else:
aparc = bg.copy_file(aparc, outdirs["anatomydir"][0])
aparcnii = bg.convert(aparc, aparcnii)
bg.remove_files([aparc])
# make pons
refdir, _ = outdirs["refdir"]
brainstem = os.path.join(refdir, "brainstem.nii.gz")
if os.path.isfile(brainstem):
logging.warning("brainstem %s exists, skipping" % (brainstem))
else:
# copy aseg+aparc to refdir
try:
caparcnii = bg.copy_file(aparcnii, refdir)
bg.make_brainstem(caparcnii)
brainstem = bg.unzip_file(brainstem)
bg.remove_files([caparcnii.replace(".gz", "")])
except:
logging.warning("Check %s" % (brainstem))
rawtracer, exists = outdirs["rawtracer"]
rawtracer_base, _ = os.path.split(rawtracer)
os.system("rm -rf %s" % rawtracer_base)
tracerdir, _ = outdirs["tracerdir"]
newname = "%s_%s" % (subid, tracer)
copied_ecats = bg.copy_files(ecats, tracerdir)
bg.convertallecat(copied_ecats, newname)
logging.info("ecats converted for %s " % (subid))
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 cerebellum
refdir, _ = outdirs['refdir']
cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
if os.path.isfile(cerebellum):
logging.warning('cerebellum %s exists, skipping' % (cerebellum))
else:
# copy aseg+aparc to refdir
try:
caparcnii = bg.copy_file(aparcnii, refdir)
bg.make_cerebellum_nibabel(caparcnii)
bg.remove_files([caparcnii])
except:
logging.warning('Fail: unable to make %s' % (cerebellum))
rawtracer, exists = outdirs['rawtracer']
os.system('rm %s' % rawtracer)
tracerdir, _ = outdirs['tracerdir']
newname = '%s_%s' % (subid, tracer)
copied_ecats = bg.copy_files(ecats, tracerdir)
bg.convertallecat(copied_ecats, newname)
logging.info('ecats converted for %s ' % (subid))
# make cerebellum
refdir,_ = outdirs['refdir']
cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
if os.path.isfile(cerebellum):
logging.warning('cerebellum %s exists, skipping'%(cerebellum))
else:
# copy aseg+aparc to refdir
try:
caparcnii = bg.copy_file(aparcnii, refdir)
bg.make_cerebellum_nibabel(caparcnii)
bg.remove_files([caparcnii])
except:
logging.warning('Fail: unable to make %s'%(cerebellum))
rawtracer, exists = outdirs['rawtracer']
os.system('rm %s'%rawtracer)
tracerdir, _ = outdirs['tracerdir']
newname = '%s_%s' % (subid, tracer)
niftis = bg.biograph_dicom_convert(tgz[0], tracerdir, subid, tracer)
## center new nifti files
orig_dir, _ = bg.make_dir(tracerdir, dirname='orig')
copied_orig = bg.copy_files(niftis, orig_dir)
bg.remove_files(niftis)
for f,nf in zip(copied_orig, niftis):
print f, nf
nicm.CMTransform(f).fix(new_file = nf)
logging.info('biograph dicoms converted for %s ' % (subid))
bg.remove_files([aparc])
# make cerebellum
refdir, _ = outdirs['refdir']
cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
if os.path.isfile(cerebellum):
logging.warning('cerebellum %s exists, skipping' % (cerebellum))
else:
# copy aseg+aparc to refdir
try:
caparcnii = bg.copy_file(aparcnii, refdir)
bg.make_cerebellum_nibabel(caparcnii)
bg.remove_files([caparcnii])
except:
logging.warning('Fail: unable to make %s' % (cerebellum))
rawtracer, exists = outdirs['rawtracer']
os.system('rm %s' % rawtracer)
tracerdir, _ = outdirs['tracerdir']
newname = '%s_%s' % (subid, tracer)
niftis = bg.biograph_dicom_convert(tgz[0], tracerdir, subid, tracer)
## center new nifti files
orig_dir, _ = bg.make_dir(tracerdir, dirname='orig')
copied_orig = bg.copy_files(niftis, orig_dir)
bg.remove_files(niftis)
for f, nf in zip(copied_orig, niftis):
print f, nf
nicm.CMTransform(f).fix(new_file=nf)
logging.info('biograph dicoms converted for %s ' % (subid))