This repos allows to perfom the virtual dissection to extract left (L) and right (R) Arnold tracts.
- L_Arnold_proper, R_Arnold_proper
- L_Arnold_lateral, R_Arnold_lateral
- L_Arnold_AR_like, R_Arnold_AR_like
- L_Arnold_OR_like, R_Arnold_OR_like
AR := Accoustic Radiations, OR := Optic Radiations
Figure from the paper
Maldonado IL, Descoteaux M, Rheault F, et al.
Multimodal study of multilevel pulvino-temporal connections: a new piece in the puzzle of lexical retrieval networks.
Brain. Published online January 18, 2024. doi:10.1093/brain/awae021
Download the paper: Mandonnet et al BRAIN 2024
The script is based on scilpy
Make sure your pip is up-to-date before trying to install:
pip install --upgrade pip
pip install scilpy==1.5.0
If you have any issues to install scilpy please post an issue here.
- The tractogram needs to be in trk format in **MNI space**.
- The tractogram quality will not be checked. Arnold tracks are "hard-to-track" anatomical pulvino-temporal
connections. See Mandonnet et al BRAIN 2024 for tractography details. In this work, an aggressive seeding
TractoFlow pipeline was used in conjunction with a Bundle-Specitifc Tractography (BST) approach.
- This script does not perform any registration or warping (see scilpy for documentation on this).
./dissect_arnold_tracks.sh -i INPUT -r MNI_binary_ROIs -o OUT_DIR
INPUT=/path/to/[INPUT] INPUT folder containing multiple subjects trk in MNI space
[INPUT]
├── S1
│ └── *.trk
├── S2
│ └── *.trk
└── *
MNI_ROI_PATH=/path/to/atlas_arnold/data/MNI_ROIs Path to MNI_binary_ROIs provided in the atlas_arnold_project
OUT_DIR=/path/to/[OUT_DIR] Output directory