Hi Sandra,
On 06/18/2004 07:15 PM, Sandra Basic wrote:
Can you tell me if it is neccessary to align lower scale mark of the
section to the origin although the contours, once I do it, appear out of
alignment.
I don't think it needs to be the origin, but it should be consistent
throughout all contours.
Are you saying your contours appear out of alignment when you choose
consistent scale marks throughout all the sections? Are you using the
tutorial dataset or your own data?
Does it matter if drawings are not always in the same position, but the
scale bar is? Scale marks should take care of this problem.?
I think it will matter, but without seeing your sections or better
understanding how the position changes from one contour to the next, I
can't be sure. The scale marks will help you keep the scale consistent
from one contour to the next, but not rotation or translation, for example.
And in a separate message wrote:
IN your tutorial, are your sections/drawings all centered, and the sale
bar/marks is to set the measure?
I'm not sure I understand what "all centered" means in this context, but
the Paxinos contours in tutorial 9 appear rotated and translated
consistently from one section to the next, with only the scale differing.
If you have completed tutorial 9, then you have at least as much
experience as I reconstructing surfaces from contours. I did ask Erin
Reid, who also works in the Van Essen Lab and *does* have real
experience doing this, about your questions. She did tell me that in
practice, the scale marks might be off a bit in some sections. In those
cases, if you faithfully stick to setting the scale marks consistent
with adjacent sections, then your contours will be clearly out of
alignment. In such cases, you have to deviate a bit, based on the
neighboring contours, and consult with the source of the contour dataset
to clear up the discrepancy. To me, this is not surprising, since I'd
expect contour reconstruction to be inherently more error prone than
reconstruction from, say, structural MRI.
If this doesn't help, let us know; perhaps David or John can provide a
more meaningful response, if we better understand the particulars of
your dataset.
Donna
