Dear Xiaowei,

I'm not familiar with MPS or LHP, but will briefly describe the coordinate
system used by FLIRT and MCFLIRT.  I suggest that you only ever
work with matrices and never the parameters (rotations, translations)
as these are *much* harder to work out, and you can always get
the matrices too.

The matrices map between coordinates in a mm coordinate space.
They are related to the nifti coordinates as follows:
 - if the qform or sform (whichever has a non-zero code) has a
       negative determinant then:
               - x, y, z mm coordinates are just the voxel coordinates
                 multiplied by the voxel sizes (in mm)
 - if the qform or sform has a positive determinant, then it is the
       same as above *except* that the x-axis is reversed
       (that is, if there were 64 voxels, then voxel number 0 would
       become number 63 and vice-versa, 1 would become 62, etc)
 - note that the qform and sform relate to each image, so you may
       need to reverse either the initial or final x (voxel) coordinates

The bvecs are in the same space as the mm coordinates, as all
FSL programs will do the above swapping in x when they read in
images.

All the best,
       Mark

On 26 Aug 2010, at 20:52, vivian wrote:

Hi all,

Sorry that I didn't specify the coordinates I mostly concerned. The main coordinate system we are using now is XYZ, MPS, or LHP. It would be truely helpful if the answer is related to these three systems.

Thank you again



On Thu, Aug 26, 2010 at 2:03 PM, Xiaowei Zou <[log in to unmask]> wrote:
Greetings,

I'm a new researcher in DTI field and my project needs to match the estimated motion parameter  (6-DOF: x,y,z,roll,yaw,pitch) to the real motion in XYZ coordinate of scanner. I've read the lecture about FLIRT but still it didn't solve my questions. I'd be very gratful if someone could help me out.

1, What's the coordinate system in which the estimated 6-DOF motion parameter defined?

The lecture mentioned voxel space coordinate which can make the problem become a pure 3D matrix. However, it requires voxel size so I think it might jump between voxel space coordinate and standard space coordinate.

2, How does this coordinate system related to the input NFITI 3D data?

In either coordinate system I found in the lecture, the definition of coordinate is corelated to the image data coordinate. For example, the voxel space coordinate defines origin at lower-left corner. Then what's the lower-left cornner in the NIFTI 3D data? Is that the same lower-left corner if I read the 3D NFITI by spm_read_vols?

3, This is a little bit extension about FDT. What's the assumption of coordinate of the input bvecs? Is it XYZ ?


FSL does a wonderful job about fiber tracking so I believe there must be some understandable transformation from real world to estimated motion parameters.

Thank you veryone who read this message. Any help from you is highly appreciated.

Best regards,

Xiaowei Zou







--
Xiaowei.Zou

Department of Biomedical Engineering
Columbia University
New York, NY, 10027
Cell: 203-506-6130