volBrain
volBrain is a pipeline dedicated to automatically analyze MRI brain data. It gets an anonymized MRI brain volume in NIFTI format and produces a pdf report. volBrain provides the volumes of subcortical structures, cerebellum, brainstem, brain hemispheres, brain tissues and intracranial cavity.
Labelling protocol
Intracranial cavity mask, hemisphere/cerebellum masks and subcortical labels were manually segmented by our expert on a set of T1w MRI. This training library is then used to perform automatic segmentation of your new cases. All structures were outlined according to our expert definition (our Lateral ventricles definition did not include choroid plexuses) with the exception of hippocampus which was segmented following the EADC protocol.
Report
Once the process is finished, you will be notified by e-mail so you will be able to download a package including some image files and two (CSV and PDF) reports providing all the volumetry values calculated from the segmentations. As you can see in the figure below, the PDF includes patient information, the volumes of parenchyma, brain tissues, macrostructures and subcortical structures as well as asymmetry indexes. Finally, it also includes several snapshots from the different labeling steps as a quality control.
References
José V. Manjón and Pierrick Coupe. volBrain: an online MRI brain volumetry system. Frontiers in Neuroinformatics, 10, 30, 2016. PDF