Hi David,
Thanks for the information.
We had actually been using layer 4 as the surface but I thought that since
atlases are based on MRI mid-thickness it would better to use mid-thickness.
But I take your point about histology quality and alignment accuracy being
a much bigger source of error.
Thanks for giving me Erin's contact details, I may need to ask her a few
things.
If you have C++ code that can do it, let us know if you're willing to share
> it.
Unfortunately, the cutting code we have is just some ad hoc python scripts
at this stage. It would be interesting to see if we could clean it up and
redo it in C++ for Caret, but like you we have other priorities.
Thanks,
Tristan
On Tue, Jan 18, 2011 at 16:24, David Van Essen <vanes...@wustl.edu> wrote:
> Tristan,
>
> On Jan 17, 2011, at 6:56 AM, Tristan Chaplin wrote:
>
> Hi,
>
> I'm working on constructing brain models from histological sections with
> cortical areas demarcated. Until now we've been writing our own progrms to
> achieve this. I'd like to start to use Caret for more of this work so
> non-programmers can do it and our data is more compatible with other
> datasets, but I've got a few questions.
>
> Firstly, with regards to drawing a contour of the cortical mid-thickness,
> the tutorial suggests that you just estimate this visually when drawing the
> contours. I was wondering, is there a standard procedure or set of tools
> for calculating the mid-thickness given the pial and GM/WM boundaries?
>
> Not for histological contours. Unless the mapping between white and pial
> surfaces has already been determined (e.g., via Freesurfer automated
> segmentation) computing the midthickness is a very hard problem.
>
> In practice, we generally achieve a reasonable outcome by drawing a contour
> along the estimated midpoint between the white matter and pial contours in a
> given section, modulated by the fact that histological layer 4 tends towards
> the pial side in gyri and near the white matter side near sulcal fundi.
>
> Unless your histological sections are exceptionally well aligned
> (overcoming tissue distortions during histology), the inaccuracies
> associated with imperfect midthickness determination are likely to be small
> on average relative to the typical between-section misalignment.
>
> Finally on this front, Erin Reid in my lab has been doing contour-based
> reconstructions on a couple of recent projects and has been helping to
> update the old tutorial. If you have specific technical questions, you can
> contact her:
> Erin Reid <e...@brainvis.wustl.edu>
>
>
> Secondly, with regards to marking cortical areas, normally we would
> represent the area boundaries as points in space ("cells" in Caret I
> believe) and using our own programs, project to the nearest mesh node.
> Then, for a given cortical area, we would use the Dijkstra algorithm to
> "cut out" the cortical area by finding the shortest path between it's
> boundary points.
>
>
> Sounds nice.
>
> However it seems that in Caret the method is to view the projected cells on
> a flat map, and draw a border around it to create a paint file.
>
> Yes, except that Caret now permits borders to be drawn on inflated or other
> closed surfaces, thereby obviating the problems along the cuts in flat maps.
>
> Is there a more precise way, perhaps similar to the one I described, of
> doing it in Caret?
>
>
> Not at present. It would be nice to have this as an automated
> process/algorithm, but given other priorities it is not something we are
> likely to undertake in the near future. If you have C++ code that can do
> it, let us know if you're willing to share it.
>
> David VE
>
>
> Thanks,
> Tristan
>
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