public:

// execute a command string in the system environment

static FslJobID runCommand(string command);

// execute a command string in the system environment and block

// until it finishes

static FslJobStatus runCommandBlocking(string command);

// perform a same-subject registration of two EPI volumes

// in:

// target image that will be registered to

// movable image that will be registered

// xfmFile file to save the transformation in (if empty a temp file

// is created)

static FslJobID registerSameSubjEPI(string target, string movable,

string xfmFile = string(tempnam(NULL,

"rtreg")),

bool block = false);

// apply a pre-computed transformation to a file

// in:

// target image that was registered to

// movable image that was registered

// input image to be transformed

// output image filename to save to

// xfmFile file to save the transformation in (if empty a temp file

// is created)

static FslJobID applyTransform(string target, string movable,

string input, string output,

string xfmFile, bool block = false);

// make a brain mask out of an epi volume

// in:

// filename of the volume to base the mask off of

static FslJobID makeBrainMask(string brainVolume,

string maskFilename,

string betOptions,

bool block = false);

// run a block design analysis

// in:

// filePrefix full path plus file prefix of volumes to include

// runNum series number of the images to include

// blockLength number of seconds per block

// numConditions number of stimulus conditions (including rest)

static FslJobID runAnalysis(string filePrefix, unsigned int runNum,

float blockLength, unsigned int numConditions);

// get a job status

static FslJobStatus getJobStatus(FslJobID jobID);

private:

static FslJobID getNextJobID();

// map job ids to system command objects

static map<FslJobID, SystemCommand*> cmdMap;