I don't know of another way to map control points. By MRI space I assume that you mean the scanner RAS space? Eg, the space defined by the nifti qform? I think this matrix will be

L = inv(T)*Q

where Q is the scanner vox2ras of the orig volume and T is the tkregister vox2ras of the orig volume. You can get both of these matrices using mri_info.

doug

Martin Reuter wrote:

Hi Gabriele,

not sure if there is an easy way (probably Doug knows). But if there isn't, I wrote a tool mri_map_cpdat to map control points from one space to another. A control points dat file is a txt file containing coordinates. The tool will be available in 5.1 where it is used to transfer manual edits in the longitudinal stream. I could send a copy of it before. So you can:

• create a control.dat file with your coordinates
• map it using a lta file.

I am not sure how you can get the lta that you need (from native to freesurfer conform space) but probably someone else can help with that. This probably has been discussed before.

Here is the format of the control.dat:

xcoord1 ycoord1 zcoord2 xcoord2 ycoord2 zcoord2 xcoord3 ycoord3 zcoord3 info numpoints 3 useRealRAS 0

So instead of the coords put your numbers, of course you can have more than three points.

Best, Martin

On Thu, 2011-01-20 at 17:26 +0200, Gabriele Arnulfo wrote:

...

Hi all,

I'm a new freesurfer user and I've a small question for you all. Which the faster and reliable way to map a list of points into the freesurfer geometrical space?

I've already read the pdf/ppt but there's no suggestion in there about which command should be used (if any). I've read about matlab tools that could be used for this purpose is it right?

My task is really simple but i cannot figure out which is the best way. I've got a list of points (basically intra-cerebral electrodes coordinates segmented from MRI) in the MRI space and I'd like to calculate the respective points in the freesurfer space.

Cheers,

gabriele

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