Hello,
on behalf of a collegue who has not yet registered for the freesurfer
mailing list I want to send you the questions below.
Thanks for your help
Claus
-----------------------------------------------------------------------
Hi,
we are currently trying to spatially transform functional data into the
anatomical 256*256*256 1mm isovoxel COR-anatomy.
We already have a register.dat and therefore a rotation-translation matrix.
Our functional data are in a 128*128*24 bshorts file (1.406*1.406*2mm voxels).
Slice orientation is approximately orthogonal to the calcarine sulcus
Our problem is that the functional data do not fall on the correct location in
the anatomical volume.
Our approach so far is:
We built a datacube from the anatomical COR* files and oriented it with respect
to the RAS system so that:
R corresponds to -X (the inverted first coordinate direction in our data cube)
A corresponds to Y
S corresponds to Z
From the functional data (in bshort format) we reconstruct a similar volume and
orient it the same way.
We assume the origin of the two coordinate system (the anatomical and the
functional) in the center voxel of the two volumes
Whe now calculate [xAnat, yAnat, zAnat,1]'=[4*4-matrix from
register.dat]*[xFunctional, yFunctional, zFunctional,1]'
The x*, y* and z*s are in millimeters.
An example: we choose the voxel in the center of gravity of the functional
volume [0,0,0,1]' and multiply it at the right of the matrix in register.dat.
Shouldn't this give us the location of that voxel in the anatomical volume ?
Our qusestions:
Can the register.dat be used to transform the functional data onto the
COR-anatomy ?
If yes how ?
How does the coordinate system look like in both volumes especially the
functional?
The *.bhdr file related to the functional bshorts contains RAS-coordinates of
the corners of the (first ?) slice. What is the corresponding coordinate system
? Scanner, COR-anatomy ...?
We already checked the wiki-site that describes the coordinate systems and
transforms but this did not solve our problem.
Thank you very much for your help.
PS. The 4*4 transformation matrix we are using:
1.081372e+00 5.667235e-02 0.000000e+00 8.327621e+00
3.764737e-02 -7.183544e-01 -6.946586e-01 -6.509724e+01
3.635561e-02 -6.937064e-01 7.193404e-01 -4.349084e+01
0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
