add-constant [value] <volume list>
subtract-constant [value] < volume list>
multiply-constant [value] < volume list>
divide-constant [value] < volume list>
For every voxel in every volume, add/subtract/multiply/divide the specified constant value with the voxel.
add [volume_ref] <volume list>
subtract [volume_ref] <volume list>
multiply [volume_ref] <volume list>
divide [volume_ref] <volume list>
For every volume in the list, add/subtract/multiply/divide the single specified reference volume.
add-stacks [stack_ref] <volume list>
subtract-stacks [stack_ref] <volume list>
multiply-stacks [stack_ref] <volume list>
divide-stacks [stack_ref] <volume list>
For every stack in the list, add/subtract/multiply/divide the specified reference stack, such that the first volume of the reference stack is added (or whatever) to all other first volumes, and so on.
ln [constant] <volume list>
exp [constant] <volume list>
Perform ln(voxel_value/constant) for every voxel in every volume, or do the same operation with exponential function. For instance, use ln() to convert signal to relaxation rate.
create-fCBV [new stack name] [pre-contrast volume] [post contrast volume] <volume list>
Convert a time series of signal intensities in the volume list to the percentage change in CBV * 100 (so that results can be written as short integers if desired). Provide a pre-constrast volume, which presumably is an average of volumes prior to injection of paramagnetic contrast agent, and provide a post-contrast volume, which presumably is an average of post-injection volumes, including potentially many volume in the volume list. This function assumes that all volume were collected using the same echo time.
create-fCBV1 [new stack name] [pre-contrast volume] [post-contrast volume] [baseline post-contrast volume] <volume list>
Perform the same basic operation as above, but allow the pre-contrast and post-contrast volumes to have one echo time, and the baseline post-contrast volume and the volume list to potentially have a different echo time. For instance, if one injected too much contrast agent and then decided to lower the echo time for a functional run, this function would be appropriate (although the example case has never happened, surely).
scale-volumes [target intensity] <volume list>
normalize-volumes [target intensity] <volume list>
Rescale volumes so that either the spatial maximum (scale-volumes) or average (normalize-volumes) is set to the target intensity. If you want to preserve the relative scaling across a time series of volumes within a stack, use “multiply-constant” rather than these commands, which are most useful for single volumes.