Thanks Marc,
I will go with img2imgcoord. It seems like the easiest option given the many complexities with orientation problems in nifti files.
Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash)
Research Officer
Developmental and Functional Brain Imaging, Critical Care and Neurosciences
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road Parkville Victoria 3052 Australia
T 9345 4306
M XXXX XXX XXX
E [log in to unmask]
www.mcri.edu.au
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
Sent: Fri 18/02/2011 5:57 PM
To: [log in to unmask]
Subject: Re: [FSL] FLIRT coordinate transformation to tracts
Dear Chris,
The tool img2imgcoord has been created precisely to allow you to
map coordinates between images, so I recommend using that.
If you really want to be able to do it yourself there have been
several past emails on the list describing how the FLIRT coordinates
work, although it isn't the easiest option.
All the best,
Mark
On 18 Feb 2011, at 22:27, Chris Adamson wrote:
> hello everyone,
>
> Sorry if this has been posted before.
>
> I have some tracts that I created using a DWI processing program (mrtrix) and I want to register these to a T1 anatomical image.
>
> I have managed to get the tract coordinates into voxel coordinates in terms of the DWI image and I have also performed a dimension swapping step (since the T1 image was in a different orientation to the DWI image).
> I have registered the B=0 image to the T1 image and have a flirt transformation matrix.
>
> My question is: what sequence of transformations do I need to apply my coordinates, which I have in voxel coordinates (so x = i, y = j, z = k) in my original image to get to the registered image?
>
> Thus far I have tried:
>
> let S be the original coordinate and T be the transformed
>
> T = multiply S by the pixel dimensions in original image
> T = qform of original * T
> T = FLIRTMatrix * T
> T = inv(qform of target) * T
> T = divide S by the pixel dimensions in target image
>
> But this did not work.
>
> Any help greatly appreciated.
>
>
> Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash)
> Research Officer
> Developmental and Functional Brain Imaging, Critical Care and Neurosciences
>
> Murdoch Childrens Research Institute
> The Royal Children's Hospital
> Flemington Road Parkville Victoria 3052 Australia
> T 9345 4306
> M XXXX XXX XXX
> E [log in to unmask]
> www.mcri.edu.au
>
>
>
>
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