Segmentation of thalamic nuclei
This functionality will be soon available in the development version of FreeSurfer.
PLEASE NOTE THAT:
1. THERE IS A BUG IN quantifyThalamicNuclei.sh IN FREESURFER 7.0, 7.1 AND 7.1.1; PLEASE REPLACE $FREESURFER_HOME/bin/quantifyThalamicNuclei.sh BY THIS FILE: quantifyThalamicNuclei.sh (no need to rerun your subjects!)
2. PLEASE NOTE THAT THIS MODULE WAS MODIFIED WITH THE FREESURFER 7 RELEASE (COMPARED WITH OLDER DEV VERSIONS) FOR IMPROVED SEGMENTATION OF THE MOST LATERAL NUCLEI, INCLUDING THE LGN.
Author: Juan Eugenio Iglesias
E-mail: e.iglesias [at] ucl.ac.uk
Rather than directly contacting the author, please post your questions on this module to the FreeSurfer mailing list at freesurfer [at] nmr.mgh.harvard.edu
If you use these tools in your analysis, please cite:
A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. Iglesias, J.E., Insausti, R., Lerma-Usabiaga, G., Bocchetta, M., Van Leemput, K., Greve, D., van der Kouwe, A., Caballero-Gaudes, C., Paz-Alonso, P. Neuroimage (accepted).
This tool implements SynthSR, a convolutional neural network that turns a clinical MRI scan (or even CT scan!) of any orientation, resolution and contrast into 1 mm isotropic MP-RAGE. You can then run your favorite neuroimaging software on these synthetic images for segmentation / registration / any other analysis.