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 greve@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

slew@nmr.mgh.harvard.edu

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 greve@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

slew@nmr.mgh.harvard.edu

-- 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: 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

slew@nmr.mgh.harvard.edu