it only affects points that are close to it in space. Pretty much every
point is corrected according to the bias field associated with the nearest
control point, with some smoothing. Why are the values near the center of
the brain so dark? Was this aquired with a surface coil?
cheers,
Bruce
On Sun, 30 Oct 2005,
Martin Ystad wrote:
Jenni Pacheco wrote:
Hi Martin,
Control points should fix the problem. Try adding some to this brighter
region, as well as a few to regions currently labeled to 110. Sometimes
this helps. After you've saved your control points (be sure to save them)
then you should run:
recon-all -normalization -usecontrolpoints -subjid <subjid>
to make sure that it uses your control points. If you look at your brain T1
volume now, those bright spots should be taken care of. If so you'll need
to re-run these steps:
recon-all -skullstrip -subcortseg -normalization2 -segmentation -subjid
<subjid>
If it hasn't worked, let me know, maybe there's another problem.
good luck,
Jenni
On Fri, 28 Oct 2005, Martin Ystad wrote:
Hi, I'm currently running the latest developmental release for RedHat 9,
but I seem to have some problems concerning the intesity-normalization.
Unfortunately, my images have some intensity inhomogenities, but the first
normalization-step seems to take care of most of these. However, some
regions inside the white matter has a somewhat high value, for example 130
-140. These regions are not included in the white matter when I run the
recon-all -segmentation program. Adding control-points to these areas does
not work, obviously, since only values lower than 110 are considered when
the normalization-step is re-runned. (right?)
Is there any way to include these areas in my final white matter whithout
manually drawing them onto the wm.mgz -volume? For instance raising the
threshold for wm-segmentation?
If so, would this produce any kind new artifacts which I need to be aware
of?
Thanks,
Martin Ystad
Medical Student
University of Bergen
Institute of Biomedicine
Jonas Lies vei 91, 5009
Bergen, Norway.
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Hi, thanks for your help.
I tried what you suggested and it turned out somewhat better. Still, there
are large areas that are not included in the wm.mgz. The problem with some of
the data sets is that the intensity inhomogenities in the center of the brain
also reaches some very low values. I'm worried that if I include these with
control-points, some of the gray matter will be misinterpreted as white
matter. Is this a legitimate concern, or does the program work in a different
way? If so, how low can the control point value be to avoid that this
happens?
Ps. If I add a control point to one area with a specific high or low value,
does this take care of all the other areas with similar values across the
brain, or do I have to add a control point to all areas that have
discrepancies in intensity?
Thanks,
Martin
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