mergecontrasts-sess - mergedcontrast name of new contrast


mergecontrasts-sess ??


Positional Arguments


Required Flagged Arguments


Optional Flagged Arguments

-conjunction name

and, or, andor

-analysis analysisname

name of session-level functional analysis


name thresch tail complement



-space spacename

tal or sph

-spacedir spacedir

if not tal or sph

-sf sessidfile


-df srchdirfile


-s sessid


-d srchdir



print version and exit


print help and exit

-umask umask

set unix file expression mask





mergecontrasts-sess will merge two or more contrasts. The merging is done by comparing each thresholded contrast on a voxel-by-voxel basis. The result depends upon the conjunction chosen. For the 'and' conjunction, each contrast must meet the threshold criteria at a voxel for the voxel to be set to 1. For the 'or' conjunction, the voxel is set to 1 if any contrast meets the threshold criteria. Otherwise, the voxel is set to zero. For the 'andor' conjunction, a voxel is set to 2 if both of the inputs meet the criteria. If the first input meets the criteria, then the voxel is set to 1. If the second input meets the criteria, then the voxel is set to 2. Otherwise, the voxel is zero. The andor only makes sense with two input. The andor conjunction allows four distinct areas to be visualized.

The output is a map with the same name as the input map which will be placed in a new contrast directory. The merged contrast can be accessed in the same was as any other contrast. However, remember that the voxel values of the merged contrast will be either 0 or 1, so set thresholds appropriately.

The contrast and threshold criteria are set with the -contrast flag. The first argument is the name of the contrast. The second is the threshold to apply. If the map is a significance map, then set the threshold based on log10(p) (eg, 2 = .01). The third argument is the tail, which can be either pos, neg, or abs for positive, negative, or ignore sign. The final arugment allows the user to use a complement. Ie, if the fourth argument is non-zero and the threshold criteria is met, then a 0 is input to the conjunction.

There is a .ovlp file created with the following three numbers:

  1. number of voxels in contrast 1 that met threshold criteria
  2. number of voxels in contrast 2 that met threshold criteria
  3. number of voxels that overlapped


Example 1




See Also




Methods Description




Reporting Bugs

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