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.
