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/ >>> >>> >>> >> >> >> > > > -- 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. 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.
