def transform_vol(invol, xfm, space_defining):
invol = bg.unzip_file(invol) # in case zipped
xfm = bg.unzip_file(xfm) # in case zipped
space_defining = bg.unzip_file(space_defining) # in case zipped
pp.apply_transform_onefile(xfm, invol)
pp.reslice(space_defining, invol)
rinvol = pp.prefix_filename(invol, prefix='r')
bg.remove_files([invol])
bg.zip_files([space_defining])
return rinvol
def transform_vol(invol, xfm, space_defining):
invol = bg.unzip_file(invol)# in case zipped
xfm = bg.unzip_file(xfm)# in case zipped
space_defining = bg.unzip_file(space_defining)# in case zipped
pp.apply_transform_onefile(xfm, invol)
pp.reslice(space_defining, invol)
rinvol = pp.prefix_filename(invol, prefix='r')
bg.remove_files([invol])
bg.zip_files([space_defining])
return rinvol
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('cant find ID in %s' % sub)
continue
logging.info('%s' % subid)
pth = os.path.join(sub, tracer.lower())
if not os.path.isdir(pth):
logging.error('%s does not exist, skipping' % pth)
continue
# get dvr
globstr = '%s/dvr/DVR*nii*' % (pth)
dat = pp.find_single_file(globstr)
if dat is None:
logging.error('%s missing, skipping' % (globstr))
continue
dat = bg.unzip_file(dat) # in case zipped
# get raparc
globstr = '%s/coreg/rB*aparc_aseg.nii*' % (pth)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('Missing %s, SKIPPING' % globstr)
continue
data = pp.nibabel.load(dat).get_data()
meand = pp.mean_from_labels(roid, raparc, data)
alld[subid] = meand
###write to file
_, roifname = os.path.split(roifile)
outf = os.path.join(userhome,
'roivalues_%s_%s_%s' % (tracer, cleantime, roifname))
fid = open(outf, 'w+')
logging.info('Coreg %s' % (subid))
coregdir, exists = bg.make_dir(pth, 'coreg')
if exists:
logging.warning('%s exists, remove to rerun' % (coregdir))
continue
# copy brainmask, aparc_aseg, cerebellum to coreg dir
basedir, _ = os.path.split(pth)
# brainmask
globstr = os.path.join(basedir, 'anatomy', 'brainmask.nii*')
brainmask = pp.find_single_file(globstr)
if brainmask is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(coregdir)
continue
cbrainmask = bg.copy_file(brainmask, coregdir)
cbrainmask = bg.unzip_file(cbrainmask)
# aparc aseg
globstr = os.path.join(basedir, 'anatomy', '*aparc_aseg.nii*')
aparc = pp.find_single_file(globstr)
if aparc is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(coregdir)
continue
caparc = bg.copy_file(aparc, coregdir)
caparc = bg.unzip_file(caparc)
# cerebellum
globstr = os.path.join(pth, 'ref_region', 'grey_cerebellum.nii*')
cere = pp.find_single_file(globstr)
if cere is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(coregdir)
if not os.path.isdir(dvrdir):
logging.error('%s doesnt exist,skipping'%(dvrdir))
continue
# make/check warp dir
warpdir, exists = bg.make_dir(dvrdir, 'warp_%s'%tname)
if exists:
logging.warning('%s exists, remove to rerun'%(warpdir))
continue
#get brainmask
globstr = os.path.join(dvrdir, 'DVR-%s*.nii*'%subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
dvr = bg.unzip_file(dvr)
# get mean 20 minute pib
globstr = os.path.join(sub,'pib','realign_QA', 'mean20min*.nii*')
mean20 = pp.find_single_file(globstr)
if mean20 is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
mean20 = bg.unzip_file(mean20)
# brainmask
globstr = os.path.join(anatdir, 'brainmask.nii*')
brainmask = pp.find_single_file(globstr)
if brainmask is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
logging.info('Coreg %s'%(subid))
coregdir, exists = bg.make_dir(pth, 'coreg')
if exists:
logging.warning('%s exists, remove to rerun'%(coregdir))
continue
# copy brainmask, aparc_aseg, cerebellum to coreg dir
basedir, _ = os.path.split(pth)
# brainmask
globstr = os.path.join(basedir, 'anatomy', 'brainmask.nii*')
brainmask = pp.find_single_file(globstr)
if brainmask is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(coregdir)
continue
cbrainmask = bg.copy_file(brainmask, coregdir)
cbrainmask = bg.unzip_file(cbrainmask)
# aparc aseg
globstr = os.path.join(basedir, 'anatomy', '*aparc_aseg.nii*')
aparc = pp.find_single_file(globstr)
if aparc is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(coregdir)
continue
caparc = bg.copy_file(aparc, coregdir)
caparc = bg.unzip_file(caparc)
# cerebellum
globstr = os.path.join(pth, 'ref_region', 'grey_cerebellum.nii*')
cere = pp.find_single_file(globstr)
if cere is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(coregdir)
logging.error('cant find ID in %s'%sub)
continue
logging.info('%s'%subid)
pth = os.path.join(sub, tracer.lower())
if not os.path.isdir(pth):
logging.error('%s does not exist, skipping'%pth)
continue
# get dvr
globstr = '%s/dvr/DVR*nii*'%(pth)
dat = pp.find_single_file(globstr)
if dat is None:
logging.error('%s missing, skipping'%(globstr))
continue
dat = bg.unzip_file(dat)# in case zipped
# get raparc
globstr = '%s/coreg/rB*aparc_aseg.nii*'%(pth)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('Missing %s, SKIPPING'%globstr)
continue
data = pp.nibabel.load(dat).get_data()
meand = pp.mean_from_labels(roid, raparc, data)
alld[subid] = meand
###write to file
_, roifname = os.path.split(roifile)
outf = os.path.join(userhome, 'roivalues_%s_%s_%s'%(tracer,
cleantime,
roifname))
if not os.path.isdir(dvrdir):
logging.error('%s doesnt exist,skipping' % (dvrdir))
continue
# make/check warp dir
warpdir, exists = bg.make_dir(dvrdir, 'warp_%s' % tname)
if exists:
logging.warning('%s exists, remove to rerun' % (warpdir))
continue
#get brainmask
globstr = os.path.join(dvrdir, 'DVR-%s*.nii*' % subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
dvr = bg.unzip_file(dvr)
# get mean 20 minute pib
globstr = os.path.join(sub, 'pib', 'realign_QA', 'mean20min*.nii*')
mean20 = pp.find_single_file(globstr)
if mean20 is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
mean20 = bg.unzip_file(mean20)
# brainmask
globstr = os.path.join(anatdir, 'brainmask.nii*')
brainmask = pp.find_single_file(globstr)
if brainmask is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
if not os.path.isdir(tracerdir):
logging.error('%s doesnt exist,skipping' % (tracerdir))
continue
# make/check warp dir
warpdir, exists = bg.make_dir(tracerdir, 'warp_%s' % tname)
if exists:
logging.warning('%s exists, remove to rerun' % (warpdir))
continue
#get ponsnormed
globstr = os.path.join(tracerdir, 'ponsnormed_%s*.nii*' % subid)
pnfdg = pp.find_single_file(globstr)
if pnfdg is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
pnfdg = bg.unzip_file(pnfdg)
# get summed fdg
globstr = os.path.join(tracerdir, 'sum_rB*.nii*')
sumfdg = pp.find_single_file(globstr)
if sumfdg is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
sumfdg = bg.unzip_file(sumfdg)
# brainmask
globstr = os.path.join(anatdir, 'brainmask.nii*')
brainmask = pp.find_single_file(globstr)
if brainmask is None:
logging.error('%s not found. skipping' % globstr)
shutil.rmtree(warpdir)
continue
logging.warning("remove %s to rerun?" % coregdir)
continue
## find brainmask
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)
if not os.path.isdir(tracerdir):
logging.error('%s doesnt exist,skipping'%(tracerdir))
continue
# make/check warp dir
warpdir, exists = bg.make_dir(tracerdir, 'warp_%s'%tname)
if exists:
logging.warning('%s exists, remove to rerun'%(warpdir))
continue
#get ponsnormed
globstr = os.path.join(tracerdir, 'ponsnormed_%s*.nii*'%subid)
pnfdg = pp.find_single_file(globstr)
if pnfdg is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
pnfdg = bg.unzip_file(pnfdg)
# get summed fdg
globstr = os.path.join(tracerdir, 'sum_rB*.nii*')
sumfdg = pp.find_single_file(globstr)
if sumfdg is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
sumfdg = bg.unzip_file(sumfdg)
# brainmask
globstr = os.path.join(anatdir, 'brainmask.nii*')
brainmask = pp.find_single_file(globstr)
if brainmask is None:
logging.error('%s not found. skipping'%globstr)
shutil.rmtree(warpdir)
continue
logging.info('%s'%subid)
pth = os.path.join(sub, tracer.lower())
if not os.path.isdir(pth):
logging.error('%s does not exist, skipping'%pth)
continue
# find roi directory
roidir, exists = bg.make_dir(pth, dirname='roi_data')
# get pons normed
globstr = '%s/nonan-ponsnormed*fdg**nii*'%(pth)
dat = pp.find_single_file(globstr)
if dat is None:
logging.error('%s missing, skipping'%(globstr))
continue
dat = bg.unzip_file(dat)# in case zipped
# get raparc
#if exists: #roidir exists so raparc_aseg should also
# globstr = '%s/rB*aparc_aseg.nii*'%(roidir)
# raparc = pp.find_single_file(globstr)
# if raparc is None:
# exists = False
#if not exists: # check coreg directory
globstr = '%s/coreg_mri2fdg/rB*aparc_aseg.nii*'%(pth)
raparc = pp.find_single_file(globstr)
if raparc is None:
exists = False
else:
exists = True
if not exists: #last chance
# find aparcaseg
if len(nifti) < 5:
logging.warning(
'fdg frames not found or too few for %s skipping' % (subid))
continue
nifti.sort()
nifti = bg.unzip_files(nifti)
hasqa = False
rlgnout, newnifti = pp.realigntoframe1(nifti)
if rlgnout is None and newnifti is None:
logging.warning('%s :existing realign_QA ' % (subid))
tmprealigned, tmpparameterfile = find_realigned(tracerdir)
if tmprealigned is None or tmpparameterfile is None:
logging.warning('%s :missing realigned, skipping ' % (subid))
continue
logging.info('found %s %s' % (tmprealigned, tmpparameterfile))
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)
logging.info('%s' % subid)
pth = os.path.join(sub, tracer.lower())
if not os.path.isdir(pth):
logging.error('%s does not exist, skipping' % pth)
continue
# find roi directory
roidir, exists = bg.make_dir(pth, dirname='roi_data')
# get pons normed
globstr = '%s/nonan-ponsnormed*fdg**nii*' % (pth)
dat = pp.find_single_file(globstr)
if dat is None:
logging.error('%s missing, skipping' % (globstr))
continue
dat = bg.unzip_file(dat) # in case zipped
# get raparc
#if exists: #roidir exists so raparc_aseg should also
# globstr = '%s/rB*aparc_aseg.nii*'%(roidir)
# raparc = pp.find_single_file(globstr)
# if raparc is None:
# exists = False
#if not exists: # check coreg directory
globstr = '%s/coreg_mri2fdg/rB*aparc_aseg.nii*' % (pth)
raparc = pp.find_single_file(globstr)
if raparc is None:
exists = False
else:
exists = True
if not exists: #last chance
# find aparcaseg
if len(nifti) < 5:
logging.warning("fdg frames not found or too few for %s skipping" % (subid))
continue
nifti.sort()
nifti = bg.unzip_files(nifti)
hasqa = False
rlgnout, newnifti = pp.realigntoframe1(nifti)
if rlgnout is None and newnifti is None:
logging.warning("%s :existing realign_QA " % (subid))
tmprealigned, tmpparameterfile = find_realigned(tracerdir)
if tmprealigned is None or tmpparameterfile is None:
logging.warning("%s :missing realigned, skipping " % (subid))
continue
logging.info("found %s %s" % (tmprealigned, tmpparameterfile))
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)
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.warning('remove %s to rerun?' % coregdir)
continue
## find brainmask
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)