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/ > > > -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/ _______________________________________________ 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. 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