Segment thalamic nuclei

This app will segment the thalamus into its multiple components using the developer version of Freesurfer’s segmentThalamicNuclei.sh function (http://freesurfer.net/fswiki/ThalamicNuclei). This app takes a Freesurfer segmentation in as an input and generates .mgz files with the appropriate thalamic segmentation inside the Freesurfer directory as an output.

Authors

• Brad Caron (bacaron@iu.edu)

Contributors

• Soichi Hayashi (hayashis@iu.edu)

Funding

Citations

Please cite the following articles when publishing papers that used data, code or other resources created by the brainlife.io community.

1. Iglesias, J. E., Insausti, R., Lerma-Usabiaga, G., Bocchetta, M., Van Leemput, K., Greve, D. N., van der Kouwe, A., Alzheimer's Disease Neuroimaging Initiative, Fischl, B., Caballero-Gaudes, C., & Paz-Alonso, P. M. (2018). A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. NeuroImage, 183, 314–326. https://doi.org/10.1016/j.neuroimage.2018.08.012

Running the App

On Brainlife.io

You can submit this App online at https://doi.org/10.25663/brainlife.app.222 via the 'Execute' tab.

Running Locally (on your machine)

1. git clone this repo

2. Inside the cloned directory, create config.json with something like the following content with paths to your input files.

{
   "freesurfer":    "testdata/freesurfer/output"
} 

Sample Datasets

You can download sample datasets from Brainlife using Brainlife CLI.

npm install -g brainlife 
bl login 
mkdir input 
bl dataset download 

3. Launch the App by executing 'main'

./main 

Output

The main output of this App is is the Freesurfer directory containing the ThalamicNuclei*.mgz files. These can be fed into the 'Generate ROIs in dMRI Space' apps under the 'thalamic' options.

Product.json

The secondary output of this app is product.json. This file allows web interfaces, DB and API calls on the results of the processing.

Dependencies

This App requires the following libraries when run locally.

• Freesurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
• FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
• jsonlab: https://github.com/fangq/jsonlab
• singularity: https://singularity.lbl.gov/quickstart