MRIcron has a View/Flip L/R option, and changing that might give you the
desired result.  You may also want to search the SPM list for the many
postings on the flip topic, here for example:

In brief, SPM2 Analyze format sometimes has a .mat file that is read only by
SPM and ignored by other packages such as FSL, MRIcro, or MRIcron.  With
SPM5/NIFTI files, the L/R flip is encoded in the file header and can be
interpreted by other software, independent of the SPM defaults.analyze.flip

Kathy Pearson
UAB Psychology

From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
Behalf Of Markus Gschwind
Sent: Wednesday, October 22, 2008 8:46 AM
To: [log in to unmask]
Subject: [SPM] IBASPM atlas116 flipped?

Hallo Experts!

I am working with IBASPM, a very nice tool btw.

However, as I have different data from different years (and  thus ANALYZE
and NIFTIs) I am confused about the behaviour of the atlas116.img in SPM2
and SPM5. 

I am facing the following problem:
Currently I am working on SPM2 with ANALYZE files and the atlas116.img

The IBASPM_atlased  brain looks fine and in spm_display it seems correct:
Vox size -1x1x1
Origin 91 127 73
global defaults.analyze.flip = 1
the + coordinates on the right, the - coordinates on the left 
according to this the odd numbers of the atlas on the left

Now, I am looking with MRICron at the same atlas116.img
Vox size -1 x 1 x 1
Origin 90 126 72
view> flip L/R activated
the + cordinates on the LEFT, the -coordinates on the RIGHT
DISACCORDING to this the odd numbers on the LEFT

Also in SPM5 this atlas116.img behaves similar like in MRICron
Vox size -1 x 1 x 1
Origin 91 127 73
global defaults.analyze.flip = 1
the + cordinates on the right, the -coordinates on the left
DISACCORDING to this the odd numbers on the RIGHT

I am very confused and as I need to treat a whole data set with this atlas,
I would like to know what is going on here!

I am even more sensitive to that problem as IBASPM under SPM5 seems to flip
ANALYSE files during the segmentation (which creates an unusable output),
however it does not flip the NIFTI files. 
Under SPM2 all the IBASPM treatment of ANALYZE works fine, but I am still
not sure if the orientation is correct. And why is it wrong in MRICron and

Could anybody shed light on this, please?
Thanks in advance!

Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH

Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]