Hi again, just a clarification. The two surfaces in the image are single subject surfaces (the original lh.white and the transformed lh.white.ico6), not fsaverage6 surfs. Best, Franz
Am 30.08.2013 um 09:51 schrieb Franz Liem: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
