nifti = glob('%s/pib/%s_PIB*.nii' % (sub, subid))
nifti.sort()
if len(nifti) < 34:
logging.error('%s only has %d frames, RUNBYHAND' %
(subid, len(nifti)))
continue
pth, _ = os.path.split(nifti[0])
realigndir = os.path.join(pth, 'realign_QA')
if os.path.isdir(realigndir):
logging.error('%s exists, remove to rerun' % (realigndir))
continue
rlgnout, newnifti = pp.realigntoframe17(nifti)
tmpparameterfile = rlgnout.outputs.realignment_parameters
realigndir, _ = os.path.split(tmpparameterfile)
sum1_5 = pp.make_summed_image(newnifti[:5], prefix='sum1_5_')
mean_img = rlgnout.outputs.mean_image
#coregister 1-5 to mean
crg_out = pp.simple_coregister(mean_img, sum1_5, newnifti[:5])
if crg_out.runtime.returncode is not 0:
logging.error('Failed to coreg 1-5 to mean for %s' % subid)
continue
# grab all realigned files
allrealigned = crg_out.outputs.coregistered_files + \
rlgnout.outputs.realigned_files
# make new mean files(s) based on fully realigned files
# 1. first 20 mins for coreg (frames 1-23)
# 2. 40-60 mins for possible SUVR (frames 28-31)
mean_20min = pp.make_mean_20min(allrealigned)
mean_40_60min = pp.make_mean_40_60(allrealigned)
tmpparameterfile = bg.unzip_file(tmpparameterfile)
tmprealigned = [bg.unzip_file(x) for x in tmprealigned]
hasqa = True
elif rlgnout.runtime.returncode is not 0:
logging.warning("Failed to realign %s" % subid)
continue
else:
tmprealigned = rlgnout.outputs.realigned_files
tmpmean = rlgnout.outputs.mean_image
tmpparameterfile = rlgnout.outputs.realignment_parameters
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
nifti = glob('%s/pib/%s_PIB*.nii'%(sub, subid))
nifti.sort()
if len(nifti) < 34:
logging.error('%s only has %d frames, RUNBYHAND'%(subid,
len(nifti)))
continue
pth, _ = os.path.split(nifti[0])
realigndir = os.path.join(pth, 'realign_QA')
if os.path.isdir(realigndir):
logging.error('%s exists, remove to rerun'%(realigndir))
continue
rlgnout, newnifti = pp.realigntoframe17(nifti)
tmpparameterfile = rlgnout.outputs.realignment_parameters
realigndir, _ = os.path.split(tmpparameterfile)
sum1_5 = pp.make_summed_image(newnifti[:5],
prefix='sum1_5_')
mean_img = rlgnout.outputs.mean_image
#coregister 1-5 to mean
crg_out = pp.simple_coregister(mean_img, sum1_5, newnifti[:5])
if crg_out.runtime.returncode is not 0:
logging.error('Failed to coreg 1-5 to mean for %s' % subid)
continue
# grab all realigned files
allrealigned = crg_out.outputs.coregistered_files + \
rlgnout.outputs.realigned_files
# make new mean files(s) based on fully realigned files
# 1. first 20 mins for coreg (frames 1-23)
# 2. 40-60 mins for possible SUVR (frames 28-31)
mean_20min = pp.make_mean_20min(allrealigned)
mean_40_60min = pp.make_mean_40_60(allrealigned)
tmpparameterfile = bg.unzip_file(tmpparameterfile)
tmprealigned = [bg.unzip_file(x) for x in tmprealigned]
hasqa = True
elif rlgnout.runtime.returncode is not 0:
logging.warning('Failed to realign %s' % subid)
continue
else:
tmprealigned = rlgnout.outputs.realigned_files
tmpmean = rlgnout.outputs.mean_image
tmpparameterfile = rlgnout.outputs.realignment_parameters
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
