DeepThalamus
DeepThalamus is a pipeline to automatically perform the whole thalamus segmentation process (left and right) and their 13 nuclei from a commonly available T1w MRI brain volume. It provides nuclei volumes and asymetry indexes. It gets an anonymized MRI brain volume in NIFTI format and produces a pdf report with the volumes of different structures.
Labelling protocol
We have used an extended protocol based on the Morel et al., 1997 atlas by adding an intermediate space label to obtain a compact thalamus segmentation.
Report
Once the process is completed, you will be notified by email and you will be able to download a package that includes some image files and two reports (CSV and PDF) with all the volumes estimated from the segmentations. As you can see in the figure below, the PDF includes the patient information, the volume of the whole thalamus and the nuclei of each hemisphere, as well as the asymmetry indices. Finally, it also includes snapshots of the result of the segmentations as a quality control.
References
Marina Ruiz-Perez, Sergio Morell-Ortega, Marien Gadea, Roberto Vivo-Hernando, Gregorio Rubio, Fernando Aparici, Mariam de la Iglesia-Vaya, Thomas Tourdias, Pierrick Coupé, José V. Manjón. DeepThalamus: A novel deep learning method for automatic segmentation of brain thalamic nuclei from multimodal ultra-high resolution MRI. arXiv Preprint arXiv:2401.07751 PDF