Dear Doug, thank you so much, the fix works great. The problem now is that when I mris_convert the newly generated surface to .gii the volume geometry is lost again and the offset reintroduced. Is there a way to fix this? I have tried to give mri_surf2surf a register.dat that would correct for the c_ras offset, but that did not work.
Thanks, Franz Am 30.08.2013 um 17:41 schrieb Douglas N Greve: > > Sorry, I'm answering your emails in reverse order. Your command should > do what youwant once you use the new version below > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2surf.snowleopard > > note the --tval-xyz requires an argument (give it the orig.mgz) > > doug > > > On 08/30/2013 03:51 AM, Franz Liem wrote: >> Hi Doug, >> >> thanks a lot. >> I am using Darwin-snowleopard and centos6_x86_64. >> >> What I am trying to do is to use the white surface as seed for probtrackx. >> Therefore, I would like to reduce the number of vertices and at the same >> time bring the surfaces into a common space (so that vertex x is meaning the >> same thing in all subjects, while respecting the individual coordinates). I >> think my command did this but did not take the c_ras offset into account. >> Is there a better way to do this. >> >> Thank you very much, >> Franz >> >> Am 29.08.2013 um 20:54 schrieb Douglas N Greve: >> >>> Hi Franz, I just programmed a fix into mri_surf2surf. What platform do >>> you use? >>> >>> As for the shift, you would not expect them to line up. In fact, that >>> command line does not make a lot of sense. What it is doing is mapping >>> the xyz coordinates in the native space to a new tesselation. The xyz >>> coorindates don't change at all. It is surprising that they are as close >>> as they are. What are you trying to do? >>> >>> doug >>> >>> >>> On 08/29/2013 07:41 AM, Franz Liem wrote: >>>> Dear Freesurfers, >>>> >>>> sorry for the bump, but my message seems to have gone unnoticed. >>>> Thanks so much for any ideas. >>>> Franz >>>> >>>> Am 22.08.2013 um 13:37 schrieb Franz Liem: >>>> >>>>> Dear Freesurfers, >>>>> >>>>> I tried to map a single subject surface to fsaverageX (for the sake of >>>>> demonstration lets take fsaverage6). I did the following: >>>>> mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject >>>>> fsaverage6 --tval-xyz --tval ./lh.white.ico6 >>>>> This produces a surface that seems systematically shifted (see figure). >>>>> Also the newly generated surface does not contain valid geomery >>>>> information (see mris_info print of lh.white and lh.white.ico6). Is there >>>>> a way to fix this? >>>>> >>>>> Another question: is there a reason why mris_decimate is not included in >>>>> the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build >>>>> >>>>> Any help is very much appreciated. >>>>> Best, Franz >>>>> >>>>> >>>>> mris_info $s/surf/lh.white >>>>>> SURFACE INFO ======================================== >>>>>> type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE >>>>>> num vertices: 118611 >>>>>> num faces : 237218 >>>>>> num strips : 0 >>>>>> surface area: 77595.6 >>>>>> AvgVtxArea 0.654202 >>>>>> AvgVtxDist 0.885026 >>>>>> StdVtxDist 0.251941 >>>>>> ctr : (-33.3535, -11.9536, 42.7693) >>>>>> vertex locs : surfaceRAS >>>>>> talairch.xfm: >>>>>> 1.045 -0.093 -0.014 1.081; >>>>>> 0.099 1.095 0.070 -4.263; >>>>>> 0.010 -0.083 1.290 -41.092; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> surfaceRAS to talaraiched surfaceRAS: >>>>>> 1.045 -0.093 -0.014 1.177; >>>>>> 0.099 1.095 0.070 13.377; >>>>>> 0.010 -0.083 1.290 -49.756; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> talairached surfaceRAS to surfaceRAS: >>>>>> 0.949 0.081 0.006 -1.900; >>>>>> -0.085 0.902 -0.050 -14.449; >>>>>> -0.013 0.058 0.772 37.650; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> volume geometry: >>>>>> extent : (256, 256, 256) >>>>>> voxel : ( 1.0000, 1.0000, 1.0000) >>>>>> x_(ras) : (-1.0000, -0.0000, 0.0000) >>>>>> y_(ras) : (-0.0000, 0.0000, -1.0000) >>>>>> z_(ras) : ( 0.0000, 1.0000, -0.0000) >>>>>> c_(ras) : ( 0.0989, 0.9660, 0.9027) >>>>>> ... >>>>> >>>>> mris_info lh.white.ico6 >>>>>> SURFACE INFO ======================================== >>>>>> type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE >>>>>> num vertices: 40962 >>>>>> num faces : 81920 >>>>>> num strips : 0 >>>>>> surface area: 75477.4 >>>>>> AvgVtxArea 1.842620 >>>>>> AvgVtxDist 1.573724 >>>>>> StdVtxDist 0.523314 >>>>>> ctr : (-33.3983, -12.0872, 42.7743) >>>>>> vertex locs : surfaceRAS >>>>>> volume geometry info is either not contained or not valid. >>>>>> ... >>>>> <surfPics.png>_______________________________________________ >>>>> 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. >>>> _______________________________________________ >>>> 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 >> >> _______________________________________________ >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
