Hi again I've finally found the exact transformation which is ... gather from the original nifti the qfrom matrix (say Qf) and then collect with mri_info vox2ras-tkr orig.mgz , the transformation matrix (say T) to map ras to index in the freesurfer space. I've finally matched the points.

Why mri_info -vox2ras 001.mgz is different (signs mismatch and also qoffset values are different) from the original qform matrix ... they do not suppose, as U have said, to share the same space?

Thanks for any support and for your hints.

g.

2011/1/21 Douglas Greve <greve@nmr.mgh.harvard.edu>
yes, 001.mgz and the DICOM share the same space.

doug


On 1/21/11 9:08 AM, Gabriele Arnulfo wrote:
Hi all,

MRI, in this context, i was considering the original DICOM T1 MRI space before the conversion to 001.mgz file. Is your suggestion still the right way to solve my task?



2011/1/20 Douglas N Greve <greve@nmr.mgh.harvard.edu>

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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In a world without wall, how needs WINDOWS??



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