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
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
$ 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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I should also note that I have had a couple problems, trying to fill the uncut area, where I get the following error: ---
tksurfer.bin: ../../src/mesa/tnl/t_vertex.c:423: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort (core dumped)
---
*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 11:34 AM, S.V.Shepherd [work] < stephen.v.shepherd@gmail.com> wrote:
$ tksurfer ${subj} lh inflated -sulc
- closed cut line around corpus callossum etc.
- four tension relief cuts
- select connected region
- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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
- closed cut line around corpus callossum etc.
- four tension relief cuts
- select connected region
- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
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
- closed cut line around corpus callossum etc.
- four tension relief cuts
- select connected region
- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Thanks for the update. This information could be of potential help if this error is ever come across again by other users.
-Zeke
On 06/23/2016 01:53 PM, S.V.Shepherd [work] wrote:
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 mailto: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 <tel:212.327.7699> On Thu, Jun 23, 2016 at 9:58 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto: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 <tel:212.327.7699> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no problem. The stride error is something buried in the depths of openGL. It seems to be OS/version specific and there isn't much we can do about it
Glad you figure out your error though Bruce
On Thu, 23 Jun 2016, S.V.Shepherd [work] wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
S.V.Shepherd [work] -
Z K