This is probably because SPM5 saves images in NIfTI format. MRIcron and many
other packages know about NIfTI format. This format overwrites many of the
old fields in ANALYZE format images, possibly also including the old image
orientation field. See http://nifti.nimh.nih.gov/nifti-1 for more
information.
Best regards,
-John
On Friday 30 May 2008 19:42, namhee kim wrote:
> Dear SPM users
>
> I have an issue of image orientation. I found that the images generated
> from SPM5 "imcalc" were saved with an Analyze format 2 ("sagittal
> unflipped") while most of the analyze images were saved in analyze format
> 0 ("transverse unflipped").
>
> I displayed the input files and an output file which was generated in
> imcalc in spm 5 by using "mricron".
>
> As default, mricron displays the images in neurological convention by
> flipping left and right.
>
> The input files (used for the arithmetic calculation) and the output file
> show different orientation, which means the left and right are flipped from
> each other. I chacked that the input files were saved in an Analyze format
> with "transverse unflipped" orientation.
>
> I thought of the reason why the images display different orientation and
> concluded that the output file which was saved in the orientation of
> "sagittal unflipped" has a coordinate system of (Z, Y, X). In mricron,
> thus, it rotates around Z axis by 180 degree, it still presents the
> radiological convention while input files which were saved in "transverse
> unflipped" present the neurological convention.
>
> Secondly, later, the output images were used for further analysis (t-test)
> in the SPM5 (with default.Analyze.flip=1). Then, spm5 (with flip=1) will
> safely display the results in the neurological convention no matter what
> the input data format is.
>
> Is it convincing? Or let me know the keys to settle down this issue.
>
> Thank you!
>
> Namhee
>
>
>
>
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