[MINC-users] conversion to analyze problem

[Alex Zijdenbos]

I suppose flipping the minc volume prior to conversion should amount
up to the same thing, e.g.,

   flip_volume <in.mnc> <out.mnc>

flip_volume is part of the 'conglomerate' package.

However, what I would like to know is whether this is a conceptually
unsolvable problem due to the specifics of ANALYZE and MINC coordinate
handling, or if this is in fact fixable (i.e., a bug). I don't believe
I have *ever* encountered a MINC <-> ANALYZE conversion that did not
require flipping of some sort, so at first glance I would assume we
are looking at a bug.

Does anybody more familiar with the inner workings of mnc2nii and the
like perhaps have some insight into this? Andrew, Bert, ...?

Thanks,

-- Alex

On 9/7/07, Najmeh Khalili M. <najma at bic.mni.mcgill.ca> wrote:
>
> Hi,
>
> Yes I have too.
> I did something like:
>              fslswapdim data.nii.gz x -y z flipped_data.nii.gz
> to correct the left-right flip problem.
>
> Hope this helps,
> Naj
>
>
> On Fri, 7 Sep 2007, Walker, Lindsay (NIH/NICHD) [V] wrote:
>
> > I need to convert some minc images to analyze format.  I have been using
> > the mnc2nii tool from minc-1.5.1 with the -analyze option.
> >
> >
> >
> > The images I converted have an indicator dot on the anatomical right of
> > the image.  When I run the minc to analyze conversion program, the
> > resulting analyze image shows the indicator dot on the anatomical left.
> > So the program appears to be flipping the labels for the left and right.
> >
> >
> >
> > I have tried opening the analyze image with multiple pieces of software
> > to make sure it is not just a display issue (i.e. radiological versus
> > neurological coordinates).  The left and right labels appear to be
> > incorrect using fslview, medx and mipav.
> >
> >
> >
> > Has anyone else encountered or noticed this problem?
> >
> >
> >
> > Thank you.
> >
> >
> >
> > Lindsay Walker.
> >
> >
> >
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
>
> =========================================================
> http://www.bic.mni.mcgill.ca/~najma
> _______________________________________________
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>
>