Dear all,
I am trying to add control points for a subject in order to improve normalization and skull stripping, but I found that the control points I added did not have much effect on the end result. I know control points should be added at points that the user feels sure are inside the white matter boundary, and that there should be about 20 spread out throughout the volume, but I am still uncertain as to how to choose them effectively. Should they be closer to the white/gray boundary? Or closer to the center? I believe I would be able to choose these points more effectively if I understood how FreeSurfer uses control points. Is it used as a high or low cut-off thresh-hold? Or is it more complex than that? Is location taken into account or is it just the intensity values that are used?
Any help is greatly appreciated. Thank you, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
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Hi Sasha,
you want to pick them in a region where the wm intensity is lower than it should be. That is, less than 110. In general, they can help recover thin wm strands that are dark by putting some at the base of the strand. Note that they will only have an effect if you put them at points that are not equal to 110 in the T1 volume. And you can pick more than 20, just make sure that none of them contain any gray matter.
Bruce
On Mon, 3 Oct 2005, Sasha Wolosin wrote:
Dear all,
I am trying to add control points for a subject in order to improve normalization and skull stripping, but I found that the control points I added did not have much effect on the end result. I know control points should be added at points that the user feels sure are inside the white matter boundary, and that there should be about 20 spread out throughout the volume, but I am still uncertain as to how to choose them effectively. Should they be closer to the white/gray boundary? Or closer to the center? I believe I would be able to choose these points more effectively if I understood how FreeSurfer uses control points. Is it used as a high or low cut-off thresh-hold? Or is it more complex than that? Is location taken into account or is it just the intensity values that are used?
Any help is greatly appreciated. Thank you, Sasha
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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Sasha Wolosin