I always wondered what is the 5th column for? Anyway seems to me it is working. I need to do more checking but this is what I did and what I got.
Source Label: #!ascii label , from subject FreeSurferClean vox2ras=TkReg 5 129756 -13.048 63.016 -1.943 1 129757 -13.268 63.132 -1.961 2 129767 -13.120 63.091 -2.173 3 129768 -13.470 63.274 -2.293 4 129870 -7.339 63.337 5.869 5 Mapped Label: #!ascii label , from subject FreeSurferClean2 vox2ras=TkReg 5 132988 -7.268 83.361 -2.195 1.0000000000 132714 -7.766 83.079 -2.603 4.0000000000 132259 -4.885 81.451 7.416 5.0000000000 132697 -7.822 82.960 -1.894 2.0000000000 133003 -6.776 83.765 -2.841 3.0000000000 Seems like when I do one by one I get the same vertex as well. Do you think this is correct? I’m running these without —norevmap and —nohash option, is that correct? Best -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razli...@gmail.com<mailto:razli...@gmail.com> Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/ On Nov 10, 2015, at 2:39 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>> wrote: You can try adding a number in the statistic field (the 5th column) On 11/10/2015 02:24 PM, Razlighi, Qolamreza R. wrote: Thanks Doug, Now with —norevmap option gives 191 vertices. See below. I’m completely confused here. I have 217 vertices that I want to map them into a another subject surface. I have no problem if multiple vertices are mapping into one vertex or one vertex in source surface maps onto multiple vertices on the target surface but there should a correspondence between these two files. Is there any way we can output that correspond ace? For example I know vertex "129756 -13.048 63.016 -1.943” maps into one or multiple vertices in the output vertices listed below, I just don’t know which one. Is there any way we can find the link between these two label files? Best #!ascii label , from subject FreeSurferClean2 vox2ras=TkReg 191 132988 -7.268 83.361 -2.195 0.0000000000 132714 -7.766 83.079 -2.603 0.0000000000 132259 -4.885 81.451 7.416 0.0000000000 132260 -5.354 81.986 6.795 0.0000000000 132609 -5.461 82.480 5.323 0.0000000000 132904 -5.190 83.525 4.692 0.0000000000 132903 -4.503 83.934 4.047 0.0000000000 133205 -3.592 84.944 3.299 0.0000000000 132913 -3.623 84.596 3.095 0.0000000000 133222 -6.863 84.768 1.300 0.0000000000 133223 -7.284 84.611 1.941 0.0000000000 133204 -3.445 84.969 2.831 0.0000000000 133211 -3.895 84.688 2.151 0.0000000000 133250 -6.409 84.885 -0.260 0.0000000000 133236 -6.568 84.963 0.611 0.0000000000 132934 -7.418 83.679 1.113 0.0000000000 133456 -3.481 85.560 2.366 0.0000000000 133470 -3.739 85.730 0.320 0.0000000000 -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razli...@gmail.com<mailto:razli...@gmail.com> <mailto:razli...@gmail.com> Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/ On Nov 10, 2015, at 2:07 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>> wrote: To get the same number of vertices, use --norevmap. I think it should give them to you in the same order, but I can't guarantee it. Try it on a few vertices in isolation to verify. On 11/10/2015 01:46 PM, Ray Razlighi wrote: Hi Guys, I'm trying to map the vertices of temporal pole in one subject into the space of another subject using mri_label2label. When I do it, the output doesn't have the same number of vertices and the other of the vertex are completely messed up. See below as the first few lines in the source and transferred labels along with the command execution. What I need to know is that where for example vertex number 129756 mapped to in the target surface space. I can't extract those information from these two files. Thanks a lot -------------------------------------------------------------------------------------------------------------------------------- Source Label file: aparc-lh-032.label #!ascii label , from subject FreeSurferClean vox2ras=TkReg 217 129756 -13.048 63.016 -1.943 0.0000000000 129757 -13.268 63.132 -1.961 0.0000000000 129767 -13.120 63.091 -2.173 0.0000000000 129768 -13.470 63.274 -2.293 0.0000000000 129870 -7.339 63.337 5.869 0.0000000000 129879 -7.347 63.505 5.024 0.0000000000 129888 -7.731 63.526 4.092 0.0000000000 129889 -8.111 63.407 3.205 0.0000000000 129893 -8.317 63.382 2.401 0.0000000000 129896 -7.864 64.313 1.332 0.0000000000 129897 -8.180 63.672 1.427 0.0000000000 129898 -12.359 64.295 1.105 0.0000000000 129899 -12.777 64.061 1.152 0.0000000000 129902 -7.780 64.251 0.861 0.0000000000 129903 -7.979 63.500 0.404 0.0000000000 129904 -11.492 64.276 0.155 0.0000000000 129905 -12.091 63.982 0.540 0.0000000000 129906 -13.264 63.628 0.557 0.0000000000 -------------------------------------------------------------------------------------------------------------------------------- Transfered Label file: aparc-lh-032-reg3.label #!ascii label , from subject FreeSurferClean2 vox2ras=TkReg 333 132988 -7.268 83.361 -2.195 0.0000000000 132714 -7.766 83.079 -2.603 0.0000000000 132259 -4.885 81.451 7.416 0.0000000000 132260 -5.354 81.986 6.795 0.0000000000 132609 -5.461 82.480 5.323 0.0000000000 132904 -5.190 83.525 4.692 0.0000000000 132903 -4.503 83.934 4.047 0.0000000000 133205 -3.592 84.944 3.299 0.0000000000 132913 -3.623 84.596 3.095 0.0000000000 133222 -6.863 84.768 1.300 0.0000000000 133223 -7.284 84.611 1.941 0.0000000000 133204 -3.445 84.969 2.831 0.0000000000 133211 -3.895 84.688 2.151 0.0000000000 133250 -6.409 84.885 -0.260 0.0000000000 133236 -6.568 84.963 0.611 0.0000000000 132934 -7.418 83.679 1.113 0.0000000000 133456 -3.481 85.560 2.366 0.0000000000 133470 -3.739 85.730 0.320 0.0000000000 -------------------------------------------------------------------------------------------------------------------------------- ray@athens-b8-e8-56-47-e6-54:~/Data/P00001613\> mri_label2label --srclabel FreeSurferClean/label/aparc-lh-032.label --srcsubject FreeSurferClean --trglabel FreeSurferClean2/label/aparc-lh-032-reg3.label --trgsubject FreeSurferClean2 --regmethod surface --hemi lh srclabel = FreeSurferClean/label/aparc-lh-032.label srcsubject = FreeSurferClean trgsubject = FreeSurferClean2 trglabel = FreeSurferClean2/label/aparc-lh-032-reg3.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Users/ray/Data/P00001613 FREESURFER_HOME /Applications/freesurfer Loading source label. Found 217 points in source label. Starting surface-based mapping Reading source registration /Users/ray/Data/P00001613/FreeSurferClean/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Users/ray/Data/P00001613/FreeSurferClean2/surf/lh.white Reading target registration /Users/ray/Data/P00001613/FreeSurferClean2/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 217 nlabel points Performing mapping from target back to the source label 134519 Number of reverse mapping hits = 142 Checking for and removing duplicates Writing label file FreeSurferClean2/label/aparc-lh-032-reg3.label 359 mri_label2label: Done ---------------------------------------------------------------------------------------------------------------------- -- Sincerely, Ray _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<http://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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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