table of contents
LIPSIA     Linear normalization
vnormalize
In order to perform group statistics, the fMRI data should be normalized to a standard size. The standard size (talairach) is 13.5 x 17.5 x 12.0 cm. The normalization amounts to a linear scaling in the x,y, and z-direction.

The parameter '-system' specifies the coordinate system. If the system is 'talairach' then the brain extent in x,y,z is set to (120 mm,175 mm,135 mm). If '-system' is set to 'mni' then the extent is (128 mm,177 mm,141 mm).

Normalization of a transformation matrix:
The program that performs the normalization is called 'vnormalize'. The normalization can be applied to the transformation matrix obtained from 'vreg3d'. In this case, the transformation matrix is multiplied by linear scaling factors. If the normalized transformation matrix is then applied using either 'vdotrans' or 'vfunctrans', the resulting 3D images will not only be registered to the 3D reference data set, but also linearly scaled to a standard size. To do this, use the following processing chain:

vreg3d -> vnormalize -> vdotrans/vfunctrans.

Example:

vnormalize -in AC1T_trans.v -out AC1T_ntrans.v

Normalization of a 3D image:
The normalization can also be applied to a 3D image such as a registered zmap or an anatomical 3D image of the image data base. Note that the reference images in the image data base '/home/newbdb/' are not normalized. Example:

vnormalize -in infile.v -out outfile.v

Parameters of 'vnormalize':
-help
Prints usage information.
-in
Input file. Default: (none)
-out
Output file. Default: (none)
-system [ talairach | mni ]
Coordinate system. Default: talairach


Max Planck Institute for Human Cognitive and Brain Sciences. Further Information: lipsia@cbs.mpg.de
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