[MINC-users] conversion to analyze problem

[Andrew Janke]

Hi Lindsay, (and others!)

As Alex has alluded to, the problems with "analyze" to MINC conversion
are systemic and not really bugs.

In short there is no way to canonically convert between the two
formats and ensure that the orientation will always be correct as it
depends on the package that you will be using with your
"analyze/Nifti" images. What generally happens is that users have to
figure out a path that works for them and stick to it.

This in itself is endemic in any Nifti/Analyze conversion but what I
can assure you of are the following...

1) mnc2nii follows the official specifications of Analyze and Nifti.

2) The issue of Radiological vs Neurological orientation _should_ have
nothing to do with a file format and only concern a file viewer. In
MINC this is the case. There is also a defined co-ordinate system for
ANALYZE and Nifti-1 but these are not always followed to the letter.

3) Further to #2 you need to very careful of what you package is doing
to your files as some like SPM define a file like "spm_defaults.m"
that defines as to whether your data is "neurological" or
"radiological" that will flip your data inside the package itself.

Sorry I cant offer a simple answer to your problems but the above is
one of the primary motivating factors that caused Peter (Neelin) to
write MINC nigh on 12 years ago! :)

That all said there is a new MINC due out very soon that will have an
updated version of Nifti conversion that may alleviate your concerns
as we  now use the same version of the Nifti Libraries that is used by
FSL and thus supports a few extra things like compression of Nifti
files and the likes.


a


On 9/8/07, Walker, Lindsay (NIH/NICHD) [V] <walkerlin at mail.nih.gov> wrote:
> That definitely helps.  I will give it a try.
>
> Is there a newer version of this tool where this bug has been addressed?
> Or is it possible for someone to fix this bug?
>
> Lindsay.
>
> -----Original Message-----
> From: Najmeh Khalili M. [mailto:najma at bic.mni.mcgill.ca]
> Sent: Friday, September 07, 2007 3:49 PM
> To: MINC users mailing list
> Subject: Re: [MINC-users] conversion to analyze problem
>
> 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.
>
> 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?


-- 
Andrew Janke   (a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883