We'd like to obtain total cerebellar volumes. There are errors within the cerebellar segmentation as revealed in the aseg.mgz file. Is there a method to manually edit the cerebellar segmentation?
Thank You, Rachel Steinhorn
Hi Rachel, Here are instructions for editing the aseg in tkmedit, it can also be done using Freeview. Be sure to run mri_segstats again when you're done editing.
https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithDat...
Alternatively, if the errors involve dura around the cerebellum being labeled as cerebellum you can edit the brainmask to remove the dura and then regenerate the aseg.mgz and stats. -Louis
On Thu, 27 Sep 2012, Rachel Steinhorn wrote:
We'd like to obtain total cerebellar volumes. There are errors within the cerebellar segmentation as revealed in the aseg.mgz file. Is there a method to manually edit the cerebellar segmentation?
Thank You, Rachel Steinhorn
Hi Rachel,
yes, you can edit them in either tkmedit or freeview. The cereballar segmentation somes suffer if you landmark too high resulting in the cerebellum being too far from isocenter. If you care more about cerebellum you might see if this is the cause of the reduced accuracy, and try landmarking lower in the future.
cheers Bruce
On Thu, 27 Sep 2012, Rachel Steinhorn wrote:
We'd like to obtain total cerebellar volumes. There are errors within the cerebellar segmentation as revealed in the aseg.mgz file. Is there a method to manually edit the cerebellar segmentation?
Thank You, Rachel Steinhorn
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Louis Nicholas Vinke -
Rachel Steinhorn