Hi David,

I use both the MINC world and the freesurfer world.

One thing which may be of use to you or others, is to get from the surface co-ordinates, back to world-coordinates (or "scanner RAS"), so that minc tools etc. display things properly. To do this, you need to apply a simple translation.

ie. for native.mnc which was your input into freesurfer do this command: mri_info --cras native.mnc my output was -2.35588 52.7907 24.8145

Then you can create the following transformation matrix: 1 0 0 -2.35588 0 1 0 52.7907 0 0 0 24.8145 0 0 0 1

If you then convert your surfaces to ascii: mris_convert lh.pial lh.pial.asc

You can then transform each co-ordinate point in lh.pial.asc with the above transformation matrix and then your surfaces will be in MNI world co-cordinates. (these are referred to as "scanner RAS" on the freesurfer wiki coordinate page).

From there, if you have a transformation that already maps your

subject to mni152, then you can apply that transformation.

I think annother way, would be to use the information provided in: $FREESURFER_HOME/average/mni152.register.dat. I'm assuming lines 5-9 of that file are a transformation that will move you from mni152 space to fsaverage (avg305) space. (though im not sure if that is moving you from a SurfaceRAS to SurfaceRAS space or just from RAS to RAS or what?) If FreeSurfer calculates the transformation matrix required to get from your subject space(native, or RAS, or SurfaceRAS) to fsaverage (RAS or SurfaceRAS) space, then you could probably combine those transformations to get what you want. Unfortunately, I don't have a good enough grasp of the coordinate system yet to guide you through this process. Perhaps Doug can guide me in the right direction?

If you are interested in any of the other things, feel free to contact me as I have some tools to convert FreeSurfer outputs to MINC outputs (.mnc, .obj).

hope that helps, mishkin

On Mon, Apr 14, 2008 at 11:52 AM, Doug Greve greve@nmr.mgh.harvard.edu wrote:

Rather than creating a subject in mni152 space, you can map your 152 data to our fsaverage (mni305) with $FREESURFER_HOME/average/mni152.register.dat, eg

tkmedit fsaverage T1.mgz -overlay yourstats152.nii \ -overlay-reg $FREESURFER_HOME/average/mni152.register.dat

or

tksurfer fsaverage lh inflated -overlay yourstats152.nii \ -overlay-reg $FREESURFER_HOME/average/mni152.register.dat

doug

Stark, David Ernest wrote:

Hi all,

I am new to Freesurfer and would like to generate a cortical (pial) surface of 1 subject's brain, but I need the surface in MNI 152 space (this is for display purposes, so that I can overlay clusters already in MNI space). What is the best way to accomplish this? I already have the subject's freesurfed output (if any of those files can be of use). Also, if a pial surface already exists for one of the standard brains out there, that would also be of use.

Thanks! David ________________________________

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