What if you specify the output of surf2surf to be a gii file?
On 9/2/13 6:47 AM, Franz Liem wrote: > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
