Not from the T1 alone. I wrote a script called intcapseg (it may or may not be in the distribution). Below is the doc for it. I can get it to you if you want it, but it is not at all tested or validated.

doug

intcapseg --s subject

--ndil ndil : default is 6 --nero nerodes : default is ndil + 1 $Id: intcapseg,v 1.1 2011/03/02 18:15:47 greve Exp $

This is program that segments the internal capsule as the white matter between the thalamus and the pallidum based on the aseg.mgz. The underlying algorithm is very crude, simply using dialations and erosions of the thalamus and the pallidum segmentations.

Vaidya, Jatin G wrote:

I see.

Doug: do you consider this to be a reliably defined white matter region? If so, would it be possible to to get some information on the tools Bruce mentioned?

On 10/31/11 4:40 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

...

Doug wrote some tools to do this, but they aren't run by default.

cheers Bruce On Mon, 31 Oct 2011, Vaidya, Jatin G wrote:

...

Hi,

We recently processed some T1 data through Freesurfer but I did not see any labels for the internal capsule. Does Freesurfer still create a label for this region?

Thanks,

Jatin

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