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. ...
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