Hello Alex,

A helpful approach when editing the lateral ventricles is to view the sagittal plane; usually the filling should not extend anterior to the point where the posterior fornix is erased. The axial plane is also useful. The tutorial focuses on the coronal plane, which isn't optimal for determining when to stop the edits (moving anteriorly).

Smoothness of the surface -- the aim of manual editing is chiefly to eliminate the defects that the subsequent automated topology fixer cannot likely handle, whether or not they are easily visible on the surface. The large defects outlined in the manual are pretty safe bets for editing in this respect, and there are other anatomical idiosyncrasies that you'll find in normal or other populations which you can anticipate having to edit in order to "force" a topologically correct surface, e.g. brain lesions resulting in large gaps of white matter voxels.

It's hard to predict what will need to be edited without having done quite a few brains, but in general your choice is to either: a) err on the side of caution and edit whatever corresponds with a visible defect on the inflated surface, or; b) run the topology fixer first to see how/whether it could handle the remaining visible defects, with the risk that you might need to edit the extra defects afterward, anyway. And of course the Euler number calculation can give you precise information about a hemisphere's topological defect index. I'd recommend routinely editing the standard areas that lead to topological defects (as per the tutorial), then running the automated topology fixer, unless it is a structurally unusual brain with quite large visible defects. The automated topology fixer by and large works, and it's usually a better use of operator time to wait on this 5-hour process rather than spend an hour or so, perhaps pointlesssly, doing extra edits first.

The surfaces are generated using the normalized brain volume and not strictly the segmented white matter volume, so edits on the WM volume do not arbitrarily affect the cortical thickness measures.

Hope this helps, if not, ask more -

Hi all, I've noticed that the tutorial's instructions for manual editing of

the ventricles stops at about slice 92 (for Bert's data). Does this mean only the posterior portion of the lateral ventricles need to be filled, and that there is no need to continue to fill in the ventricles up to the anterior horns as well?

Also, a couple more queries re: manual editing:

• Sometimes I can see handles emanating from the surface that are not

in the areas listed in the manual. Are there any guidelines re: what should be deleted as opposed to what should be filled?

• Are there any guidelines for just how smooth the brain surface

should be before moving on to create the final surface? Some of my surfaces appear quite smooth (ie., no obvious handles), although somewhat bumpy, esp. around the posterior-dorsal areas.

• Am I correct in assuming that what is tissue is edited or not will

affect surface generation and hence estimates of cortical thickness? In this case, is it advisable to carry out some kind of reliability analysis for morphmoteric studies?

Thanks for your help, Alex

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