logging.info("realigned %s" % subid)
# make final mean image
meanimg = pp.make_summed_image(tmprealigned)
# move data back to main directory
nifti_dir, _ = os.path.split(nifti[0])
movedmean = bg.copy_file(meanimg, nifti_dir)
# QA
if not hasqa:
logging.info("qa %s" % subid)
qa.plot_movement(tmpparameterfile, subid)
# get rid of NAN in files
no_nanfiles = pp.clean_nan(tmprealigned)
# make 4d volume to visualize movement
img4d = qa.make_4d_nibabel(no_nanfiles)
bg.zip_files(tmprealigned)
# save qa image
# qa.save_qa_img(img4d)
qa.plot_movement(tmpparameterfile, subid)
qa.calc_robust_median_diff(img4d)
qa.screen_pet(img4d)
# remove tmpfiles
bg.remove_files(no_nanfiles)
bg.remove_files(newnifti)
# coreg pons to pet
# find PONS
indir='%s/'%root)
subs.sort()
for sub in subs:
_, subid = os.path.split(sub)
logging.info('%s'%subid)
# check is ponsnormed exists
searchstring = '%s/fdg/nonan-ponsnormed_*.nii*'%sub
pn = pp.find_single_file(searchstring)
if pn is not None:
logging.info('%s exists, skipping'%(pn))
continue
# find sum
searchstring = '%s/fdg/sum_rB*.nii*' % sub
sum = pp.find_single_file(searchstring)
if sum is None:
logging.error('%s not found'%(searchstring))
continue
searchstr = '%s/fdg/ref_region/rpons_tu.nii*' % sub
pons = pp.find_single_file(searchstr)
if pons is None:
logging.error('%s not found'%(searchstring))
continue
outfname = os.path.join(sub, 'fdg',
'ponsnormed_%s_%s.nii'%(subid,
tracer.lower()))
pp.make_pons_normed(pet, newpons, outfname)
no_nanfiles = pp.clean_nan([outfname])
logging.info('saved %s'%(outfname))
logging.info('realigned %s' % subid)
# make final mean image
meanimg = pp.make_summed_image(tmprealigned)
# move data back to main directory
nifti_dir, _ = os.path.split(nifti[0])
movedmean = bg.copy_file(meanimg, nifti_dir)
#QA
if not hasqa:
logging.info('qa %s' % subid)
qa.plot_movement(tmpparameterfile, subid)
# get rid of NAN in files
no_nanfiles = pp.clean_nan(tmprealigned)
#make 4d volume to visualize movement
img4d = qa.make_4d_nibabel(no_nanfiles)
bg.zip_files(tmprealigned)
#save qa image
#qa.save_qa_img(img4d)
qa.plot_movement(tmpparameterfile, subid)
qa.calc_robust_median_diff(img4d)
qa.screen_pet(img4d)
#remove tmpfiles
bg.remove_files(no_nanfiles)
bg.remove_files(newnifti)
# coreg pons to pet
# find PONS