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 greve@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 greve@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