table of contents
LIPSIA     Movement correction
vmovcorrection
The aim of motion correction is to realign the images acquired in an fMRI time series such that they are geometrically compatible. Misalignments occur when subjects move during the course of the experiment. As experiments may sometimes last for more than 40 minutes, some form of motion is usually inevitable. In motion correction, each scan of an fMRI time series is geometrically rotated and shifted until it matches a reference scan. The reference scan must be specified by the user.

The program 'vmovcorrection' performs a 3D motion correction using 6 degrees of freedom (3 translational and 3 rotational).

vmovcorrection -in EA1T.v -out mEA1T.v -tref 50 -report list.txt
Format of the report file
You can use the parameter '-report' to obtain a report file in ASCII.

  scan             shift              pitch    jaw    roll
  -------------------------------------------------------------
    0     -0.974   1.255   3.001     -0.285  -0.423  -0.154
    1     -0.645   1.051   2.806     -0.452  -0.320  -0.364
    2     -0.613   0.781   3.174     -0.447  -0.284  -0.263
    3     -0.683   1.031   3.188     -0.403  -0.302  -0.202
    4     -0.653   1.011   2.910     -0.324  -0.297  -0.214

The report file shows the 3 translational parameters (x,y,z) ('shift') in millimeters, and the 3 rotational parameters in degrees.

Visualization with gnuplot
To visualisize the values in the report file you can use gnuplot. For instance, to view the translational motion in x,y,z-direction between the reference time step and all other time steps you have to type

gnuplot <enter>

gnuplot> plot "list.txt" title 'x' with lines,"" using 1:3 title 'y' w l, "" using 1:4 title 'z' w l

gnuplot example (44kb)


Parameters of 'vmovcorrection':
-help
Prints usage information.
-in
Input file. Default: (none)
-out
Output file. Default: (none)
-tref
reference time step. Default: 50
-report
report file. Default:
-iterations
Max number of iterations. Default: 100
-minval
Signal threshold. Default: 0


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.