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
