thanks re: saggital and horizontal: forget that then.
so the question returns to: can I use contours as a mechanism to correct artifact in the mri and make a wm segmentation that is helpful? I RTFM (the caret tutorial dated about 2008) on contours and while the examples are midthickness it mentions WM tracing as valid. So you say "I doubt it" but the docs suggest it can work the idea is: trace the wm at 0.5mm intervals. make into a surface. fill with voxels. if i like it, that's my wm seg. if not, adjust the contours till I do like it. we really need to make this segmenation. it's turning out out to be hard due to the artifact. we've even pulled old (1999) scans of this brain from tapes in germany but those were corrupted. only part of the scan has artifact (ripple). we are really working hard to solve this problem so if anyone knows for sure if tracing the WM wouldn't make a WM surface I'd be grateful to know before I plow into it head first. Otherwise It's voxel by voxel correction of the segmentation volume in the problem region for me. thanks Colin
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