Thanks Bruce and Eugenio,

Suppose I had two identical images of a subject, but in one image I reduced the contrast of internal lamina while leaving the rest of the image intact...just removing internal intensity differences, but leaving the outer boundary contrast intact.

Would the images result in very different subfield segmentations?

Josh

- Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805

On Fri, Jun 7, 2013 at 12:33 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Josh

it depends on intensity differences if it can find them as well as boundary/geometry.

cheers Bruce

On Fri, 7 Jun 2013, Joshua Lee wrote:

I'm trying to understand Leemput's subfield algorithm better as

...

implemented in Freesurfer. Does the algorithm make use of intensity differences in the internal hippocampal lamina from the subject's T1 image to warp meshes and assign subfield probabilities? Or does it depend only on outward boundaries of the hippocampus and probability priors to determine the inner boundaries between CAs and dentate gyrus?

Josh

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That is interesting and good to know. Thanks.

I am looking for a reference that provides validation metrics on the Van Leemput (2010) method as implemented in Freesurfer. To your knowledge, is there such a reference?

Best,

Joshua

On Fri, Jun 7, 2013 at 12:49 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:

Koen, please correct me if I'm wrong, but I'd say the answer is no. Since these tissue classes share the same Gaussian parameters, their likelihood term is the same, and the posterior is fully determined by the prior (i.e., the atlas). /E

On Fri, 2013-06-07 at 12:42 -0700, Joshua Lee wrote:

...

Thanks Bruce and Eugenio,

Suppose I had two identical images of a subject, but in one image I reduced the contrast of internal lamina while leaving the rest of the image intact...just removing internal intensity differences, but leaving the outer boundary contrast intact.

Would the images result in very different subfield segmentations?

Josh

Joshua Lee

Graduate Student Center for Mind and Brain &

Department of Psychology

University of California, Davis 530.747.3805

On Fri, Jun 7, 2013 at 12:33 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Josh

    it depends on intensity differences if it can find them as
    well as boundary/geometry.

    cheers
    Bruce



    On Fri, 7 Jun 2013, Joshua Lee wrote:

            I'm trying to understand Leemput's subfield algorithm
            better as implemented
            in Freesurfer. Does the algorithm make use of
            intensity differences in the
            internal hippocampal lamina from the subject's T1
            image to warp meshes and
            assign subfield probabilities? Or does it depend only
            on outward boundaries
            of the hippocampus and probability priors to determine
            the inner boundaries
            between CAs and dentate gyrus?
            -
            Josh





    The information in this e-mail is intended only for the person
    to whom it is
    addressed. If you believe this e-mail was sent to you in error
    and the e-mail
    contains patient information, please contact the Partners
    Compliance HelpLine at
    http://www.partners.org/complianceline . If the e-mail was
    sent to you in error
    but does not contain patient information, please contact the
    sender and properly
    dispose of the e-mail.

-- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.