Hi Michelle
if you visualize your cuts on the inflated surface by loading the patch
into tksurfer, then clicking the "I" button. you can see that the cut
down the calcarine doesn't reach either the occipital pole or the end of
the patch. This makes it impossible for the flattening to find a solution
with minimal metric distortion. You need to extend the cut in both
directions - so it reaches the edge of the cut patch allowing the
flattening to unfold the patch, and to occipital pole to remove the high
curvature there. Think about it as cutting down the side of a conical piece
of paper. If you cut all the way you can unroll the paper perfectly without
any distortion
Bruce
On Fri, 7 Oct 2011, Michelle Umali wrote:
Hi Bruce,
I've uploaded a tar file called umali_fieldsign_swirl.
It contains two directories one anatomical and the other retinotopy both from
the same subject 29:
ld29 which contains the recon-all output anatomical data
sj29 which contains all the retinotopy data. the subjectfilename says ld29
The fieldsign map on the flattened patch has some out-of-plane swirls.
Is it from incorrect cuts or something else?
Thanks.
Michelle
On Fri, Oct 7, 2011 at 8:32 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Michelle,
the odd shaped shards and triangles usually means you recreated the
surfaces after flattening, so the flattening needs to be redone. The swirls can
be a number of
things, possibly incorrect cuts. If you want to upload an example I'll
take a look.
cheers
Bruce
On Thu, 6 Oct 2011, Michelle Umali wrote:
Dear freesurfers,
I've been analyzing my retinotopy , have finally been able to run
fieldsign-sess without running into dimension mismatch errors.
Everything seemed ok until I tried looking at the fieldsign maps on flat
patches. Some patches are warped with odd out of plane swirls. In
others,
all i get are odd shaped shards and triangles.
What might be the cause?
thanks,
Michelle
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