Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, when the wmparc is loaded on, we are seeing that the wmparc ROIs sometimes do not follow the white surface----the ROIs are going into the gray matter regions.
Are the white matter surfaces converted to volumes and then convolved with the aseg/aparcs/etc or are they only used for the cortical thickness computations? It almost seems as if the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)?
Any help is much appreciated!
-Ryan
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, when the wmparc is loaded on, we are seeing that the wmparc ROIs sometimes do not follow the white surface----the ROIs are going into the gray matter regions.
Are the white matter surfaces converted to volumes and then convolved with the aseg/aparcs/etc or are they only used for the cortical thickness computations? It almost seems as if the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)?
Any help is much appreciated!
-Ryan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
The images are attached. Thanks again for your help!
-Ryan
On Dec 6 2007, Doug Greve wrote:
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, when the wmparc is loaded on, we are seeing that the wmparc ROIs sometimes do not follow the white surface----the ROIs are going into the gray matter regions.
Are the white matter surfaces converted to volumes and then convolved with the aseg/aparcs/etc or are they only used for the cortical thickness computations? It almost seems as if the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)?
Any help is much appreciated!
-Ryan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they look in that area?
Ryan Muetzel wrote:
Hi Doug,
The images are attached. Thanks again for your help!
-Ryan
On Dec 6 2007, Doug Greve wrote:
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, when the wmparc is loaded on, we are seeing that the wmparc ROIs sometimes do not follow the white surface----the ROIs are going into the gray matter regions.
Are the white matter surfaces converted to volumes and then convolved with the aseg/aparcs/etc or are they only used for the cortical thickness computations? It almost seems as if the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)?
Any help is much appreciated!
-Ryan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
The white matter in aseg seems to follow the same pattern as the white matter in wmparc...it goes into the ribbon (through the white matter surface into gray matter).
-Ryan
On Dec 7 2007, Doug Greve wrote:
Can you load and examine the aseg.mgz, {lh.rh}.ribbon.mgz? How do they look in that area?
Ryan Muetzel wrote:
Hi Doug,
The images are attached. Thanks again for your help!
-Ryan
On Dec 6 2007, Doug Greve wrote:
Can you send a pic?
Ryan Muetzel wrote:
Hello,
We are running Freesurfer version 4.0.1 and seem to be having problems with the white matter/gray matter parcellation borders. When viewing the pial and the main white surfaces in tkmedit, everything looks good against the t1 brain. However, when the wmparc is loaded on, we are seeing that the wmparc ROIs sometimes do not follow the white surface----the ROIs are going into the gray matter regions.
Are the white matter surfaces converted to volumes and then convolved with the aseg/aparcs/etc or are they only used for the cortical thickness computations? It almost seems as if the intensity based wm seg is used and not the wm surface based (?h.dwhite.ribbon.mgz)?
Any help is much appreciated!
-Ryan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Ryan Muetzel