Nismaps
The application Nismaps produces variance maps and mean images given a
directory with functional images.
Invocation
java Nismaps
This starts up the java interpreter and runs the Nismaps
application. You need to have
set up your environment for java
in order for this to work.
In this window, you select the directory containing the functional
images as well as set certain options for Nismaps.
- Images file/directory
Directory containing the images (or a text file with image filenames) to be
used in creating the variance maps and mean images.
- Output directory
Directory where the variance maps and mean images will be placed. If
this directory does not exist, Nismaps will try to create it; if Nismaps
cannot create it, Nismaps will return an error.
- Produce mean image
If this checkbox is checked, Nismaps will produce an image that equals
the mean of all the input images. The filename for the output mean
image can be provided in the corresponding text field. If it is left
blank, "mean" will be used by default.
Do not include .img or .hdr extensions in the filename.
- Produce variance map
If this checkbox is checked, Nismaps will produce a variance map for the
input images. The filename for the output variance map can be provided
in the text field. If it is left blank, "variance" will be used by default.
Do not include .img or .hdr extensions in the filename.
- Variance scale
Scaling factor for variance maps (optional).
(default: smallest power of 10 that will keep variance
map pixels in default range [0 10000])
- Produce signal-to-noise map
If this checkbox is checked, Nismaps will produce a signal-to-noise ratio
image, which is the mean divided by the variance for each voxel. The
filename for the output variance map can be provided
in the text field. If it is left blank, "snr" will be used by default.
Do not include .img or .hdr extensions in the filename.
- Threshold
Pixel value threshold for calculating images (default is 0).
Any pixels below this threshold will not be included in calculations.
- View results
If this checkbox is checked, Nismaps will start a slice viewer to visualize
the results.
- Verbose mode
Reports progress in output window while Nismaps is running.
Last updated Fri Mar 10 16:59:07 EST 2000