Hi Mike can you tar and gzip a subject dir with strange results? All manually specified CPs are included. Then there is an initial intensity segmentation for stuff that is very likely to be wm, after-which there are a set of region-growing steps. That's actually the cortical one.The subcortical is a bit gentler and more complex as it includes spatial priors and multiple structures.
Bruce On Mon, 30 Jan 2012, Michael Harms wrote: > > 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
