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
