table of contents
LIPSIA     Apply a brain mask
vbrainmask
The program 'vbrainmask' applies a brain mask to a zmap or some other type of activation map. The brain mask is obtained by thresholding fMRT raw data. For example:

vbrainmask -in zmap.v -raw ntbsm.v -minval 2000 -out zmap_new.v

This program call does the following: the raw data are thresholded using 2000 as threshold. The resulting mask is cleaned along its borders and then applied to the zmap. The raw data file must have the same geometrical properties as the zmap. In particular, it must have been transformed into AC/PC space, if the zmap is in AC/PC space. The image below illustrates the process.




Parameters of 'vbrainmask':
-help
Prints usage information.
-in
Input file. Default: (none)
-out
Output file. Default: (none)
-raw
Raw data. Required.
-minval
Signal threshold. Required.
-radius.
Radius for cleaning the brain mask. Default: 2


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.