table of contents
LIPSIA     Rotation into Talairach space - brain peeling
vtal
The program 'vtal' rotates a high-resolution T1-weighted MR image into the stereotactic coordinate system. The origin of the cordinate system is located at CA. Our coordinate differs from the standard Talairach system in that the data sets are not scaled to a standard size. To scale images into a standard size, use the program 'vnormalize'.

In addition, 'vtal' optionally also performs a "brain peeling", i.e. it removes non-brain matter from the image.

Usage
Here is an example:

vtal -in infile.v -out outfile.v -type 0 -ca 100 120 103 -cp 100 130 105 -angle 5

The input into 'vtal' is an MR-image with isotropic voxels. The voxel coordinates of CA and CP must be known beforehand. They can be obtained either manually or automatically by calling the program 'vcacp'.

The parameter '-type' specifies the type of operation to be performed. If type=0, then both brain peeling and the coordinate transformation are performed.

If type=1, then the coordinate transformation but no brain peeling is performed. However, 'vtal' internally performs a brain segmentation in order to obtain the brain size and adds the attribute 'extent' to the file header. The output image is not segmented. The brain size is needed in many applications to compute Talairach coordinates and perform linear scaling operations.

If type=2, then only the coordinate transformation but no brain peeling is performed. This option is useful in cases where a reliable brain segmentation is impossible. Note that in this case, the brain size (attribute 'extent') is NOT computed. Thus, it is not possible to obtain Talairach coordinates for such images. However, the parameter 'extent' may be added manually using the program 'vattredit'.

Brain peeling is performed by using a sequence of morphological operations. These operations can optionally be influenced by the parameters '-d1', '-d2'.

The parameter '-size' controls the size of the output image matrix. The default size ('-size small') is 160x200x160 (160 slices with 160 columes and 200 rows per slice). In this case, the inter-hemispheric cleft resides at column 80. If '-size' is set to 'big', the output image matrix is set to 180x230x190. An even larger matrix size can be obtained using '-size xxl'.

The parameter '-system' controls the type of coordinate system to be used. If '-system' is set to 'neurological' then the coordinate system follows the neurological convention (lower border of CA and upper border of CP). If '-system' is set to 'atlas', then the coordinate system follows the Talairach atlas convention (upper border of CA and lower border of CP).

Parameters of 'vtal':
-help
Prints usage information.
-in
Input file. Default: (none)
-out
Output file. Default: (none)
-d1
Erosion (peeling parameter). Default: 1.3
-d2
Dilation (peeling parameter). Default: 5.2
-t
Segmentation threshold (peeling parameter). Default: 120
-ca
CA position. Required.
-cp
CP position. Required.
-p
3rd Point position. Default: 0 0 0
-angle
Rotation angle. Required.
-type [ 0 | 1 | 2 ]
Type of operation: 0=peel+extent, 1=no_peel+extent, 2=no_peel+no_extent. Default: 0
-system [ 0 | 1 ]
Type of talairach convention: 0=atlas, 1=neurological. Default: atlas
-extent
extent parameter (if peeling impossible). Default: 0 0 0
-size [ small | big | xxl | huge]
Size of output image matrix, small=160x200x160, big=180x230x190, xxl=210x240x200, huge. Default: small


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.