Best segmentation routine for CSF Volume count in children with hydrocephalus

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Dear all,
I just discovered this platform. I am currently helping a neuropediatric radiologist to develop a pipeline for CSF Volume quantification before and after shunt surgery. We have tried spm and cat12 but in roughly 50% of the cases these algorithms fail, because of the disproportionate intracranial anatomy of the children that don’t match any reasonable tpm. I am thinking about ways for only signal based segmentation in native space. Does anyone know of such algorithms or software solutions?

Any help is mich appreciated.

Best wishes
Julian

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Hi Julian,
Hope this reply wasn’t too late. We have recently collect a dataset of children with hydrocephalus and just started data analyses.
We found FSL’s tissue segment works well. But freesurfer don’t.
Just wondering how your data analyses go.

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Do you find this even after using the new SynthSeg (included in recent Freesurfer distributions)?