| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
|
<<BR>> <<BR>> '''''PLEASE NOTE THAT:''''' <<BR>> '''''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: [[attachment:quantifyThalamicNuclei.sh]] (no need to rerun your subjects!)''''' <<BR>> '''''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.''''' |
|
| Line 24: | Line 17: |
| If you use these tools in your analysis, please cite: | If you use this tool in your analysis, please cite: |
| Line 26: | Line 19: |
| * [[https://arxiv.org/abs/1806.08634|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). |
* [[https://www.sciencedirect.com/science/article/pii/S1053811921004833|Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast]]. JE Iglesias, B Billot, Y Balbastre, A Tabari, J Conklin, RG Gonzalez, DC Alexander, P Golland, BL Edlow, B Fischl, for the ADNI. Neuroimage, 2021 (in press). <<BR>> Since the robustness against MR contrast / orientation /resolution with a single model was not presented in the original SynthSR paper, we would also greatly appreciate it if you could please also cite: * [[https://arxiv.org/pdf/2107.09559.pdf|SynthSeg: Domain Randomisation for Segmentation of Brain MRI Scans of any Contrast and Resolution]]. B Billot, DN Greve, O Puonti, A Thielscher, K Van Leemput, B Fischl, AV Dalca, JE Iglesias. Under revision. |
Segmentation of thalamic nuclei
This functionality will be soon available in the development version of FreeSurfer.
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 this tool in your analysis, please cite:
Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. JE Iglesias, B Billot, Y Balbastre, A Tabari, J Conklin, RG Gonzalez, DC Alexander, P Golland, BL Edlow, B Fischl, for the ADNI. Neuroimage, 2021 (in press).
Since the robustness against MR contrast / orientation /resolution with a single model was not presented in the original SynthSR paper, we would also greatly appreciate it if you could please also cite:
SynthSeg: Domain Randomisation for Segmentation of Brain MRI Scans of any Contrast and Resolution. B Billot, DN Greve, O Puonti, A Thielscher, K Van Leemput, B Fischl, AV Dalca, JE Iglesias. Under revision.
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.