def RunStatsOnVols(subject,Regressor):
mainDir,subID=os.path.split(subject)
for meth in Methods:
WrkFile=subject
if os.path.exists(WrkFile):
trash='.exe'
FileBase=subID
while trash:
FileBase,trash=os.path.splitext(FileBase)
subID=FileBase
if meth=='Uncorrected':
target=subject
else:
target=os.path.join(mainDir,'{}_{}.nii.gz'.format(subID,meth))
print target
if not os.path.exists(target):
if meth=='FS':
Runfs.main(WrkFile,1./tr,itl)
elif meth=='FSL':
Runfsl.main(WrkFile,1./tr,itl)
elif meth=='SPM':
Runspm.main(WrkFile,1./tr,itl)
time.sleep(20)
else:
print 'found {} for {}'.format(meth,subID)
CheckOutput=os.path.join(mainDir,'tPython',meth,con,'Beta.nii.gz')
print CheckOutput
if not os.path.exists(CheckOutput):
pr=sp.Popen('fslmaths {} -s 5 {}/Smooth{}_{}'.format(target,mainDir,subID,meth),shell=True)
print 'Blurring:\nfslmaths {} -s 5 Smooth{}_{}'.format(target,subID,meth)
pr.wait()
target=os.path.join(mainDir,'Smooth{}_{}.nii.gz'.format(subID,meth))
Runglm.main(target,con,Regressor,meth)
else:
print 'Ran for {} {}, skipping'.format(subject,meth)
else:
print ('No Nii File For {}'.format(subID))
def main(WrkFile,tr,itl):
Files=[]
MethOrder=[]
base,subID=os.path.split(WrkFile)
print subID
subID=re.search('(.*)(.nii.*)',subID).group(1)
print 'subID: {}'.format(subID)
########################### FS #############################
target=os.path.join(base,'{}_FS.nii.gz'.format(subID))
print target
if not os.path.exists(target):
Runfs.main(WrkFile,1./tr,itl)
Files.append(target)
MethOrder.append('FS')
else:
print 'found FS for {}'.format(subID)
Files.append(target)
MethOrder.append('FS')
########################### SPM #############################
target=os.path.join(base,'{}_SPM.nii.gz'.format(subID))
if not os.path.exists(target):
Runspm.main(WrkFile,1./tr,itl)
Files.append(target)
MethOrder.append('SPM')
else:
print 'found SPM for {}'.format(subID)
Files.append(target)
MethOrder.append('SPM')
########################### FSL #############################
target=os.path.join(base,'{}_FSL.nii.gz'.format(subID))
if not os.path.exists(target):
Runfsl.main(WrkFile,1./tr,itl)
Files.append(target)
MethOrder.append('FSL')
else:
print 'found FSL for {}'.format(subID)
Files.append(target)
MethOrder.append('FSL')
########################### Filt #############################
target=os.path.join(base,'{}_Filt.nii.gz'.format(subID))
if not os.path.exists(target):
RunFilt.main(WrkFile,1./tr,itl)
Files.append(target)
MethOrder.append('Filt')
else:
print 'found Filt for {}'.format(subID)
Files.append(target)
MethOrder.append('Filt')
########################### Uncorrected #############################
target=os.path.join(base,'{}_Uncorrected.nii.gz'.format(subID))
if not os.path.exists(target):
cmd='cp {} {}/{}_Uncorrected.nii.gz'.format(WrkFile,base,subID)
pr=sp.Popen(cmd,shell=True)
pr.wait()
Files.append(target)
MethOrder.append('Uncorrected')
else:
print 'found Uncorrected for {}'.format(subID)
Files.append(target)
MethOrder.append('Uncorrected')
return Files,MethOrder
#
# if __name__ == '__main__':
# Subjects=glob.glob(sys.argv[1])
# print sys.argv[1]
# print len(Subjects)
# for sub in Subjects:
# RunStatsOnVols(sub)
target = os.path.join(subject, "{}_FS.nii.gz".format(subID))
print target
if not os.path.exists(target):
Runfs.main(WrkFile, 1.0 / tr, itl)
else:
print "found FS for {}".format(subID)
target = os.path.join(subject, "{}_SPM.nii.gz".format(subID))
if not os.path.exists(target):
Runspm.main(WrkFile, 1.0 / tr, itl)
else:
print "found SPM for {}".format(subID)
target = os.path.join(subject, "{}_FSL.nii.gz".format(subID))
if not os.path.exists(target):
Runfsl.main(WrkFile, 1.0 / tr, itl)
else:
print "found FSL for {}".format(subID)
InputNii = os.path.join(subject, "{}_{}.nii.gz".format(subID, meth))
InputNii = WrkFile
Regressor = os.path.join(subject, "SuperiorFrontalL.txt")
CheckOutput = os.path.join(subject, "tPython", meth, con, "Beta.nii.gz")
if not os.path.exists(CheckOutput):
Runglm.main(InputNii, con, Regressor, meth)
else:
print "Ran for {} {}, skipping".format(subject, meth)
else: