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Deep-MI / FastSurfer

PyTorch implementation of FastSurferCNN
Apache License 2.0
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Brain Stem Substructures Module #270

Open fmcalcagno opened 1 year ago

fmcalcagno commented 1 year ago

Feature Description

We would like to train and create a new sub-module to obtain from a T1 weighted image all 4 substructures of the Brain Stem (Pons, MidBrain, Medule, SCP) ...

Motivation

The volume of the Pons can be very important to understand the state of certain degenerative diseases. We are using this module https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures from FreeSurfer to calculate the volumes of each region. We believe that FastSurfer could include a module with this substructures and deliver results Faster.

We propose to generate a Dataset including this regions using the same Open Source Datasets that where used to train FastSurfer, and generate a dataset using the FreeSurfer Module. The next step would be to create a new Deep Learning model to detect all these 4 different substructures using FastSurferCNN and deliver the module to the community.

We're open to discusion and to new ideas.

m-reuter commented 1 year ago

Hi @fmcalcagno , we already prepare a dataset with manually segmented/cleaned brainstem labels and plan to add it later to the upcoming cerebellum sub-segmentation module.

fmcalcagno commented 1 year ago

Hi @m-reuter , thank you for you quick response. Is the new upcoming cerebellum sub-segmentation module including an output (both volumetric and in nifti files) for the four regions of the brain stem (Pons, MidBrain, Medule, SCP) ?

m-reuter commented 1 year ago

The upcoming module will only include the cerebellum (see the cerebnet paper). We are working on an extension to also include the Brainstem regions. Until then you need to use FreeSurfer module for it.

fmcalcagno commented 1 year ago

We propose to help you with the training of the FastSurferCNN Brain Stem module, we have the hardware and the time if needed.

DimToum commented 10 months ago

Hi! Any update on that? (i.e. segmentation module for the subregions of the brain stem)

m-reuter commented 10 months ago

No, currently no updates. Still waiting for the manual labels (the usual bottleneck). In the meantime, you should be able to run FreeSurfer's brain stem module on top of FastSurfer.

DimToum commented 9 months ago

Ok, thank you. Please let me know if I can help with the manual labeling, I am an academic neuroradiologist.