[MINC-development] minc 2.0 file format definition

[Robert VINCENT]

Romain,

You are correct about equation (4).  I had updated it in the source TeX
files but I had not updated the document on the website.  I will update
the website to reflect this correction.

Regarding the definition of the coordinate spaces, the meaning of the
"true" xspace, yspace, and zspace dimensions is invariant with respect to
the acquisition order of the image.  X is always from patient left to
patient right, Y is from patient posterior to anterior, and Z is from
patient to inferior to superior.  A MINC file may have any of these
dimensions chosen as the fastest-varying dimension, so a coronal image and
a transverse image may share precisely the same definitions of X, Y, and Z
even though the organization of the data in the file may change.

The direction cosines simply represent (in a very general fashion) the
rotation that must be applied to the voxel (IJK) coordinates in order to
derive the world (XYZ)  coordinates.

	-bert


On Tue, 10 May 2005, romain wrote:

> /Hello/
>
>
> /I have carefully read the MINC 2.0 File Format document written
> by Robert D Vincent, and I have a few question, in order to
> fully understand how the orientation is handle./
>
>
> /First, I wonder if the formula (4) from section 2.1 describing
> the relation between voxel space and world space is not false ?
> I would have put Ox, Oy, Oz in the last colon rather than in the last line./
>
>
> /Then I have a problem with the definition of xspace, yspace and zspace : /
>
> in the definition of direction_cosines it is say :
> "Numeric vector with 3 elements giving the direction cosines of the axes.
> Although axes are labeled x, y and z, they may in fact have a significantly
> different orientation - this attribute allows the direction relative to
> the true axes to be specified exactly. "
>
>
> The definition of the true axes is clear : this is the patient
> coordinate system,
>  but then the precise definition of the axes (that is xspace, yspace and
> zspace)
> is not clear to me.
>
>
> In the dicom format the equivalent definition is clear. The first given
> cosines direction is the direction of the first row in the patient
> coordinate
> system. (and the first row is the faster varying index of the stored data)
>
>
> If you use the same definition then the name is really confusing... if not
> cant someone precise it  ?
>
>
> If someone could give me an example for the definition of those
> dimension variables,
> in the case of coronal acquired volume (ie, where the data is stored in
> the order,
> x axis, z axis and y axis.)
>
>
> Thanks for the help
>
> Romain
>
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