table of contents
LIPSIA     How to get started using an example data set
How to transform anatomical/functional MRI data into the 3D Talairach space

In this section, we will use the example data to demonstrate how to transform anatomical and functional data into the 3D Talairach space. Note that anatomical and functional data are required to be in the 3D Talairach space, if they are to be analyzed further (shown in the next section).

Transformation of the 3D high-resolution anatomical data set into the Talairach space

To transform the example high-resolution structural data set 'structural.v' into the Talairach space, the data set must have isotropic voxels. However, our example structural data set has a non-isotrop resolution of 1x1x1.5mm. Therefore, we have to convert the data set to an isotropic resolution of 1x1x1mm using 'visotrop'.

visotrop -in structural.v -out structural_iso.v -reorder false -reso 1

'visotrop' needs to be called in case of non-isotropic voxels. Moreover, if the slices have been sagitally acquired, the program can transpose them into axial slices, as is required for further processing. Finally, axial slices can be reordered if necessary using the option '-reorder true'.

In the next step, we would like to rotate our high-resolution MR image into the stereotactic coordinate system. The origin of the coordinate system is located at CA. This origin can be detected automatically using the command:

vcacp -in structural_iso.v -report cacp.txt

The report file 'cacp.txt' contains the location of CA and CP. Just do 'more cacp.txt'. This data can be used to rotate the 3D anatomical data set into the Talairach space using 'vtal'.

vtal -in structural_iso.v -out structural_isotal.v -ca 87.9 104.0 112.0 -cp 87.4 133.0 116.0 -angle 0.0 0.2 2.9

The parameters '-ca', '-cp', and '-angle' can be taken from the report file 'cacp.txt'. Note that 'vtal' performs a brain peeling per default. The result can be displayed using

vlview -in structural_isotal.v

This peeled 3D data set can be used as a reference data set for registration of functional MRI slices. The brain peeling can be switched off using 'vtal' with the command line option '-type 1'. Then the brain is rotated into the talairach space without brain peeling.

Registration of the functional data into the 3D Talairach space

For registration of the functional data, we need an isotropic 3D high-resolution structural data set, which is already transformed into the Talairach space. In our example (see above), we generated the data set 'structural_isotal.v' which can be used as a reference data set to align the functional slices into the Talairach space. Then, the program 'vreg3d' obtains the parameters necessary for rotation and shifting in the alignment. These parameters are saved in the output file 'reg.v'.

vtimestep -in data.v -out tmp.v -step 0

vreg3d -in tmp.v -out reg.v -ref structural_isotal.v -type MI

The result of registration should be checked by applying the registration matrix 'reg.v' to the functional data (to the image 'tmp.v'). This can be done using the program 'vdotrans'.

vdotrans -in tmp.v -out image.v -trans reg.v -object all

Now both data sets 'image.v' and 'structural_isotal.v' can be visualized using 'vlv'. The registration was successful if both data sets 'image.v' and 'structural_isotal.v' show the same location (see image below).

vlv -in image.v structural_isotal.v

If the registration was successful, the transformation matrix 'reg.v' can later be applied to the functional slices using 'vfunctrans', which transforms the entire functional data set into the 3D Talairach space (see next section).



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.