The program 'anatov' converts Analyze data into a vista file. Note that 'anatov'
supports only a single input file and not a series of images. If the input Analyze
file contains an anatomical image, e.g. ana.img and ana.hdr, 'anatov' can be called
in the following way:
anatov -in ana.img -out ana.v
Note that Lipsia is using the neurological convention of the data, i.e. L=L and R=R.
Per default, 'anatov' expects the image in the radiological convention,
and flips the image to the natural convention. This flip can be controlled
using the command-line options '-flipx', '-flipy', and '-flipz'.
Functional data can only be converted, if they are stored as 4D image in a single image file
(see above). A correct repetition time must be specified (in seconds) for converting functional data.
Example:
anatov -in functional3D.img -out functional3D.v -tr 2
Important: In Lipsia, raw functional slices (i.e. before preprocessing) must be ordered from ventral to
dorsal (i.e. upside down). Therefore, for (2D-)functional raw data, the correct command line is:
anatov -in functional.img -out functional.v -tr 2 -zflip true
To do a correct data conversion from the NIfTI to the Lipsia data format, please read the chapters
'The Lipsia data format' and
'How to convert data into the Lipsia data format'.
'vtoanalyze' expects a Vista image dataset as input and converts
it to Analyze format, which is e.g. SPM-compatible. For converting an anatomical image use:
vtoanalyze -in ana.v -out ana -anatomic true
To change the orientation in the resulting Analyze image, 'vtoanalyze' can be called with
the command-line options '-xflip', '-yflip', and '-zflip'. The slice ordering can be changed using '-zflip true'.
Lipsia is using the neurological convention, i.e., L=L and R=R. Per default, 'vtoanalyze' transforms
the images into radiological convention, i.e. L=R and R=L. If the neurological convention must
be preserved in the Analyze data files, 'vtoanalyze' can be called with '-flipx true'.
To convert functional data into the Analyze format, 'vtoanalyze' can be called as follows:
vtoanalyze -in fnc.v -out fnc -functional true
Because in Lipsia, raw functional slices (i.e. before preprocessing) are ordered from ventral to
dorsal (i.e. upside down), the option '-zflip true' is neccessary.
vtoanalyze -in fnc.v -out fnc -functional true -zflip true
For functional data,'vtoanalyze' generates a file in the 4D Analyze format. If you wish
the 3D data format, then the command-line option '-4D false' can be specified.
The resulting 3D-images are saved in separate files for each timestep. Thus, if there is
a functional data set with 600 timesteps in the vista file, there are 600 Analyze image output files
and 600 Analyze header output files.
vtoanalyze -in fnc.v -out fnc -functional true -zflip true -4D false
NB: The Analyze data can be visualized in SPM (using the 'Display' button), or in FSL using 'fslview'.