This info is probably not stored in the gii header. I'll have to take a look which could take a while. Depending on what you are doing, it might not be important. doug
On 9/2/13 2:58 PM, Franz Liem wrote: > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
