table of contents
LIPSIA     Parameters of average time courses
vimagetimecourse, vdifftimecourse, vextractparam

The program 'vimagetimecourse' caluclates an average time course for each voxel. Inputs are preprocessed raw data. Length and resolution of the time course can be predefined. Output files contain time courses for each voxel inside the brain. Output files can be handled like raw data. In particular, visualization is possible using the option -raw within 'vlview':

Example output:



Average time courses can be subtracted from each other using 'vdifftimecourse'. In this program, the second average timecourse (parameter ' -second') is subtracted from the first (parameter '-first'). This is useful, in particular, for subtracting null events from another condition.

Average time courses as produced by 'vimagetimecourse' and 'vdifftimecourse' can be further processed using the program 'vextractparam'. This program caluclates characteristic parameters of average time courses. They include 'amplitude', 'slope', 'dispersion', and four time points depicted in the figure below:


Output of 'vextractparam' is a file that can be handled like a z-map, but contains the values of the extracted parameter in every voxel. Visualization is possible using the option '-zmap' within 'vlview' or 'vlv'.

Important! Extracted parameters can only be meaningfully interpreted, if the underlying BOLD signal resembles (roughly) that of an activation as depicted above. The result images of 'vextractparam' should therefore be masked by a z-map or contrast image including only significantly activated voxels. This can be done with the program 'vimagemask'.

Parameters of 'vimagetimecourse':
-help
Prints usage information.
-in
Input file (raw data). Default: (none)
-out
Output file (raw data). Default: (none)
-length
Length of average time course (in sec). Default: 15
-cond
Condition. Required.
-reso
Temporal resolution (in sec). Default: 0.2
-tr
TR (in sec). Default: 0
-minval
Signal threshold. Required.
-des
Design file. Required.
-report
Report file. Default: report.txt
Parameters of 'vdifftimecourse':
-help
Prints usage information.
-out
Output file. Default: (none)
-first
first input file. Required.
-second
second input file. Required.
Parameters of 'vextractparam':
-help
Prints usage information.
-in
Input file. Default: (none)
-out
Output file. Default: (none)
-param [maxtime | mintime | peaktime | onsettime | slope | amp | disp ]
Parameter to be extracted. Required.
-reso
temporal resolution of time course (in sec). Default: 0.2
-onstart
first possible time for onset (in sec). Default: 0
-onend
last possible time for onset (in sec). Default: 5
-offstart
first possible time for peak (in sec). Default: 5
-offend
last possible time for peak (in sec). Default: 15
-minval
minval of first timestep. Required.
-psc [ true | false ]
Whether to report percent signal change. Default: true
-report
report file. Default: report.txt
Literature:

J. Neumann, G. Lohmann, S. Zysset, D.Y. von Cramon. Within-subject variability of BOLD response dynamics. NeuroImage 19(3), 784-796, 2003.



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.