Thank you ! I successfully projected the pial surface normals in the volume. Now I wanted to project the normals in the inner gm boundary voxels (i.e. gm boundary voxels with wm). What I tried is scaling up the wm surface by
mris_convert -s 1.01 lh.white lh.white101 and then projected the normals on the volume by mri_surf2surf -- hemi lh --sval-nxyz white101 --tval wn101.mgz mri_surf2vol --surfval wn101.mgz --hemi lh --surf white101 --volreg reg2ana.dat --template vol.mgz --outvol wn101_b.mgz However, the projection seemed not in the scaled-up layers, but in the original wm layers. The scaling seemed not effective. Would you have any ideas what could project normals in the gm boundary voxels with wm? Eventually what I wanted to do is assign normal vectors in all gm voxels somehow. Thanks, Seok On Mar 9, 2011, at 5:44 PM, Douglas N Greve wrote: > That is the file created by registering your orig.mgz to the mni152 > brain (assuming you are using the 152). You can create this > registration file with the mni152reg script. > > doug > > Seok Lew wrote: >> Thanks, first of all. >> >> I tried with the following scripts, but ended up with an error. I >> am not sure which format or file is required for the --volreg. >> >> # >> mri_surf2surf --s FS --hemi lh --sval-nxyz pial --tval ./ttt.mgz >> # >> mri_surf2vol --surfval ttt.mgz --hemi lh --volreg mri/transforms/ >> talairach.xfm --outvol ooo.mgz --template mri/T1.mgz >> >> gdiagno = -1 >> regio_read_register(): No such file or directory >> Error reading inplaneres from mri/transforms/talairach.xfm >> >> Thanks, >> Seok >> >> On Mar 9, 2011, at 2:00 PM, Douglas N Greve wrote: >> >>> Try using mri_surf2surf with the --sval-nxyz. The output have 3- >>> frame, one for each component in the normal. Then use mri_surf2vol >>> to stuff this back into a volume. >>> >>> doug >>> >>> Seok Lew wrote: >>>> Hello users, >>>> >>>> My colleagues and I are trying to create a gray matter electric >>>> conduction model where a preferable conduction direction is >>>> aligned with the normal direction induced from the pial and >>>> white surface normals. >>>> >>>> Freesurfer reconstruction already gives pial and white matter >>>> surface normals and correspondences between them. Now I want to >>>> have the freesurfer surface normals projected on the mri volumes >>>> and interpolated for gray matter voxels (regions between the >>>> pial surface and the white surface), such that each voxel of >>>> gray matter can have a normal direction. >>>> >>>> Is it possible to do the job with freesurfer scripts ? If so, >>>> what scripts might work for this? >>>> >>>> Thanks in advance, >>>> >>>> Seok >>>> _______________________________________________ >>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >> >> Seok Lew, Ph.D. >> MEG Core Laboratory >> Athinoula A. Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> Harvard Medical School >> >> s...@nmr.mgh.harvard.edu >> >> >> >> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School s...@nmr.mgh.harvard.edu _______________________________________________ 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.
