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I think you want fslswapdim.  Just make sure you heed any left/right flip
warnings (and flip the sign of x to compensate).

Peace,

Matt.

-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Silviu Podariu
Sent: Monday, August 10, 2009 12:17 PM
To: [log in to unmask]
Subject: [FSL] orientation problem for SPM-imported image (dcm2nii did not
work)

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