Hi Michael
I usually check visually to see if things worked. Failures occur if you
dno't cut all the way through. For example, if you are cutting down the
fundus of the calcarine but miss a spot so that there is a connection from
upper to lower bank. You could cut down the lateral surface instead if you
want to analyze visual cortex. If you load the flat map in tksurfer you can
tell it's correct if the sulci all look about the same size (which means
there is relatively little distortion)
cheers
Bruce
On Mon, 11 May 2015, Michael Waskom wrote:
Hi Bruce,
Is there some way to know when cuts have been made correctly so that
distortion can be minimized? (Or conversely, some way to know when a given
patch has or will undergo "too much" distortion during flattening?
Thanks!
Michael
On Mon, May 11, 2015 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Sarah
the unfolding tries very hard to preserve exactly this - the
metric properties. If you cut off the occipital third of cortex
and flatten it (after introducing some cut along the axis of the
"cone") you should be able to get to around 10% distortion or
below, which I assume is good enough.
cheers
Bruce
On Mon, 11 May 2015, Sarah Finnegan wrote:
Dear all,
I am looking to take two measures within the visual
cortex.
1) A measure of width and length for each activation
cluster overlaid onto
the flattened cortical surface.
2) A measure of spacing between each cluster
I can find how to take measures of area but I
specifically want to know the
width and length separately to correlate this to
potential stripe systems.
My plan was to fit an oval to each of these clusters
and measure length
through the cardinal axis and width through the
minor, spacing would be
calculated from a line fit to the minor axis of each
cluster. Unfortunately
I think the unfolding process will have changed the
spacing relationships
between clusters to make this inappropriate.
I wonder if there is a command or established
pipeline to take such
measures?
Thanks for your help!
Sarah
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