The program pvc_relabel can be used to transform a 3-D parcellation from region definition to another. The mapping is controlled by a CSV file which is passed as one of the inputs.
pvc_relabel -i <INPUT> -o <OUTPUT> --parc <CSVFILE> --type <COLID>
where <INPUT> is the 3-D image of parcellated regions, <OUTPUT> is the newly labeled image, <CSVFILE> is a comma separated file (see below) that maps from one labelling scheme to another and <COLID> refers to the desired mapping contained in a column of the <CSVFILE>.
An example mapping from FreeSurfer's aparc+aseg is provided in parc/FS.csv. pvc_relabel always expects the first row to comprise the column headers:
REGION,SOURCE,XXX
The REGION column contains a text description of the region (optional) and SOURCE holds the numeric ID of the original label (mandatory). The header XXX can be any desired name for the new mapping scheme. In FS.csv this is called DST. The column must contain the new numeric ID to be applied. It is this name that must be passed as the <COLID> when executing pvc_relabel. Multiple columns can be added to the CSV file for different applications:
REGION,SOURCE,MYSCHEME1,MYSCHEME2
Calling pvc_relabel with --type MYSCHEME1 will produce an image with the label scheme defined by the MYSCHEME1 and --type MYSCHEME2 will use the second column.
Note that FS.csv is an example and that region definitions should be created and validated for each application.
Most of the methods provided in the toolbox expect a 4-D mask image as input. The application pvc_make4d will create a 4-D image from a 3-D label image. Each volume in the 4-D file represents a single region. The set of labels do not need to be continuous. pvc_make4d will write the volumes in ascending order.
pvc_make4d -i <3DMASK> -o <4DMASK>
where <3DMASK> is a single 3-D volume of labels and <4DMASK> is the output 4-D file.