You'll need to do this in steps.
1. Create a registration matrix R between your axial and conformed data: tkregister2 --mov axial.nii --targ orig.mgz --regheader --reg axial.reg.dat --noedit --s subjectname
2. Get the tkreg vox2ras matrix T from your axial: mri_info --vox2ras axial.nii
3. Compute a new matrix M = inv(T)*R. Put it into a file with the same format as axial.reg.dat (call it axia.crs.reg.dat). Just replace the 4x4 matrix.
4. Convert the surfaces with mri_surf2surf, something like
mri_surf2surf ---hemi --subject subjectname --sval-xyz lh.white --reg axial.crs.reg.dat --tval lh.white.axial.crs --tval-xyz
doug
Navid Shiee wrote:
Hi,
I need coordinates in col-row-slice space of my axial data. The reason for this is that I have manually picked landmarks on the cortex in the axial data space and I want to compute landmark errors for the generated surface. I work with vtk files. I think after all it is a simple scale+translation of coordinates, but not sure if freesurfer provides such a tool.
I know "mri_label2vol" does this for segmentation image. Is there an equivalent command for surfaces?
Thanks a lot for your help.
On Wed, Aug 31, 2011 at 12:03 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Navid, it is still not clear what you want. Each surface coordinate has an xyz. This space that this xyz is in is a peculiar space defined by FS. You want to use a different xyz space. It could be scanner space. It could be col-row-slice of your axial data. Or is it that you just want to visualize the surfaces on the axial. In that case, you'll have to indicate what tool you are going to use (you cannot use tkmedit for this -- it will just conform it to 256^3). doug Navid Shiee wrote: Hi, Thanks for your reply. I make an examaple to clarify myself. I have a 256x256x128 axial image which has 0.83^3 resolution. I am intrested in generating the cortical surfaces and overlay it on this image. Freesurfer first converts this image to 256^3 voxels and 1^3 resolution and then generates the surfaces. Thus if I want to intersect freesurfer surfaces with my axial data, I can not because surface is in a different space. Is there a way to transform the freesurfer surfaces to 256x256x256 axial space? Thanks a lot for your help. Navid / Connected by MOTOBLUR™ on T-Mobile / -----Original message----- *From: *Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>* To: *Navid Shiee <navid@jhu.edu <mailto:navid@jhu.edu>>* Cc: *freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>* Sent: *Tue, Aug 30, 2011 20:13:09 GMT+00:00* Subject: *Re: [Freesurfer] Freesurfer surfaces in the original space Hi Navid, what do you mean by "the original image space"? Ie, what coordinates do you specifically want? Voxel? Scanner? doug Navid Shiee wrote: > Dear Freesurfer team, > > I have a question regarding Freesurfer surfaces. I submitted this > questions to the wiki but did not get any response and I was wondering > if you can help me on this issue. > I am doing some experiments with Freesurfer and would like to have > surfaces in the original image space. FS converts everything to 1mm^3 > 256x256x256 grid in the coronal space. I have axial images which does > not have homogenous grid (although it has isotropic resolution). I > know there is a command to convert the volumetric structural > segmentation into the original space but could not find the command > for surfaces. I would be very grateful if you can provide me with some > information for doing this. > > I appreciate your kind help in advance. > > Regards, > > -- > Navid Shiee > Ph.D. Candidate > Laboratory of MEDical Image Computing (MEDIC) > Image Analysis and Communication Laboratory (IACL) > Johns Hopkins University > ------------------------------------------------------------------------ > > _______________________________________________ > 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> 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. -- 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>-- Navid