Introduction

Singularity repository for 

Qi Yang, Colin B. Hansen, Leon Y. Cai, Francois Rheault, Ho Hin Lee, Shunxing Bao, Bramsh Qamar Chandio, Owen Williams, Susan M. Resnick, Eleftherios Garyfallidis, Adam W. Anderson, Maxime Descoteaux, Kurt G. Schilling, Bennett A. Landman, "Learning white matter subject‐specific segmentation from structural MRI." Medical physics 49.4 (2022): 2502-2513.

Due to Zenodo's default storage limit, this repository contains only 1 out of 6 Singularity images: TractSeg.

The remaining three Singularity images can be found in the following Zenodo project at: 

For usage details—including commands, expected inputs, and outputs—please refer to the primary GitHub repository at White matter learning

Compare to Test Data

For testing data, we use a scanning session from version 1.2.1 of the AOMIC ID1000 dataset (https://openneuro.org/datasets/ds003097/versions/1.2.1).

• Lukas Snoek and Maite van der Miesen and Andries van der Leij and Tinka Beemsterboer and Annemarie Eigenhuis and Steven Scholte (2021). AOMIC-ID1000. OpenNeuro. [Dataset] doi: 10.18112/openneuro.ds003097.v1.2.1
• The scanning session is from sub-0001
  • The T1w scan comes from the anat subfolder and is called sub-0001_run-1_T1w.nii.gz in the dataset
• For reproducibility, we also uploaded the AFQclipped processing results on the test data (TractSeg_Test_OUTPUTS.tar.gz) for your comparison.