glad to hear it Bruce On Wed, 24 Jul 2013, Lingqiang Kong wrote: > Running autorecon3 fixed the mri_label2label conversion problem. > > Thank you everyone! > > L >> 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
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