Dear Bruce thank you for the quick answer. I saved the vox2ras matrix by assigning to it the voxel to millimiters transformation matrix the nifti converter read from dicom data (Siemens Magnetom Trio, 3T, sequence: standard mprage T1 't1_mprage_sag_std'). The tessellated mesh is saved in the millimiters space too (which means i applied the homogeneous transformation of voxel coordinates into millimiters) and in the millimiters space the volume and the mesh coincide. Actually the volume has been acquired as a 256X256X192 cube, and this could also cause a problem. I know realize that the volume has to be saved in RAS convention in order to be read in FreeSurfer correctly, about which i did not bother enough because the original voxel to nifti conversion matrix seems to have positioned the volume already in a convenient position. This is at least what i see when i visualized the so saved volume with tkmedit (coronal/sagittal/etc. are correctly positioned).
Is everything clear about what i did? I though that since the two coordinate systems are the same they could be handled similarly in FS. How should i act on the surface in order to align it to the volume? If i would apply a topology fix on the mesh i will need the information about the white matter too, also saved in the same nifti format. In order to use this routine, do i also have to convert the volume in the proper RAS format or is it sufficient that volume and surface coincide in tkmedit visualization? (that was my intuitive criterion).
About Freesurfer documentation that is what i found so far: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?highlight=%28vox2... Do you have other suggestions? There is a disclaimer on the documentation wiki.
Sorry for the long email and i hope to hear from you soon. Happy Christmas!
Cristiano
----- "Bruce Fischl" fischl@nmr.mgh.harvard.edu schreef:
Van: "Bruce Fischl" fischl@nmr.mgh.harvard.edu Aan: "C. Micheli" c.micheli@fcdonders.ru.nl Cc: freesurfer@nmr.mgh.harvard.edu Verzonden: Woensdag 22 december 2010 15:26:37 Onderwerp: Re: [Freesurfer] volume - surface shift in tkmedit
Where did you get the vox2ras matrix that save_mgh takes? And what space are the surface fiords in? There is extensive documentation on our wiki fir the various coordinate systems we use Cheers Bruce
On Dec 21, 2010, at 8:06 PM, "Micheli, C." c.micheli@fcdonders.ru.nl wrote:
Dear all I would like to write an MRI anatomical volume and a surface in
freesurfer format.
The surface is correspondent to the white matter tessellation, while
the volume represents T1 anatomical slices, both obtained from softwares external to FreeSurfer.
Using the two functions save_mgh.m and write_surf.m from the
freesurfer matlab interface files I am able to write the variables in the proper freesurfer folders.
In the original nifti format volume and surface match both in voxel
space and in millimiters space, but as soon as i visualize them in tkmedit the surface is shifted. Any clue why this happens? Is there any matrix that automatically translates the surface coordinates when it is read in tkmedit?
I hope to get your feedback soon
Best regards Cristiano
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Micheli, C.