## find brainmask
globstr = os.path.join(s, 'anatomy', 'brainmask.nii')
brainmask = pp.find_single_file(globstr)
## find sum
globstr = os.path.join(s, 'fdg', 'sum_r*.nii')
sum = pp.find_single_file(globstr)
if brainmask is None or sum is None:
logging.error('pet2mri sum: %s brainmask: %s' % (sum, brainmask))
continue
## coreg pet 2 brainmask
cpons = bg.copy_file(ponsnormed, coregdir)
csum = bg.copy_file(sum, coregdir)
corg_out = pp.simple_coregister(str(brainmask),
str(csum),
other=str(cpons))
if not corg_out.runtime.returncode == 0:
logging.error(corg_out.runtime.stderr)
continue
rpons = corg_out.outputs.coregistered_files
# copy ponsnormed to freesurfer subjects petdir
cponsnormed = bg.copy_file(rpons, petdir)
globstr = os.path.join(fsdir, 'mri', 'T1.mgz')
t1 = pp.find_single_file(globstr)
if t1 is None:
logging.error('%s not found' % globstr)
continue
xfm = fst.fs_generate_dat(cponsnormed, t1, subid)
outfiles = fst.pet_2_surf(cponsnormed, xfm, mridir)
if brainmask is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
brainmask = bg.unzip_file(brainmask)
# copy to warp dir
cmean20 = bg.copy_file(mean20, warpdir)
cdvr = bg.copy_file(dvr, warpdir)
cbm = bg.copy_file(brainmask, warpdir)
# coreg pet to brainmask
logging.info('Run coreg')
# cast everything to string
cbm = str(cbm)
cmean20 = str(cmean20)
cdvr = str(cdvr)
corgout = pp.simple_coregister(cbm, cmean20, other=cdvr)
if not corgout.runtime.returncode == 0:
logging.error('coreg pet to mri failed %s'%subid)
shutil.rmtree(warpdir)
continue
rcmean20 = corgout.outputs.coregistered_source
rdvr = corgout.outputs.coregistered_files
# warp brainmask to template, apply to dvr
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rdvr)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s'%subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s'%subid)
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)
# clean up
# remove copied unrealigned frames
bg.remove_files(newnifti)
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)
# clean up
# remove copied unrealigned frames
bg.remove_files(newnifti)
if brainmask is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
brainmask = bg.unzip_file(brainmask)
# copy to warp dir
csumfdg = bg.copy_file(sumfdg, warpdir)
cpnfdg = bg.copy_file(pnfdg, warpdir)
cbm = bg.copy_file(brainmask, warpdir)
# coreg pet to brainmask
logging.info('Run coreg')
# cast everything to string
cbm = str(cbm)
csumfdg = str(csumfdg)
cpnfdg = str(cpnfdg)
corgout = pp.simple_coregister(cbm, csumfdg, other=cpnfdg)
if not corgout.runtime.returncode == 0:
logging.error('coreg pet to mri failed %s' % subid)
shutil.rmtree(warpdir)
continue
rcsumfdg = corgout.outputs.coregistered_source
rpnfdg = corgout.outputs.coregistered_files
# warp brainmask to template, apply to pnfdg
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rpnfdg)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s' % subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s' % subid)
globstr = os.path.join(s, "anatomy", "brainmask.nii")
brainmask = pp.find_single_file(globstr)
## find sum
globstr = os.path.join(s, "pib", "realign_QA", "mean20min*.nii")
sum = pp.find_single_file(globstr)
if brainmask is None or sum is None:
logging.error("pet2mri sum: %s brainmask: %s" % (sum, brainmask))
continue
# move dvr and sum to coregdir, unzip if necessary
cdvr = bg.copy_file(dvr, coregdir)
csum = bg.copy_file(sum, coregdir)
cdvr = bg.unzip_file(cdvr)
csum = bg.unzip_file(csum)
## coreg pet 2 brainmask
corg_out = pp.simple_coregister(str(brainmask), str(csum), other=str(cdvr))
if not corg_out.runtime.returncode == 0:
logging.error(corg_out.runtime.traceback)
continue
rdvr = corg_out.outputs.coregistered_files
# copy dvr to freesurfer subjects petdir
cdvr = bg.copy_file(rdvr, petdir)
globstr = os.path.join(fsdir, "mri", "T1.mgz")
t1 = pp.find_single_file(globstr)
if t1 is None:
logging.error("%s not found" % globstr)
continue
xfm = fst.fs_generate_dat(cdvr, t1, subid)
outfiles = fst.pet_2_surf(cdvr, xfm, mridir)
# zip files in coregdir
allf = glob("%s/*" % coregdir)
if brainmask is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
brainmask = bg.unzip_file(brainmask)
# copy to warp dir
csumfdg = bg.copy_file(sumfdg, warpdir)
cpnfdg = bg.copy_file(pnfdg, warpdir)
cbm = bg.copy_file(brainmask, warpdir)
# coreg pet to brainmask
logging.info('Run coreg')
# cast everything to string
cbm = str(cbm)
csumfdg = str(csumfdg)
cpnfdg = str(cpnfdg)
corgout = pp.simple_coregister(cbm, csumfdg, other=cpnfdg)
if not corgout.runtime.returncode == 0:
logging.error('coreg pet to mri failed %s'%subid)
shutil.rmtree(warpdir)
continue
rcsumfdg = corgout.outputs.coregistered_source
rpnfdg = corgout.outputs.coregistered_files
# warp brainmask to template, apply to pnfdg
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rpnfdg)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s'%subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s'%subid)
if brainmask is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
brainmask = bg.unzip_file(brainmask)
# copy to warp dir
cmean20 = bg.copy_file(mean20, warpdir)
cdvr = bg.copy_file(dvr, warpdir)
cbm = bg.copy_file(brainmask, warpdir)
# coreg pet to brainmask
logging.info('Run coreg')
# cast everything to string
cbm = str(cbm)
cmean20 = str(cmean20)
cdvr = str(cdvr)
corgout = pp.simple_coregister(cbm, cmean20, other=cdvr)
if not corgout.runtime.returncode == 0:
logging.error('coreg pet to mri failed %s' % subid)
shutil.rmtree(warpdir)
continue
rcmean20 = corgout.outputs.coregistered_source
rdvr = corgout.outputs.coregistered_files
# warp brainmask to template, apply to dvr
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rdvr)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s' % subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s' % subid)
