looks like it works. I don't think not hashing will have an effect (except to slow it down)
On 11/10/2015 02:49 PM, Razlighi, Qolamreza R. wrote: > 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. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu >>>> <mailto: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> >>>> <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><mailto: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. >>> >>> >>> >>> _______________________________________________ >>> 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 > > > > _______________________________________________ > 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
