The error on flattening was caused by my saving the surface, instead of the patch, to lh.full.patch.3d.  I apologize -- it was a dumb mistake. 

I am unsure what caused the """ Assertion `a[j].inputstride == vptr->stride' failed. """ error, but it only occurred on a few attempts, so I was able to work around it.

Thanks for thinking about the problem and sorry to report it was simply user error!

stephen

stephen v. shepherd   phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

On Thu, Jun 23, 2016 at 1:00 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
hmmm, are you sure that the partition isn't full or something? On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote:

$     tksurfer ${subj} lh inflated -sulc

1) closed cut line around corpus callossum etc.
2) four tension relief cuts
3) select connected region
4) save as patch



stephen v. shepherd   phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699

On Thu, Jun 23, 2016 at 9:58 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Stephen

      how did you create the patch? It looks like it is corrupted
      since that vertex # is way too big. The total # of vertices in
      the patch is also wrong.

      cheers
      Bruce
       On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote:

            Hello all,

            I'm trying to make a patch and have run into the
            'bad vertex' error. It's
            come up a few times on the listserv, but I never saw
            a public resolution.
            One possible source of errors is that I had to do a
            manual correction in
            FreeView, including a 'remove intersections' in
            FreeView. However, tksurfer
            had no trouble mapping the curvature to the finished
            surface, so I assume
            this was not likely to be the source of the error.
            Details below:

            $    mris_flatten -w 0 -distances 20 7
            lh.cort.patch.3d lh.cort.patch.flat
            using write iterations = 0
            sampling 7 neighbors out to a distance of 20 mm
            reading patch lh.cort.patch.3d with 1919246708
            vertices (2846533.5% of
            total)
            MRISreadPatch: bad vertex # (1701060705) found in
            patch file
            No such file or directory

            stephen

            stephen v. shepherd   phd
            The Rockefeller University / 1230 York Avenue / New
            York NY 10065-6307 USA
            // 212.327.7699


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