Hi Bruce,

It is pretty erratic what happens after adding them. Sometimes the wm.mgz is more accurate and the wm surface is less accurate, but more often they are both less accurate. The points themselves do typically get brighter (on wm.mgz).

I've included a screenshot of an example of what's going on as an attachment (.pdf)

Best,
Peter


On Thu, Jul 12, 2012 at 3:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Peter and Mike

yes, 5.2 will undo those changes, although I still wouldn't expect this behavior. Peter: are the points brighter (closer to 110) after adding them? Is the wm.mgz more accurate?

cheers
Bruce



On Thu, 12 Jul 2012, Michael Harms wrote:


Hi Peter,
This sounds very familiar (including the effect on the opposing
hemisphere) to something I've observed previously under FS v5.1 -- see
the posts titled "control point guidance" from late Jan 2012.  This may
be related to a change in how CP's were used in FS v5.1, which I believe
they are planning on backing out in the next release.

I've personally always found it much easier to predict what would occur
using direct edits to the wm.mgz, rather than control points.  And in
this case, wm edits are what we did.

cheers,
-MH

On Thu, 2012-07-12 at 13:15 -0400, Peter McNally wrote:
Dear FreeSurfer,

Hello, I am currently working on a project using FreeSurfer (version
5.1.0) at the Kable Labs at the University of Pennsylvania, and I have
come across a problem when using control points to add incorporate
more of the white matter into the white matter surface. After
highlighting the parts of the white matter that have yet to be brought
into the white matter surface with CPs, it will sometimes do what I
intend it to but often  will not. The strange part is that when it
fails to incorporate more wm into the wm surfs it often actually
removes a considerable amount the white matter both from the wm.mgz
volume and from the white matter surface. Once it even did so on the
opposite hemisphere as where I had put down control points. This
problem seems to occur exclusively in the anterior end of the temporal
lobe (everywhere else my use of control points has presented me with
no problems), and it happens both when using control points sparingly
and aggressively (I did a bit of experimenting, and the quantity of
CPs that I used seemed to make no difference). Do you have any advice
for how I might be able to get around this dilemma and/or why it
likely is occurring? Thank you very much for your time.

Best,
Peter McNally
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