Hi Tetiana,
I think what you're seeing are just the consequences of a voxel-based segmentation. The borders have to be voxelated. Note that much of this will be corrected in the volume calculation that performs a partial-volume correction.
cheers Bruce
On Wed, 23 Feb 2011, Tetiana Dadakova wrote:
Dear Bruce, dear all,
I attach several images to show where I would like to manually interfere into segmentation process.
img1: Hippocampus' volume covers part of amygdala and parahippocampal area. The intensity in these non-hippocampal regions are between 75-95.
img2: Segmentation of brain stem (problem point are shown by arrows). This problem repeats more or less for every subject.
img3: Edges of thalamus are too "pixelated". I mean, shouldn't the line be smoother? Can this cause overestimation of thalamus' volume?
Manual correction (drawing) of all the mis-segmented parts would take a lot of time, so I would like to find out other way of controlling the segmentation process. (Something like "putting control points" would be perfect).
Thank you, Tanja.
On Mon, Feb 21, 2011 at 2:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tanja, Can you send us an image? Is parahippocampal white matter significantly darker than 110? Bruce
On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova tetiana.d@gmail.com wrote:
Dear Freesurfer users,
For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)?
Thank you, Tanja. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer