[MINC-users] changing the coordinate in mnc

[Andrew Janke]

On Mon, 24 May 2004, Agatha Lee wrote:

> Does anyone know how to change orientation in mnc? When I open
> mnc in Display, I am seeing different orientation in different box of
> window which will interfere when I try to register with average brain.  I
> tried "mincreshape -coronal(transverse)". However, it would not change any
> orientaion

Agatha,

You appear to be wanting to rotate your MINC volume, mincreshape is not designed
to do this, rather it's purpose is to reorganise the data within a MINC file
such that reading the data in a coronal or sagittal fashion is faster.

What you need to do is either:

  1) Figure out what went wrong with the conversion process and fix it

  2) rotate your volume

To do the second use param2xfm to generate a transformation matrix that will
correctly orient your volume remembering to be very carefull that you don't
confuse left and right in this process!  Then apply this transformation to your
volume using mincresample.  (and likely with a -nearest_neighbour option)


--
Andrew Janke  ( rotorATcmr.uq.edu.au || www.cmr.uq.edu.au/~rotor )
Australia->University of Queensland->Centre for Magnetic Resonance
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