Tractfinder atlases and training streamlines
Description
Atlases and source data for the tractfinder tract segmentation method. "atlases" is all you need to run tractfinder on your own data. The source streamlines are provided in "data" for completeness only.
Install tractfinder here: https://github.com/fionaEyoung/tractfinder
Files
atlases
Contains the left and right tractfinder atlases for the arcuate fasciculus (AF), corticospinal tracts (CST), inferior fronto-occipital fasciculus (IFOF) and optic radiation (OR). It also contains the template T1w weighted file MNI152.nii.gz which is provided for convenience as a template space anatomical image alongside the atlases. It is a copy of mni_icbm152_t1_tal_nlin_sym_09a.nii from the MNI152 ICBM 2009a Nonlinear Symmetric template.
data
Contains the individual streamline bundles (16 adult volunteer subjects) from which the atlases are derived, in subject and MNI space. Source dataset (raw diffusion and T1w MRI data) available here: OSF | EEG, fMRI and NODDI dataset.
Additionally, transform files are provided for registering to and from MNI space (see below).
Author: Fiona Young, fiona.young.15@ucl.ac.uk
Notes
Important information about transforms
Each subject directory in data.zip contains the files
- MNI152_2_scanner.nii.gz
- MNI152_2_scanner.txt
- scanner_2_MNI152.nii.gz
- scanner_2_MNI152.txt
Each .txt file contains the corresponding transform in reverse convention, i.e. in a format suitable for transforming images in the expected direction:
mrtransform -linear scanner_2_MNI152.txt T1w.nii.gz T1w_in_MNI152_space.nii.gz
Each .nii.gz file contains the corresponding transform in forward convention, i.e. in a format suitable for transform track files:
tcktransform streams.tck scanner_2_MNI152.nii.gz streams_in_MNI152_space.tck
All are affine transforms derived from FSL's flirt tool.
Files
atlases.zip
Additional details
Related works
- Is derived from
- Dataset: https://osf.io/94c5t/ (URL)
- Is described by
- Journal article: 10.1002/hbm.26578 (DOI)
- Is part of
- Software: https://github.com/fionaEyoung/tractfinder (URL)
Funding
- UK Research and Innovation
- EPSRC Centre for Doctoral Training in Intelligent, Integrated Imaging In Healthcare (i4health) EP/S021930/1