, Smallwood J (2014) A correspondence between individual differences in the brain’s intrinsic functional architecture and the content and form of self-generated thoughts PLoS One 9(5): e97176


Nighres is a Python package for processing of high-resolution neuroimaging data developed by Julia Huntenburg, Pierre-Louis Bazin, and Chris Steele.

  •  PDF |  Link | Huntenburg JM, Steele CJ, Bazin P-L (2018) Nighres: processing tools for high-resolution neuroimaging GigaScience 7(7): giy082