Reading in Data
fslr implicitly is partnered with the nifti
format from oro.nifti. All functions use the
system command to implement the FSL functions. All
functions will check to see whether the file passed in a character path
to a filename. If the object is a nifti object, the
programs will create a temporary file using tempfile() and
then return the name of this file with the checkimg
command. If a character path is passed to the file argument
into an fslr command, then this will run in FSL assuming
that file exists.
Checking if FSL exists
If R is run using a GUI, then fsl.path must
be set using options(fsl.path='/path/to/fsl').
have.fsl() checks to see if FSL is in the PATH or the
options are correctly set and returns TRUE and returns
FALSE otherwise.
Printing out FSL Version
For example, you can wrap example functions with a logical check for
have.fsl() to have the execute if FSL exists:
if (have.fsl()) {
print(fsl_version())
}
## [1] "6.0.4"
Returning Objects
In functions where an image is the end result, the
outfile and retimg arguments are present. If
outfile is specified, the user wants a file to be saved to
disk. If outfile is not specified, a temporary file (using
tempfile) will be created for the result and deleted at the
end of the R session. If retimg=TRUE, then the
user specified that an object of class nifti will be
returned to R. If both retimg=TRUE and
outfile is specified, the image will be written to disk,
read into R and the nifti object will be
returned. If retimg=FALSE and outfile is not
specified, the function will fail as fslr would be
calculating an image and no result would be able to be obtained since
the outfile is deleted.
Main functions
The main functions implemented are fslmaths and
fslstats. fslmaths usually returns images as
the result and fslstats usually returns a vector of
information.
Functions functions such as fslmask,
fslerode, fslsmooth, and fslfill
are implemented wrappers for ease of use, but are essentially calling
fslmaths with specific options. Functions such as
fslrange is an example of a wrapper for
fslstats. As fslstats outputs are variable in
their format, the results are returned simply as a character vector
which needs to be parsed. This GitHub repository
will be used for development and issues.