Dear Bruce,

Thanks for your detailed answer!

> it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show up on a single slice, but actually isn't a significant inaccuracy.

Yes, when scrolling throug the slides it really appears consistent across several slides (actually the attached screenshots showed Freeview in coronal, sagittal and axial perspective of the same region). Here is the orig attached together with the wm, pial and white.
So how should I treat it?

> As for the dura, that certainly looks like a problem for thickness estimates. Have you tried using the graph cuts skull stripping? That is more aggressive than mri_watershed. You can also play with the watershed parameters to try to get more dura removed. Finally, if you have a T2-space FLAIR scan we can use that to properly reposition the surfaces (or less ideally, a T2-space scan without a FLAIR inversion).

No, unfortunately there are no other images at disposition.

How would one go with the graph cuts ?
I found "mri_gcut [-110| -mult <filename> |-T <value>] in_filename out_filename",

but how is it run within recon-all in order to repair (FS version 5.3)?

Thank you so much!
Markus

2014-04-07 14:47 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:

Hi Markus

it's tough to tell for sure on just a single slice, particularly if it is the intensity normalized one that removes a lot of the contrast if it is (as you suspect) doing the wrong thing. What does the orig look like? We try pretty hard to avoid including deep, highly myelinated gray matter inside the white matter surface, but of course if the contrast is low enough we can fail. If you scroll backwards and forward a few slices does or look in a different orientation does it look different/better? Sometimes the surface is curving sharply and this kind of thing will show up on a single slice, but actually isn't a significant inaccuracy.

As for the dura, that certainly looks like a problem for thickness estimates. Have you tried using the graph cuts skull stripping? That is more aggressive than mri_watershed. You can also play with the watershed parameters to try to get more dura removed. Finally, if you have a T2-space FLAIR scan we can use that to properly reposition the surfaces (or less ideally, a T2-space scan without a FLAIR inversion).

cheers
Bruce

On Mon, 7 Apr 2014, Markus Gschwind wrote:

Dear all,
I would like to show some very frequent and typical cases of segmentation
problems in my bunch of data of normal subjects (after recon-all), of which
I couldn't find a description in the wiki(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWith
Data/FreeviewEditingaRecon).

I am therefore not sure if these types of error are serious and will affect
later results like thickness, curvature, GWR, etc.

Here are the examples (c.f. attached screenshots from Freeview)

1) In the primary sensory-motor cortex it frequently happens that the
"?h.white" line lies several mm within the wm border (c.f. yellow arrow), I
did not observe this behavior in other places.
>>Would I need to edit that?

2) Sometimes the "?h.pial" line includes also dura or parts of the skull
(green arrow).
>>Is it necessary to edit that as well?

3) Another question concerns the yellow parts of the wm which sometimes are
much larger than the ventricles and also include both caudate nuclei (not
shown).
>>Is this a problem?

Thanks in advance!!

Markus