Re: [Freesurfer] normal vector in gm
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.
Re: [Freesurfer] normal vector in gm
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.
Re: [Freesurfer] normal vector in gm
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 ___ 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.
Re: [Freesurfer] normal vector in gm
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 ___ 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.
Re: [Freesurfer] normal vector in gm
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 ___ 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] normal vector in gm
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 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.
