floIm = os.path.join(itDir, 'T1MD.nii.gz')
resIm = os.path.join(itDir, 'T1_MD_Regged.nii.gz')
affIn = os.path.join(topDir, 'aff.txt')
cppName = os.path.join(itDir, 'trans.cpp.nii')
segResName = os.path.join(nextDir, 'Segs_diffspace.nii.gz')
maskOutName = os.path.join(nextDir, 'T1_Brain_mask.nii.gz')
if os.path.isdir(itDir) and not os.path.isdir(nextDir) and os.path.isfile(
floIm):
os.mkdir(nextDir)
if not os.path.isfile(resIm) and os.path.isfile(floIm):
other_args = '-rmask ' + rMask
DPD.NR_reg(refIm,
floIm,
cppName,
resIm,
dbg=False,
other_args=other_args)
## This is for when we don't want to keep resampling the matrix
T1segName = os.path.join(itDir, 'T1_Segmentation.nii.gz')
T1tmpName = os.path.join(itDir, 'T1_Segmentation_Regged.nii.gz')
T1MaskName = os.path.join(itDir, 'T1_Brain_mask.nii.gz')
MaskTempName = os.path.join(itDir, 'T1_Brain_Mask_Regged.nii.gz')
NextT1SegName = os.path.join(nextDir, 'T1_Segmentation.nii.gz')
if (not os.path.isfile(segResName)) and os.path.isfile(cppName):
DPD.reg_resample(refIm,
T1segName,
