Hi all! We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not.
Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised. We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later. Could anyone help us in this? And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity). And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ). Thank you very much. Gergely Orsi
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