nipy/mindboggle repository overview

Mindboggle’s open source brain morphometry platform takes in preprocessed T1-weighted MRI data, and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. This cross-platform Docker container was built to conveniently and reproducibly run FreeSurfer, ANTs, and Mindboggle. See https://mindboggle.info⁠ for more information.

This Docker image contains most of Mindboggle's dependencies, including preprocessing software packages FreeSurfer and ANTs, and visualization software roygbiv.

The Dockerfile performs the following setup:

1. Set up neurodebian and miniconda and install conda packages.
2. Install FreeSurfer and ANTS.
3. Install Mindboggle templates from the Open Science Framework.
4. Install Mindboggle.
5. Install roygbiv for output visualization.

UPDATES (mirrored in Mindboggle's CHANGELOG):

November 4, 2019 (v1.3.8):

• Fix issue #190 in v1.3.7, an error caused by a unicode character within docstrings in three files
• Introduce Singularity recipe in neurodocker.sh

September 24, 2019 (v1.3.7): Satrajit Ghosh added etelemetry capabilities.

June 14, 2019 (v1.3.6): Joachim Giard patched the curvature C++ code to support non-default curvature measures.

June 11, 2019 (v1.3.5):

• Conda installed a version of vtk that broke the C++ code (https://github.com/nipy/mindboggle/issues/171⁠).
  • updated neurodocker.sh to install VTK 8.2
• Nipype is breaking with "UnicodeEncodeError" when it tries to generate reports
  • added "encoding='utf-8'" in nipype files in the docker image to resolve issue #175
• Zernike moments stopped working because scipy.misc was deprecated.
  • replaced with scipy.special
• Non-default (Gaussian, min, max) curvature file names were incomplete.
  • fixed the names so that they have the same filestem as the mean curvature file
• Image links broken in docs and in the Jupyter notebook tutorial.
  • moved images to a new GitHub repository "nipy/mindboggle-assets"

September 14, 2018: neurodocker.sh updated to remove __macosx files to allow for Singularity builds.

August 26, 2018: neurodocker.sh replaces the earlier Dockerfile-creating scripts.

March 8, 2018: mindboggle123 script revised to run antsCorticalThickness.sh with "-u 0" flag, which turns off a default setting in ANTs that introduces a stochastic element in the Atropos segmentation algorithm.