Program name: threshold_tmap

Function: Thresholding Student’s t statistical parametric maps. Specifically the ones outputted by the vancova program.

Author: Babak A. Ardekani, Ph.D.

Usage:

threshold_tmap [–v/–verbose] [–o prefix] [-log logFile] [–pvox voxel P value]

[–pclus cluster P value] [-cc cluster size threshold] –t tmap –df dfmap

Required arguments:

–t tmap

Specifies an ANALYZE image of type ‘float’. Each image voxel is interpreted as a Student’s t-value. Specifically, the tmap is the prefix_t image outputted by the vancova program.

–df dfmap

Specifies an ANALYZE image of type ‘char’. This image is expected to have the same matrix size and number of slices as tmap. The value at each voxel in dfmap gives the degrees of freedom for the corresponding t-value at the same voxel of tmap. dfmap is also created by the vancova program.

Optional arguments:

–log logFile

Specifies a log file name. Default = “threshold_tmap.log”.

–o or –output prefix

This option can be used to specify a prefix for the output files. The default value is prefix=V.

–v or –verbose

Runs the program in verbose mode.

–pvox voxel P value

Specifies a two-tailed P-value for thresholding the t-values. The program performs the thresholding in such a way that only voxels with P-values less than voxel P value are retained. This is the first level of thresholding. The default value is 0.05.

–pclus cluster P value

After the first level of thresholding specified using the –pvox option, a number of contiguous cluster of voxels remain. When this option is specified, the program ensures that each of those clusters has at least one voxel for which the (two-tailed) P-value is less than cluster P value. This is the second level of thresholding. The default value for this variable is voxel P value.

–cc cluster size threshold

When this option is specified, a third level of thresholding is performed, in which it is ensured that all remaining clusters have sizes greater or equal to cluster size threshold.

Outputs:

Outputs the ANALYZE image: prefix_cluster.hdr(img). The image is of type ‘float’ and stores the t-values in tmap that survive all levels of thresholding. The program also appends the logFile.

Bugs:

No known bugs.