table of contents
LIPSIA     Vista images to Analyze data format and vice versa
anatov

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

'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'.

Parameters of 'anatov':
-help
Prints usage information.
-in
Input file. Required.
-out
Output file. Default: (none)
-precision auto | original
precision of anatomical data. Default: auto
-black
lower histogram cutoff for contrast scaling. Default: 0.1
-white
upper histogram cutoff for contrast scaling. Default: 0.1
-xflip
[ true | false ] flip x axis. Default: false
-yflip
[ true | false ] flip y axis. Default: false
-zflip
[ true | false ] flip z axis. Default: false
-tr
repetition time in ms. Default: 0.
-orientation
axial | sagittal | coronal orientation of slices. Default: axial
Parameters of 'vtoanalyze':
-help
Prints usage information.
-in
Input files. Default: (none)
-out
Output filename stub. Required.
-anatomic [ true | false ]
Convert anatomic image(s).
-functional [ true | false ]
Convert functional image(s).
-zmap [ true | false ]
Convert zmap(s).
-4D [ true | false ]
Generate 4D Analyze file format. Default: false
-xflip [ true | false ]
flip x axis. Default: false
-yflip [ true | false ]
flip y axis. Default: false
-zflip [ true | false ]
flip z axis. Default: false


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.