Well, if the volumes do not line up, then you're register.dat is wrong.
Use tkregister2 to register the original functinoal to the anatomical
(use the --regheader the first time), then use mri_vol2vol to resample
the functional into anat space (make sure to use the --invxfm flag with
vol2vol).
doug
Claus Tempelmann wrote:
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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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