Adapting FreeSurfer (HCP pipeline) for pediatric subjects with ventriculomegaly

[Armin Allahverdy]

Hello everyone,

I am using the HCP FreeSurfer processing pipeline on T1-weighted MRI data from 5-year-old children. In some cases, the subjects present with ventriculomegaly, which seems to affect the accuracy of the cortical and subcortical segmentations.

Is there a recommended way to modify or adapt the FreeSurfer pipeline to better handle pediatric subjects with enlarged ventricles? For example, are there parameter adjustments, alternative initialization steps, or custom pediatric templates that could improve segmentation quality in these cases?

Any guidance or references to studies that have addressed this issue would be greatly appreciated.

Thanks in advance

Armin

[Glasser, Matthew]

There is a FreeSurfer recon-all -bigventricles flag (use --extra-reconall-arg when calling the HCP FreeSurfer pipeline).  It was developed for aging brains, but you can give a try for ventriculomegaly in children.

 

Matt.

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