Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

white matter mask
by Oya, Hiroyuki 03 Jan '10

03 Jan '10

Hello All, I'd like to create mask of white matter. Would it be possible to use white matter surface to do this? Tx. Hhiroyuki

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calculate the deformation in the anatomical configurition space after spherical registration
by Zhong Jidan 02 Jan '10

02 Jan '10

Hi Freesurfer experts, I have a 3D fiducial surface ('anatomical' surface configuration), based on this fiducial surface ,let's say, "template", I generated some simulated fiducial surface with some deformation, let's say "subject". So here I know the "deformation vectors" for each vertex between the template and the subject in the original 3D fiducial surface "space". Then I use FreeSurfer to generate the spheres and do spherical registration from those subjects to the template. I want to check how these " deformation vectors " I got from Freesurfer are different from my generated "deformation vectors". But the problem for me is, after Freesurfer registration, the " deformation vectors" is based on the spherical space. While my generated "deformation vectors" are in the 3d fiducial surface space, it's not comparible for these two vectors. I want to know whether I can put the deformed subject sphere back into the fiducial surface representation. In that way, I can calculate the difference in the fiducial space. If getting the deformed subject sphere into the fiducial surface space is not possible, could you give me some suggestions about how to calculate the difference of the deformation vectors which are not in the same space? Generating the deformation vectors in the spherical space is the last thing I want to do because you never know how it likes in the real fiducial surface representation. Thank you. Jidan On Mon, May 4, 2009 at 8:48 PM, Zhong Jidan <jidanz(a)gmail.com> wrote: > Hi, > > I have a question about the sphere registration. The registration of > surface is spherical registation, so the outpput of the surface is > also a sphere. When we have the inflated and smoothwm, we can convert > the surface into sphere using mris_sphere, but reversely, how to > convert the deformed sphere in the form of white surface or pial > surface? > > Also, if I want to use the surface between the white and pial surface > to do registration, do I need to make the sphere myself? > > Thanks, > > > -- > Regards, > > Jidan > -- Regards, Jidan

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bad segmentation ?
by Gonzalo Rojas Costa 01 Jan '10

01 Jan '10

Hi: I have some questions about the segmentation of a patient with a cortical displasia: why the aparc+aseg.tif labeled "none" in the segmentation of the cortical displasia section (red cross in T1.tif) and the other segmentation method (aseg.tif) labeled ok that area ?... How can I fix it ?... How can I fix the cortical thickness of that section ?... Sincerely, Gonzalo Rojas Costa

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Freesurfer January 2010