yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote:
> Yes. The input label looks fine on fsaverage. > > But I just realized something. After editing the surface, I re-ran > autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the > spherical mapping correctly, I also have to re-run autorecon3 right? I > did not realize that. So I'm running autorecon3 now, and hopefully this > will resolve the problem. > > Lingqiang > >> Are you sure the label was generated on fsaverage? Does it look ok if >> you run >> >> tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label >> >> >> >> On 07/22/2013 05:13 PM, Lingqiang Kong wrote: >>> Yes. The label file is attached. >>> >>> Although since this error did not happen with the old surface of the >>> same >>> subject, I suspect editing it and running autorecon2-wm created a new >>> surface that had some unknown issues. >>> >>> Lingqiang >>> >>> >>> >>>> Can you send the first 100 lines (or point me to the label on the file >>>> system)? >>>> doug >>>> On 07/22/2013 05:01 PM, Lingqiang Kong wrote: >>>>> The input label is one from a set published 1000 brain functional >>>>> connectivity label from the Buckner lab (Yeo & Krienen, et al., 2011). >>>>> >>>>> No. The first number of all lines are integers ranging from 5 to >>>>> 132000. >>>>> >>>>> Just adding some details: >>>>> 1) when we first ran recon did the same label conversion and >>>>> mri_label2label worked fine. Later >>>>> we edited the white matter and added control points, and re-ran >>>>> autorecon2-cp and autorecon2-wm. The surface looked better after the >>>>> editing, but we have this label conversion problem now. >>>>> >>>>> 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, >>>>> and >>>>> mri_label2label haults. However, on the other hemi, although >>>>> mri_label2label runs through without reporting error, the converted >>>>> labels >>>>> on subject surface looks like gibberish and out of place. So it's >>>>> likely >>>>> there are problem with both hemis, but with different severity. >>>>> >>>>> Thank you. >>>>> >>>>> Lingqiang >>>>> >>>>>> what is the input label? How was it created? Does it have -1 as the >>>>>> first number on any line? >>>>>> >>>>>> On 07/22/2013 03:54 PM, Lingqiang Kong wrote: >>>>>>> Dear Freesurfer list, >>>>>>> >>>>>>> I was converting a surface label from 'fsaverage' space to >>>>>>> individual >>>>>>> subjects and got this error: >>>>>>> >>>>>>> ###---------------------### >>>>>>> Performing mapping from target back to the source label >>>>>>> ERROR: srcvtxno = -1 < 0 >>>>>>> trgvtxno = 140122, dmin = 1000 >>>>>>> trgregxyz = 0, 0, 0 >>>>>>> This means that a vertex in the target surface could >>>>>>> not be mapped to a vertex in the source surface >>>>>>> because the xyz of the target is outside of the >>>>>>> range of the hash table >>>>>>> ###---------------------### >>>>>>> >>>>>>> The command I used was: >>>>>>> mri_label2label --srclabel $fsaverage_brain_label --trg >>>>>>> $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj >>>>>>> --regmethod surface --hemi $hemi >>>>>>> >>>>>>> It's worth noting that this subject is from a patient population >>>>>>> with >>>>>>> lesion and we had to manually edit the white matter and re-run >>>>>>> autorecon. >>>>>>> This error only happens for one hemisphere of this patient, the >>>>>>> other >>>>>>> hemi >>>>>>> is fine. >>>>>>> >>>>>>> Did anyone have this problem before or know how to resolve this? >>>>>>> Thank >>>>>>> you. >>>>>>> >>>>>>> BTW. I found this >>>>>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html >>>>>>> in the archive but it was never followed up. >>>>>>> >>>>>>> >>>>>>> >>>>>>> Lingqiang >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> gr...@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> >>>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > > > _______________________________________________ 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.
