logging.info(subid)
### XXXXXXXXXXXXXXXXX
## set_up_dir
outdirs = pp.set_up_dir(root, subid, tracer)
## set up MRI
brainmask = os.path.join(outdirs["anatomydir"][0], "brainmask.nii")
fsmri = pp.find_single_file(os.path.join(mridir, subid, "mri/brainmask.mgz"))
if os.path.isfile(brainmask):
logging.warning("%s has existing anatomy," "skipping" % (brainmask))
elif fsmri is None:
logging.error("%s NO MRI: %s" % (subid, fsmri))
else:
fsmri = bg.copy_file(fsmri, outdirs["anatomydir"][0])
brainmask = bg.convert(fsmri, brainmask)
bg.remove_files([fsmri])
# copy aseg+aparc
aparcnii = os.path.join(outdirs["anatomydir"][0], "%s_aparc_aseg.nii.gz" % subid)
aparc = pp.find_single_file(os.path.join(mridir, subid, "mri/aparc+aseg.mgz"))
if os.path.isfile(aparcnii):
logging.warning("%s has existing anatomy," "skipping" % (aparcnii))
elif aparc is None:
logging.error("%s NO APARC ASEG: %s" % (subid, aparc))
else:
aparc = bg.copy_file(aparc, outdirs["anatomydir"][0])
aparcnii = bg.convert(aparc, aparcnii)
bg.remove_files([aparc])
# make pons
refdir, _ = outdirs["refdir"]
## set_up_dir
outdirs = pp.set_up_dir(root, subid, tracer)
## set up MRI
brainmask = os.path.join(outdirs['anatomydir'][0], 'brainmask.nii')
fsmri = pp.find_single_file(
os.path.join(mridir, subid, 'mri/brainmask.mgz'))
if os.path.isfile(brainmask):
logging.warning('%s has existing anatomy,'\
'skipping'%(brainmask))
elif fsmri is None:
logging.error('NO MRI: %s' % (fsmri))
else:
fsmri = bg.copy_file(fsmri, outdirs['anatomydir'][0])
brainmask = bg.convert(fsmri, brainmask)
bg.remove_files([fsmri])
# copy aseg+aparc
aparcnii = os.path.join(outdirs['anatomydir'][0],
'%s_aparc_aseg.nii.gz' % subid)
aparc = pp.find_single_file(
os.path.join(mridir, subid, 'mri/aparc+aseg.mgz'))
if os.path.isfile(aparcnii):
logging.warning('%s has existing anatomy,'\
'skipping'%(aparcnii))
elif aparc is None:
logging.error('NO APARC ASEG: %s' % aparc)
else:
aparc = bg.copy_file(aparc, outdirs['anatomydir'][0])
aparcnii = bg.convert(aparc, aparcnii)