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