Re: [Freesurfer] skull stripping of IBSR using freesurfer

Hi Jinyoung ,

those images have labels - why not just zero out everything with a zero label? And make sure you are trying to srip the intensity image, not the label one. You probably don't want to use a -T1 flag unless you used our intensity normalization.

cheers Bruce On Sat, 5 Jun 2010, Jinyoung Hwang wrote:

Hi all, I'm trying to obtain skull stripped images using freesurfer.

Unfortunately, I couldn't perform the skull stripping function for 7_8 data within IBSR dataset (http://www.cma.mgh.harvard.edu/ibsr/). I used following command.

...

mri_watershed -T1 7_8.img f7_8.img

The error message was

mri_watershed error: w=White Matter =Intensity too high (>240)... valid input?

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How can I deal with this kind of error?

regards, Jinyoung