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 fischl@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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.