Hi,
Our experience is that this is really tricky.
The coordinate systems used by the scanner console or dicom can
be different from what ends up embedded in the nifti image (including
the info in the qform/sform). If you are lucky then you can just apply
the inverse of the qform (or sform) matrix to your coordinates and
it will give you the nifti voxel coordinates. When we tried this recently,
however, we also needed to swap some axes to make it work as the
reported coordinates (for a spectroscopy voxel in our case) did not
match any of the existing coordinate systems but was a whole new
one again. So you'll just have to proceed with trial and error and
see if you can get it to work. Unfortunately, this is the problem with
the scanners and dicoms not having a single, unified coordinate
system.
All the best,
Mark
On 11 Dec 2010, at 03:18, Alex Ramos wrote:
> Hello all,
>
> When the MRI is acquired, the scanner is set to map out a fixed rectangular ROI. Using a dicom viewer the MRI scan and the predetermined rectangular ROI can be seen. The dicom viewer allows us to record the corner coordinates of the ROI in an LPS coordinate system.
>
> We convert the dicom images to nifti using dcm2nii to view them in the FSLviewer. We are hoping to use fslroi to extract the rectangular ROI from the image to do further manipulations with other fsl tools.
>
> We have tried things with fslorient and fslswapdim, but we cannot seem make the X,Y,Z coordinate space or scanner anatomical values match LPS coords. I have read much of the information from http://www.fmrib.ox.ac.uk/fsl/avwutils/index.html and understand that there is probably a rotation matrix that is available for converting from LPS coords to FSLviewer coords, but I am at a loss.
>
> Any comments will be greatly appreciated - Thank you,
> Alex
>
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