Hi Bruce, Can you elaborate briefly on the 6-connected bit? e.g., if one places a CP manually in a voxel, and that CP is not face-connected on all sides to either other manually-placed CPs, or CPs determined automatically by FS, then it doesn't get counted as a CP after all?
Is there any volume that allows one to see the automatically generated CPs? Something definitely seems wonky about the inclusion of the manually- specified CPs as part of the aseg normalization (mri_ca_normalize), because the resulting norm.mgz (and thus eventually brain.mgz) ends up differing appreciably in locations distant from the manually placed CPs. In contrast, if you skip the re-creation of the norm.mgz by using the - nocanorm flag, the resulting brain.mgz is much more reasonably behaved, with its largest differences in the vicinity of the CPs. thanks, -MH On Fri, 2012-01-27 at 14:58 -0500, Bruce Fischl wrote: > 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
