Hi Doug, this gives exactly the same surface as surf2surf followed by mris_convert (i.e. with offset).
Thanks, Franz Am 02.09.2013 um 16:50 schrieb Douglas Greve: > > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
