Dear FS-Experts,
While checking the results of the autorecon2 process and editing the brainmask.mgz and wm.mgz I regularly encounter quite a few spots per brain where - in my eyes - the red pial line seems to get far too close to the yellow line making the calculated cortex appear too thin in these regions (see the three examples attached). Sometimes the lines get so close that hardly any room for the cortex is left.
I wonder what might be the best way to deal with these spots. Can I simply ignore them or should I try to remove some parts of the white matter in the wm.mgz (which will of course add another subjective factor into the analysis) or is there another way of handling them that i did not think of?
Any help is greatly appreciated.
Best wishes, Christian Scheel
hmmm, that's pretty bad ringing in your data. You could try editing the wm to remove incorrect segmentations in these regions (if the orig surface also extends out too far).
On Fri, 5 Sep 2008, Christian Scheel wrote:
Dear FS-Experts,
While checking the results of the autorecon2 process and editing the brainmask.mgz and wm.mgz I regularly encounter quite a few spots per brain where - in my eyes - the red pial line seems to get far too close to the yellow line making the calculated cortex appear too thin in these regions (see the three examples attached). Sometimes the lines get so close that hardly any room for the cortex is left.
I wonder what might be the best way to deal with these spots. Can I simply ignore them or should I try to remove some parts of the white matter in the wm.mgz (which will of course add another subjective factor into the analysis) or is there another way of handling them that i did not think of?
Any help is greatly appreciated.
Best wishes, Christian Scheel
Christian,
I suspect that in example3-frontal and example2-frontal you have motion artifacts causing increased intensity in the cortex. On the other, example1-horizontal and example1-sagittal seem to have pretty low SNR, specially in GM, but very good GM-WM contrast. I wonder, if they were not acquired after gadolinium injection?
I don't have a recipe to correct either of the problems, but I don't have good experiences with the images after Gd. They seem to have cortex overestimated.
Good luck,
Martin
On Friday 05 September 2008 15:00:17 Christian Scheel wrote:
Dear FS-Experts,
While checking the results of the autorecon2 process and editing the brainmask.mgz and wm.mgz I regularly encounter quite a few spots per brain where - in my eyes - the red pial line seems to get far too close to the yellow line making the calculated cortex appear too thin in these regions (see the three examples attached). Sometimes the lines get so close that hardly any room for the cortex is left.
I wonder what might be the best way to deal with these spots. Can I simply ignore them or should I try to remove some parts of the white matter in the wm.mgz (which will of course add another subjective factor into the analysis) or is there another way of handling them that i did not think of?
Any help is greatly appreciated.
Best wishes, Christian Scheel
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Christian Scheel -
Martin Kavec