[MINC-users] Fwd: Minc to Analyze issue

[Andrew Janke]

> 1. It seems that the mnc2nii and nii2mnc are the preferred scripts to
> convert between minc and analyze formats.
> Can these scripts use and produce analyze (i.e. *.img and *.hdr) format
> files in addition to nifti (*.nii) format
> files?

Yes, use 'mnc2nii -help' to see the various output options.

> 2. We currently make use of the scripts minc2analyze and analyze2minc to
> perform conversions, I believe that are
> part of the minc tools.  How would these scripts compare with mnc2nii and
> nii2mnc?

minc2analyze?  If you mean mnc2ana || ana2mnc then they are now old
unsupported perl scripts of mine that may produce the same results and
may not dependant on where your "analyze" file came from.

> 3. I currently need to align two analyze format images.  I first convert
> them to minc format and then run an algorithm that produces the xfms.  Next
> I convert the xfm files to .mat format.  However the .mat transforms do not
> align the original analyze format images.  I'm guessing that this is a
> result of the missing direction cosine information that pertains to analyze
> format images.  However I would like to know if there is
> a way to convert from analyze to minc with no changes to alignment.

It could be the direction cosiones and it might also be that you are
using the spm_defaults type approach to handle left-right flips "radio
and neuro" orientation.  In which case, all bets are off.  My
suggestion would be that if you really do want to mess with both
analyze and minc would be to register and then resample in MINC before
converting back.


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