table of contents
LIPSIA     Identification of AC and PC
vcacp
To rotate a high-resolution T1-weighted MR image into the stereotactic coordinate system using 'vtal', the voxel cordinates of Commissura anterior (CA) and Commissura posterior (CP) and rotation angels are necessary. They can be obtained automatically by performing 'vcacp'.

'vcacp' requires a 3-D template of each CA and CP. They depend on the MRT and must be obtained manually. For some MRT's (e.g. 3 Tesla Bruker MRT) a template is appropriated.

CA/CP-Template
The 3-D CA/CP-template consists of three images - CA-template, CP-template and an averaged anatomical image - and can be generated as follows:
  1. Select approx. 15 high-resolution T1-weighted MR images which are already rotated into the stereotactic coordinate system by calling 'vtal' with manually obtained voxel coordinates of CA and CP.

  2. Perform an anatomical image averaging by calling 'vaverage'.

  3. Crop an approx. 13 x 13 x 13 voxel image for each template by calling the vista program 'vcrop'. The voxel coordinate of the landmark must be in the center of the template!

  4. Concatenate the CA/CP templates and the average anatomical image by performing 'vcat'.

We recommend to store the 3-D CA/CP-template in '/usr/share/lipsia/MRT-name.v'
Usage
Here is an example:

vcacp -in mr024_t1_or.v -out ctrlimg.v -template /usr/share/lipsia/bruker.v -id 024 -report ascii.txt

The parameter '-in' is required and specifies the input image. The image must be an anatomical image (ubyte).

The parameter '-out' is optional and specifies an control image for experts used to retrace a failing of CA/CP identification.

The parameter '-template' is optional and specifies the path of the 3-D CA/CP-template. The default path is '/usr/share/lipsia/bruker.v'. (This template is validated for the MPI CNS 3 Tesla Bruker MRT)

The parameter '-id' is optional and specifies an identification. It can be used for inhouse database coding. The default value is 001.

The parameter '-report' is optional and specifies the path of an ASCII-file which reports the voxel coordinates of CA/CP and the rotation angles. The data output is appended to the existing file and has the following representation:

-ca ca.x ca.y ca.z -cp cp.x cp.y cp.z -angle roll yaw pitch

Parameters of 'vcacp':
-help
Prints usage information.
-in
Image to be processed. Required.
-out
Latent image for internal use. Default: (none)
-template
CA/CP template. Default: /usr/share/lipsia/vcacp/bruker.v
-report
Report file. Default: (none)


Max Planck Institute for Human Cognitive and Brain Sciences. Further Information: lipsia@cbs.mpg.de
Copyright © 2007 Max Planck Institute for Human Cognitive and Brain Sciences. All rights reserved.