I obtain this for sagittal data... while correct all the time (i.e. not
flipped) the the X,Y,Z labeling is strange. I just run the command:
fslswapdim input.nii.gz RL PA IS output.nii.gz
best regards,
Costin Tanase
On Mon, 2009-08-10 at 18:17 +0100, Silviu Podariu wrote:
> Hello,
>
> I have a set of DICOMs which I could not convert to anything useful with
> dcm2nii but which I did convert to NIFTI with SPM instead. However, they
> only look normal when opened in the SPM window, but they have a funny
> orientation when displayed in FSLview, MRIcron.
>
> I looked at the images and figured a "-90 deg roll" rotation in MRIcron
> would fix the image, orientation-wise, which it did, but there still remains
> the problem of the initially imported boundaries along the axes, which trim
> skull & brain a bit...
>
> I was wondering if anybody knew an easy fix to this problem (I know I could
> also apply transformations at will with FLIRT in FSL, but I am not sure what
> is considered the origin of the 3D affine space, so I would have to work
> harder along this route with rotations, translations and a contraction to
> adjust for the tight boundaries)
>
> Thank you very much,
> Silviu Podariu
> UNMC, Omaha
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