[Freesurfer] normal vector projection
Hi, After freesurfer reconstruction, I tried to project surface normal vectors on the ribbon. I used the following scripts, but the projected vectors were out of the ribbon when I visualized it freeview. The vectors were placed outside of the ribbon. Anyone knows any idea ? fslregister --mov mri/orig.mgz --s xDS --reg rrr.dat --dof 12 --tmp ./tmp/ mri_surf2surf --s xDS --hemi lh --sval-nxyz pial --tval ./pl_100.mgz mri_surf2vol --surfval pl_100.mgz --hemi lh --surf pial --volreg rrr.dat --outvol pln_pribbon.mgz --fillribbon --template mri/orig.mgz Thank in advance, 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
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
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.
[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.
[Freesurfer] transform to original mri
Dear all, I am trying to transform the reconstructed surface like rh.pial into the original mri's (like 001.mgz) coordinate. I found some matrices in the ./transform directory, but not sure of which one (or a set of matrices) would do the transform? Seok 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.
[Freesurfer] MRIread and MRIwrite
Hi, I am using matlab functions of MRIread and MRIwrite for a MRI correction. When running mri_normalize with the corrected MRI, I came up with the error like 'unsupported src format 3'. For a debug, I simply MRIread a mri and MRIwrite the mri without anything done, but had the same src format error. Anyone know what went wrong ? Thanks, 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.
