table of contents
LIPSIA     Slicetime correction
vslicetime
Slices in an fMRI time sequence are not acquired simultaneously. A typical example is shown here:

slice time (ms)
0 5.93
1 259.81
2 386.75
3 640.62
4 767.56
5 1021.44
6 1148.38
7 1402.26
8 1783.07
9 1910.02

In this experiment, the second slice was acquired 259.81 milliseconds and the last slice was acquired 1910.02 milliseconds after the start of each time step. In other words, the last slice is closer in time to the subsequent time step (assuming a repetition time of 2000 milliseconds) than to the time step to which it belongs.

This may cause significant problems in the statistical evaluation of the data. The last slices are particularly effected by this problem. The order of slice acquisition is usually from ventral to dorsal, i.e. the dorsal slices are most strongly effected.

The program 'vslicetime' corrects for this problem by using cubic-spline-interpolation. The time courses in each voxel of each slice are virtually moved backwards in time as if all slices had been acquired simultaneously at the start of the time step.

'vslicetime' should be called after movement correction ('vmovcorrection') and before any other type of processing takes place. The program is typically called as follows:

vslicetime -in AC1T.v -out sAC1T.v -del 5

Note that the first few time steps of the time courses usually have extremely high values due to saturation effects. This can be corrected for by replacing the first time steps of the time course by mean values. The correction should be done early in the processing sequence and is therefore part of 'vslicetime'. The parameter '-del' determines the number of the first few seconds that are replaced by a mean value.

In some cases, it can be useful to apply the program 'vslicetime' only for correcting the first few time steps (parameter '-del') without performing a slicetime correction. This is particularly the case if the interscan intervals are very large (> 5 seconds). In this case, the parameter '-correction' should be set to 'false'.

If the interscan intervals (repetition times) are not constant, then an ASCII text file must be supplied. Each line in this file must contain the scan time in seconds for each scan. The parameter '-scanfile' is used to specify this file.

Parameters of 'vslicetime'
-help
Prints usage information.
-in
Input image. Default: (none)
-out
Corrected output image. Default: (none)
-minval
Signal threshold. Default: 0
-correction [ true | false ]
Whether to perform slicetime correction. Default: true
-slicetime
ASCII file containing slice times in milliseconds. Default:
-scanfile
ASCII file containing scan times in seconds. Default: (none)
-del
First few seconds to be ignored. Default: 5


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.