Can I transform a surface-based volume back into its corresponding surface rendering using the transformation matrix used to create the surface-based volume to begin with? I'm using Freesurfer to register individual statistics generated by FSL onto the surface-map of an average brain, and then transforming these maps into mni305.cor.mgz space. At this point, I now have individual statistical surface maps in MNI space that have the benefit of Freesurfer's surface-based registration. From these MNI maps, I conducted a group analysis with FSL, resulting in a group zstat map I would like to transform back onto the average brain surface-map that I initially used to register the individuals.
So basically, I need help transforming a volume in mni305.cor.gz space back onto its surface-based map. I was thinking of running mri_vol2surf, but I would need a register.dat file that contained the exact inverse parameters to go from surf->mni305. I could use tkregister2 to create a serviceable register.dat, but I'm certain that a perfect transformation is necessary for these surface-mapped volumes.
How would I create this register.dat from mni305->surf, or is there a more direct way to accomplish this?
Thanks, Eric
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
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If you just want to view it on the surface, you can just
tksurfer fsaverage lh inlfated -overlay stats-on-mni305.nii
You can also use an average that you have created (either way, they will be in mni305 coords). If you want an actual surface file, then you can
mri_vol2surf --mov stats-on-mni305.nii --hemi lh --regheader fsaverage --o lh.stats-on-mni305.mgz
doug
Eric Moulton wrote:
Can I transform a surface-based volume back into its corresponding surface rendering using the transformation matrix used to create the surface-based volume to begin with? I'm using Freesurfer to register individual statistics generated by FSL onto the surface-map of an average brain, and then transforming these maps into mni305.cor.mgz space. At this point, I now have individual statistical surface maps in MNI space that have the benefit of Freesurfer's surface-based registration. From these MNI maps, I conducted a group analysis with FSL, resulting in a group zstat map I would like to transform back onto the average brain surface-map that I initially used to register the individuals.
So basically, I need help transforming a volume in mni305.cor.gz space back onto its surface-based map. I was thinking of running mri_vol2surf, but I would need a register.dat file that contained the exact inverse parameters to go from surf->mni305. I could use tkregister2 to create a serviceable register.dat, but I'm certain that a perfect transformation is necessary for these surface-mapped volumes.
How would I create this register.dat from mni305->surf, or is there a more direct way to accomplish this?
Thanks, Eric
Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772
Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Eric Moulton