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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
