def find_realigned(pth):
""" finds realigned files in realign_QA directory"""
realigndir = 'realign_QA'
globstr = os.path.join(pth, realigndir, 'rB*_FDG_*nii*')
tmprealigned = glob(globstr)
if len(tmprealigned)< 1:
tmprealigned = None
tmprealigned.sort()
globstr = os.path.join(pth, realigndir, 'rp_B*.txt*')
tmpparameterfile = pp.find_single_file(globstr)
return tmprealigned, tmpparameterfile
tmpparameterfile = rlgnout.outputs.realignment_parameters
anatdir = os.path.join(sub, 'anatomy')
if not os.path.isdir(anatdir):
logging.error('%s doesnt exist,skipping'%(anatdir))
continue
dvrdir = os.path.join(sub,'pib','dvr')
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*')
anatdir = os.path.join(sub, 'anatomy')
if not os.path.isdir(anatdir):
logging.error('%s doesnt exist,skipping' % (anatdir))
continue
dvrdir = os.path.join(sub, 'pib', 'dvr')
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*')
tracer = 'FDG'
user = os.environ['USER']
logging.info('###START %s :::'%(__file__))
logging.info('###TRACER %s :::'%(tracer))
logging.info('###USER : %s'%(user))
subs = bg.MyDirsDialog(prompt='Choose Subjects ',
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',
for item in sorted(outdict):
if outdict[item][0] is None:
logging.info("skipping %s, no FDG found" % (item))
continue
else:
ecats = outdict[item]
subid = item
logging.info(subid)
### XXXXXXXXXXXXXXXXX
## set_up_dir
outdirs = pp.set_up_dir(root, subid, tracer)
## set up MRI
brainmask = os.path.join(outdirs["anatomydir"][0], "brainmask.nii")
fsmri = pp.find_single_file(os.path.join(mridir, subid, "mri/brainmask.mgz"))
if os.path.isfile(brainmask):
logging.warning("%s has existing anatomy," "skipping" % (brainmask))
elif fsmri is None:
logging.error("%s NO MRI: %s" % (subid, fsmri))
else:
fsmri = bg.copy_file(fsmri, outdirs["anatomydir"][0])
brainmask = bg.convert(fsmri, brainmask)
bg.remove_files([fsmri])
# copy aseg+aparc
aparcnii = os.path.join(outdirs["anatomydir"][0], "%s_aparc_aseg.nii.gz" % subid)
aparc = pp.find_single_file(os.path.join(mridir, subid, "mri/aparc+aseg.mgz"))
if os.path.isfile(aparcnii):
logging.warning("%s has existing anatomy," "skipping" % (aparcnii))
elif aparc is None:
logging.info('###USER : %s' % (user))
subs = bg.MyDirsDialog(prompt='Choose Subjects ', indir='%s/' % root)
for s in subs:
_, subid = os.path.split(s)
# mk tracer directory in freesurfer
fsdir = os.path.join(mridir, subid)
if not os.path.isdir(fsdir):
logging.warning('%s missing, skipping' % fsdir)
continue
petdir, exists = bg.make_dir(fsdir, dirname='fdg')
if exists:
logging.warning('%s exists, skipping' % (petdir))
continue
globstr = os.path.join(s, 'fdg', 'nonan*pons*nii*')
ponsnormed = pp.find_single_file(globstr)
if ponsnormed is None:
logging.warning('%s missing, skipping' % (globstr))
continue
coregdir, exists = bg.make_dir('%s/fdg' % s, 'pet2mri')
if exists:
continue
## 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))
logging.info("###USER : %s" % (user))
subs = bg.MyDirsDialog(prompt="Choose Subjects ", indir="%s/" % root)
for s in subs:
_, subid = os.path.split(s)
# mk tracer directory in freesurfer
fsdir = os.path.join(mridir, subid)
if not os.path.isdir(fsdir):
logging.warning("%s missing, skipping" % fsdir)
continue
petdir, exists = bg.make_dir(fsdir, dirname="pib")
if exists:
logging.warning("%s exists, skipping" % (petdir))
continue
globstr = os.path.join(s, "pib", "dvr", "DVR*nii*")
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.warning("%s missing, skipping" % (globstr))
continue
coregdir, exists = bg.make_dir("%s/pib" % s, "pet2mri")
if exists:
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:
if 'None' in outdict[item][0]:
#print 'skipping %s'%(item)
logging.info('skipping %s' % (item))
continue
else:
petdir = outdict[item][0]
subid, _ = os.path.split(item)
print subid
logging.info(subid)
### XXXXXXXXXXXXXXXXX
## set_up_dir
outdirs = pp.set_up_dir(root, subid, tracer)
## set up MRI
brainmask = os.path.join(outdirs['anatomydir'][0], 'brainmask.nii')
fsmri = pp.find_single_file(
os.path.join(mridir, subid, 'mri/brainmask.mgz'))
if os.path.isfile(brainmask):
logging.warning('%s has existing anatomy,'\
'skipping'%(brainmask))
elif fsmri is None:
logging.error('NO MRI: %s' % (fsmri))
else:
fsmri = bg.copy_file(fsmri, outdirs['anatomydir'][0])
brainmask = bg.convert(fsmri, brainmask)
bg.remove_files([fsmri])
# copy aseg+aparc
aparcnii = os.path.join(outdirs['anatomydir'][0],
'%s_aparc_aseg.nii.gz' % subid)
aparc = pp.find_single_file(
os.path.join(mridir, subid, 'mri/aparc+aseg.mgz'))
anatdir = os.path.join(sub, 'anatomy')
if not os.path.isdir(anatdir):
logging.error('%s doesnt exist,skipping'%(anatdir))
continue
tracerdir = os.path.join(sub,'fdg')
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*')
except:
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
# find roi directory
roidir, exists = bg.make_dir(pth, dirname='stroke_masked_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 strokemask
globstr = '%s/rfs_cortical_mask_tu.nii*'%roidir
stroke_mask = pp.find_single_file(globstr)
if stroke_mask is None:
globstr = '%s/anatomy/fs_cortical_mask_tu.nii*'%sub
strokem = pp.find_single_file(globstr)
if strokem is None:
logging.error('%s missing, skipping'%(globstr))
continue
cstrokem = bg.copy_file(strokem, roidir)
globstr = '%s/coreg_mri2fdg/*.mat*'%pth
except:
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
# 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
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
pons_searchstr = '%s/ref_region/pons_tu.nii*' % tracerdir
pons = pp.find_single_file(pons_searchstr)
if 'gz' in pons:
pons = bg.unzip_file(pons)
if pons is None:
logging.warning('no pons_tu found for %s' % (subid))
continue
# find MRI
searchstring = '%s/anatomy/brainmask.nii' % sub
mri = pp.find_single_file(searchstring)
if mri is None:
logging.warning('no brainmask found for %s' % (subid))
continue
# find aparc_aseg
searchstring = '%s/anatomy/B*aparc_aseg.nii*' % sub
aparc = pp.find_single_file(searchstring)
if aparc is None:
subs = bg.MyDirsDialog(prompt='Choose Subjects ',
indir='%s/'%root)
for s in subs:
_, subid = os.path.split(s)
# mk tracer directory in freesurfer
fsdir = os.path.join(mridir, subid)
if not os.path.isdir(fsdir):
logging.warning('%s missing, skipping'%fsdir)
continue
petdir, exists = bg.make_dir(fsdir, dirname = 'fdg')
if exists:
logging.warning('%s exists, skipping'%(petdir))
continue
globstr = os.path.join(s, 'fdg','nonan*pons*nii*')
ponsnormed = pp.find_single_file(globstr)
if ponsnormed is None:
logging.warning('%s missing, skipping'%(globstr))
continue
coregdir,exists = bg.make_dir('%s/fdg'%s, 'pet2mri')
if exists:
continue
## 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))
m = pp.re.search('B[0-9]{2}-[0-9]{3}',fullsubid)
subid = m.group()
except:
logging.error('cant find ID in %s'%fullsubid)
continue
logging.info('%s'%subid)
# subjects tracer specific path
pth = os.path.join(sub, tracer.lower())
pvcdir, exists = bg.make_dir(dvrdir, 'pvc_rousset')
if exists:
logging.error('%s exists, remove to re-run'%(pvcdir))
continue
# get pons normed
globstr = '%s/nonan-ponsnormed_%s*nii*'%(pth,subid)
ponsnormd = pp.find_single_file(globstr)
if ponsnormd is None:
logging.error('%s missing, skipping'%(globstr))
continue
# copy ponsnormd to pvc directory
cponsnormd = bg.copy_file(ponsnormd, pvcdir)
# get raparc
corgdir = os.path.join(pth, 'coreg_mri2fdg')
globstr = '%s/rB*aparc_aseg.nii'%(corgdir)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('%s missing, skipping '%(globstr))
continue
#copy raparc_aseg to pvd dir
craparc = bg.copy_file(raparc, pvcdir)
# make brainamsk
try:
m = pp.re.search('B[0-9]{2}-[0-9]{3}', sub)
subid = m.group()
except:
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
# find roi directory
roidir, exists = bg.make_dir(pth, dirname='stroke_masked_roi_data')
if exists:
globstr = '%s/rfs_cortical_mask_tu.nii*' % roidir
stroke_mask = pp.find_single_file(globstr)
if stroke_mask is None:
exists = False
if not exists:
globstr = '%s/anatomy/fs_cortical_mask_tu.nii*' % sub
strokem = pp.find_single_file(globstr)
if strokem is None:
qa.plot_movement(tmpparameterfile, subid)
qa.calc_robust_median_diff(data4d)
qa.screen_pet(data4d)
# Coregister cerebellum, brainmask and aparc_aseg to pet space
#
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)
anatdir = os.path.join(sub, 'anatomy')
if not os.path.isdir(anatdir):
logging.error('%s doesnt exist,skipping' % (anatdir))
continue
tracerdir = os.path.join(sub, 'fdg')
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*')
subid = m.group()
except:
logging.error('cant find ID in %s'%fullsubid)
continue
logging.info('%s'%subid)
pth = os.path.join(sub, tracer.lower())
dvrdir = os.path.join(pth, 'dvr')
if not os.path.isdir(dvrdir):
logging.error('%s missing. skipping'%(dvrdir))
continue
pvcdir, exists = bg.make_dir(dvrdir, 'pvc_rousset')
if not exists:
logging.error('%s does not exist, skipping'%(pvcdir))
continue
globstr = '%s/rB*aparc_aseg.nii'%(pvcdir)
craparc = pp.find_single_file(globstr)
if craparc is None:
logging.error('%s missing, skipping '%(globstr))
continue
transferf = os.path.join(pvcdir, 'transfer_matrix.npy')
try:
transfer_mtx = rousset.np.load(transferf)
except:
logging.error('%s missing, skipping'%(transferf))
continue
obsf = os.path.join(pvcdir, 'observed.npy')
try:
obs = rousset.np.load(obsf)
except:
logging.error('%s missing, skipping'%(obsf))
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
pons_searchstr = "%s/ref_region/pons_tu.nii*" % tracerdir
pons = pp.find_single_file(pons_searchstr)
if "gz" in pons:
pons = bg.unzip_file(pons)
if pons is None:
logging.warning("no pons_tu found for %s" % (subid))
continue
# find MRI
searchstring = "%s/anatomy/brainmask.nii" % sub
mri = pp.find_single_file(searchstring)
if mri is None:
logging.warning("no brainmask found for %s" % (subid))
continue
# find aparc_aseg
searchstring = "%s/anatomy/B*aparc_aseg.nii*" % sub
aparc = pp.find_single_file(searchstring)
if aparc is None:
m = pp.re.search('B[0-9]{2}-[0-9]{3}', fullsubid)
subid = m.group()
except:
logging.error('cant find ID in %s' % fullsubid)
continue
logging.info('%s' % subid)
# subjects tracer specific path
pth = os.path.join(sub, tracer.lower())
pvcdir, exists = bg.make_dir(dvrdir, 'pvc_rousset')
if exists:
logging.error('%s exists, remove to re-run' % (pvcdir))
continue
# get pons normed
globstr = '%s/nonan-ponsnormed_%s*nii*' % (pth, subid)
ponsnormd = pp.find_single_file(globstr)
if ponsnormd is None:
logging.error('%s missing, skipping' % (globstr))
continue
# copy ponsnormd to pvc directory
cponsnormd = bg.copy_file(ponsnormd, pvcdir)
# get raparc
corgdir = os.path.join(pth, 'coreg_mri2fdg')
globstr = '%s/rB*aparc_aseg.nii' % (corgdir)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('%s missing, skipping ' % (globstr))
continue
#copy raparc_aseg to pvd dir
craparc = bg.copy_file(raparc, pvcdir)
# make brainamsk
qa.plot_movement(tmpparameterfile, subid)
qa.calc_robust_median_diff(data4d)
qa.screen_pet(data4d)
# Coregister cerebellum, brainmask and aparc_aseg to pet space
#
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)
except:
logging.error('no visit marker in %s' % fullsubid)
try:
m = pp.re.search('B[0-9]{2}-[0-9]{3}', fullsubid)
subid = m.group()
except:
logging.error('cant find ID in %s' % fullsubid)
continue
logging.info('%s' % subid)
pth = os.path.join(sub, tracer.lower())
# 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
# get raparc
corgdir = os.path.join(pth, 'roi_data')
globstr = '%s/rB*aparc_aseg.nii*' % (corgdir)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('%s missing, skipping ' % (globstr))
continue
data = pp.nibabel.load(dat).get_data()
meand = pp.mean_from_labels(roid, raparc, data)
alld[subid] = meand
###write to file
logging.info('###USER : %s' % (user))
subs = bg.MyDirsDialog(prompt='Choose Subjects ', indir='%s/' % root)
for s in subs:
_, subid = os.path.split(s)
# mk tracer directory in freesurfer
fsdir = os.path.join(mridir, subid)
if not os.path.isdir(fsdir):
logging.warning('%s missing, skipping' % fsdir)
continue
petdir, exists = bg.make_dir(fsdir, dirname='pib')
if exists:
logging.warning('%s exists, skipping' % (petdir))
continue
globstr = os.path.join(s, 'pib', 'dvr', 'DVR*nii*')
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.warning('%s missing, skipping' % (globstr))
continue
coregdir, exists = bg.make_dir('%s/pib' % s, 'pet2mri')
if exists:
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:
