Hi,
I've been working with Freesurfer and FSL in order to compare the two softwares. However the last one has a tool called "Brain Extraction Tool" (BET) that provides all the brain volume including cerebellum. Is there any option in Freesurfer that makes the same as *BET*?
Thank you for your attention,
Ana Arruda
Hi Ana
the binary mri_watershed does skull stripping in FreeSurfer.
cheers Bruce On Sun, 23 Sep 2012, Ana Arruda wrote:
Hi,
I've been working with Freesurfer and FSL in order to compare the two softwares. However the last one has a tool called "Brain Extraction Tool" (BET) that provides all the brain volume including cerebellum. Is there any option in Freesurfer that makes the same as BET?
Thank you for your attention,
Ana Arruda
Thank you.
But in the last message I forgot to say my final aim. After the skull stripping, how can I measure the volume?
Ana Arruda
I've just seen the output from mri_watershed. And from the file aseg.stats, is there any measure that provide the brain volume?
Thank you once again,
Ana Arruda
Depends on how you define "brain volume". If you're using BET, then I assume that you are just counting the number of voxels in the mask? If so, you can use mri_binarize and use the --count countfile to give you a count of the voxels. doug
On 09/22/2012 08:22 PM, Ana Arruda wrote:
I've just seen the output from mri_watershed. And from the file aseg.stats, is there any measure that provide the brain volume?
Thank you once again,
Ana Arruda
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