Hi Seok, Try using "--projfac .01" in the surf2vol command. doug Seok Lew wrote: > 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 > > > > >
-- 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 _______________________________________________ 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.
