def main(InputFile, ContrastName, Interleave, TR, Regressor, RunMC=""):
print "RunFillPipelineOnFile_SC.py"
print "RunMC:\t{}".format(RunMC)
print 'RunMC=="first":\t{}'.format(RunMC == "first")
print 'RunMC=="last":\t{}'.format(RunMC == "last")
print 'RunMC=="none":\t{}'.format(RunMC == "none")
if RunMC == "first":
print "Running MC first"
InputFile = RMC.main(InputFile)
print InputFile
STCFiles, Methods = STC.main(InputFile, TR, Interleave)
for stcfile, meth in zip(STCFiles, Methods):
if RunMC == "last":
MCstcfile = RMC.main(stcfile)
else:
MCstcfile = stcfile
print MCstcfile
GLM.main(MCstcfile, meth, Regressor, ContrastName, TR, Interleave)
pr.wait()
WrkFile=os.path.join(OutputDir,'Smooth_{}'.format(InputID))
RegPaths=[os.path.join(InputBase,'Regressors_0.5Hz.txt'),os.path.join(InputBase,'Regressors_20Hz.txt')]
for r in RegPaths:
cmd='cp {} {}'.format(r,CPdir)
print cmd
pr=sp.Popen(cmd,shell=True)
pr.wait()
reg=os.path.join(CPdir,'Regressors_0.5Hz.txt')
WrkDir,trash=os.path.split(WrkFile)
#main(InputNii,meth,Regressor,con,tr,itl)
GLM.main(WrkFile,meth,reg,'1028',float(tr),itl)
