Generates list of filenames output by CIVET
civet.getAllFilenames(gf, idvar, prefix, basedir, append = TRUE, civetVersion = "1.1.9", cnf = NULL)
| gf | Data Frame with subject information |
|---|---|
| idvar | column name in gf with subject IDs |
| prefix | Prefix specified when CIVET was run |
| basedir | directory where all CIVET output was stored |
| append | Whether to append the results to the input gf |
| civetVersion | Version of CIVET |
| cnf | A list of configuration information used to parse CIVET files produced by CBRAIN. Unnecessary for CIVETs < 2. Should be read from CBRAIN yaml config file, but can be input manually as a list containing thickness_method (tlink or laplacian), thickness_kernel (in mm), and atlas as either AAL or DKT |
gf is returned with CIVET filenames
Prior to running, read.csv may be called to generate the input argument gf. The results will be stored under the column name CIVETFILES either in the input gf (if append = TRUE) or in a new gf. Currently only CIVET versions 1.1.9 and 1.1.12 are supported.
civet.readAllCivetFiles
# NOT RUN { getRMINCTestData() gf = read.csv("/tmp/rminctestdata/CIVET_TEST.csv") gf = civet.getAllFilenames(gf,"ID","TEST","/tmp/rminctestdata/CIVET","TRUE","1.1.12") # }