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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