Dear freesurfers I used bbregister to coregister diffusion images with anatomical. I would like to apply the bbregistration transformation to the white and pial surfaces What I've done is: I calculated new transformation matrix using fs_read_dat.m and then apply it to the surfaces with mri_surf2surf. When overlaying the new surface on the diffusion data- it seems that the transformation is inaccurate.(screenshot is attached) Any idea why?.
Thanks, Shani
Hi Shani, what is fs_read_dat.m? I've never seen it before. Why do you need to transform the surface? What are you using to create the display below (ie, command line)? doug
On 01/31/2013 10:53 AM, Shani Ben Amitay wrote:
Dear freesurfers I used bbregister to coregister diffusion images with anatomical. I would like to apply the bbregistration transformation to the white and pial surfaces What I've done is: I calculated new transformation matrix using fs_read_dat.m and then apply it to the surfaces with mri_surf2surf. When overlaying the new surface on the diffusion data- it seems that the transformation is inaccurate.(screenshot is attached) Any idea why?.
Thanks, Shani
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Hi Doug
I'm sorry it's fs_read_regdat.m a matlab script I found in the mail archive which converts the register.dat file into ras2ras transformation matrix.I want to use thess surfaces to extract vector normals in the diffusion space. Hope it's clear now Thanks! Shani
On Thu, Jan 31, 2013 at 10:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Shani, what is fs_read_dat.m? I've never seen it before. Why do you need to transform the surface? What are you using to create the display below (ie, command line)? doug
On 01/31/2013 10:53 AM, Shani Ben Amitay wrote:
Dear freesurfers I used bbregister to coregister diffusion images with anatomical. I would like to apply the bbregistration transformation to the white and pial surfaces What I've done is: I calculated new transformation matrix using fs_read_dat.m and then apply it to the surfaces with mri_surf2surf. When overlaying the new surface on the diffusion data- it seems that the transformation is inaccurate.(screenshot is attached) Any idea why?.
Thanks, Shani
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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Hi Shani, I don't know anything about that program and can't vouch for it (which probably means that I wrote it:). Anyway, the way that I would do it would be to compute a new matrix: K = M*inv(T)*R where R is the register.dat and T is the vox2tkrRAS and M is the vox2scannerRAS of the DTI. These can be gotten using mri_info --vox2ras dti.nii mri_info --vox2ras-tkr dti.nii Create a new registration file same format as register.dat but with K instead of R Run something like:
mri_surf2surf --reg newreg.dat dti.nii --sval-xyz white --hemi lh --tval lh.white.dti --tval-xyz
doug
On 02/01/2013 12:35 PM, Shani Ben Amitay wrote:
Hi Doug
I'm sorry it's fs_read_regdat.m a matlab script I found in the mail archive which converts the register.dat file into ras2ras transformation matrix.I want to use thess surfaces to extract vector normals in the diffusion space. Hope it's clear now Thanks! Shani
On Thu, Jan 31, 2013 at 10:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Shani, what is fs_read_dat.m? I've never seen it before. Why do you need to transform the surface? What are you using to create the display below (ie, command line)? doug On 01/31/2013 10:53 AM, Shani Ben Amitay wrote: > Dear freesurfers > I used bbregister to coregister diffusion images with anatomical. > I would like to apply the bbregistration transformation to the white > and pial surfaces > What I've done is: > I calculated new transformation matrix using fs_read_dat.m and then > apply it to the surfaces with mri_surf2surf. > When overlaying the new surface on the diffusion data- it seems that > the transformation is inaccurate.(screenshot is attached) > Any idea why?. > > Thanks, Shani > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Hi Doug
I've tried it and the surface is still not aligned with the diffusion image. The visualization is done using FREEVIEW.
Thanks again! Shani
On Fri, Feb 1, 2013 at 9:19 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Shani, I don't know anything about that program and can't vouch for it (which probably means that I wrote it:). Anyway, the way that I would do it would be to compute a new matrix: K = M*inv(T)*R where R is the register.dat and T is the vox2tkrRAS and M is the vox2scannerRAS of the DTI. These can be gotten using mri_info --vox2ras dti.nii mri_info --vox2ras-tkr dti.nii Create a new registration file same format as register.dat but with K instead of R Run something like:
mri_surf2surf --reg newreg.dat dti.nii --sval-xyz white --hemi lh --tval lh.white.dti --tval-xyz
doug
On 02/01/2013 12:35 PM, Shani Ben Amitay wrote:
Hi Doug
I'm sorry it's fs_read_regdat.m a matlab script I found in the mail archive which converts the register.dat file into ras2ras transformation matrix.I want to use thess surfaces to extract vector normals in the diffusion space. Hope it's clear now Thanks! Shani
On Thu, Jan 31, 2013 at 10:33 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
Hi Shani, what is fs_read_dat.m? I've never seen it before. Why do you need to transform the surface? What are you using to create the display below (ie, command line)? doug On 01/31/2013 10:53 AM, Shani Ben Amitay wrote: > Dear freesurfers > I used bbregister to coregister diffusion images with anatomical. > I would like to apply the bbregistration transformation to the white > and pial surfaces > What I've done is: > I calculated new transformation matrix using fs_read_dat.m and then > apply it to the surfaces with mri_surf2surf. > When overlaying the new surface on the diffusion data- it seems that > the transformation is inaccurate.(screenshot is attached) > Any idea why?. > > Thanks, Shani > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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