Hi Mike
it's a bit hard to state the region of effect for the control points.
Essentially we go through and label voxels as control points or not based
on their intensity, intensity gradient and connectivity (that is, the must
be 6-connected to other control points) then build a Voronoi diagram and
each control point sets the scaling for its Voronoi triangle. Thus if you
have a control point surrounded by others its region of effect is small,
but one control point all by itself can have a large region of effect.
Also, 5.1 applies the manually specified control points to the aseg
normalization (norm.mgz), whereas older versions didn't. Not everyone is
happy with this, so I think there is a backwards compatibility flag. Nick
would know.
Bruce
On Fri, 27 Jan 2012, Sabin Khadka wrote:
Hi Michael,I had the same problem too. It might be because of the type of
scanner you are using. I added -washu_mprage flag, it pretty
much helped me (I did not had to add a lot of controls points and so on so
forth. You can go through the link below.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011695.html
Hope it helps.
-SK
On Fri, Jan 27, 2012 at 12:06 PM, Michael Harms <mha...@conte.wustl.edu> wrote:
Hi guys,
We are currently trying to fix some errors in the white/pial surfaces
where there are thin white matter strands by using control points, and
are noticing a couple things:
1) The resulting WM surface in the area of the CPs can end up too far
into the GM instead. Given that, is there any practical guidance for
how to think about the surrounding spatial extent that is impacted by a
given CP? i.e., How do CP's actually get used within mri_normalize in
an algorithmic sense?
2) The surfaces are being impacted in places distant from the CPs.
e.g., CP's placed in the left anterior temporal lobe are resulting in
surface changes in the right anterior temporal lobe. And when I
difference the original norm.mgz vs. the one obtained after using CP's,
I'm seeing an odd pattern of intensity differences which is clearly not
limited to just the area of the CP's (which would be my expectation).
This is version 5.1.
thanks,
-MH
--
Michael Harms, Ph.D.
--------------------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6604 Tel: 314-747-6173
660 South Euclid Ave. Fax: 314-747-2182
St. Louis, MO 63110 Email: mha...@wustl.edu
--------------------------------------------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
