def main(tgz, newid, outdir=None):
""" untars tgz, replaces PatientID PatientName
with new id, and save to outdir (default origdir/newtgz"""
# mv dicom to tmp directory
tgz = os.path.abspath(tgz)
origdir, orignme = os.path.split(tgz)
tmptgz = bg.copy_tmpdir(tgz)
# un-archive
pth = bg.tar_cmd(tmptgz)
newdir, exists = bg.make_dir(pth, dirname='dicomfiles')
startdir = os.getcwd()
os.chdir(pth)
dcms = bg.find_dicoms(pth)
keys = dcms.keys()
keys = [x for x in keys if not newdir in x]
for k in keys:
for dcm in dcms[k]:
plan = dicom.read_file(dcm)
plan.PatientID = newid
plan.PatientName = newid
_, dcm_name = os.path.split(dcm)
newdcm = os.path.join(newdir, dcm_name)
dicom.write_file(newdcm, plan)
# create tar archive of updated dicoms
if outdir is None:
outdir, _ = bg.make_dir(origdir, dirname="newtgz")
newtgz = os.path.join(outdir, orignme)
cmd = 'tar cfvz %s dicomfiles' % (newtgz)
os.system(cmd)
os.chdir(startdir)
print 'removing %s' % pth
os.system('rm -rf %s' % (pth))
print 'wrote ', newtgz
return newtgz
def main(tgz, newid, outdir=None):
""" untars tgz, replaces PatientID PatientName
with new id, and save to outdir (default origdir/newtgz"""
# mv dicom to tmp directory
tgz = os.path.abspath(tgz)
origdir, orignme = os.path.split(tgz)
tmptgz = bg.copy_tmpdir(tgz)
# un-archive
pth = bg.tar_cmd(tmptgz)
newdir, exists = bg.make_dir(pth, dirname='dicomfiles')
startdir = os.getcwd()
os.chdir(pth)
dcms = bg.find_dicoms(pth)
keys = dcms.keys()
keys = [x for x in keys if not newdir in x]
for k in keys:
for dcm in dcms[k]:
plan = dicom.read_file(dcm)
plan.PatientID = newid
plan.PatientName = newid
_, dcm_name = os.path.split(dcm)
newdcm = os.path.join(newdir, dcm_name)
dicom.write_file(newdcm, plan)
# create tar archive of updated dicoms
if outdir is None:
outdir, _ = bg.make_dir(origdir, dirname="newtgz")
newtgz = os.path.join(outdir, orignme)
cmd = 'tar cfvz %s dicomfiles'%(newtgz)
os.system(cmd)
os.chdir(startdir)
print 'removing %s'%pth
os.system('rm -rf %s'%(pth))
print 'wrote ', newtgz
return newtgz
def setup_dir(root, subid, tracer):
""" check for and Make Subjects Target Directories
Returns Dict of final directories and if they exist"""
outdirs = {}
subdir, exists = bg.make_dir(root, dirname=subid)
outdirs.update(dict(subdir=[subdir, exists]))
tracerdir,exists = bg.make_dir(subdir,
dirname = '%s' % (tracer.lower()) )
outdirs.update(dict(tracerdir=[tracerdir, exists]))
rawdatadir, exists = bg.make_dir(subdir, dirname = 'raw')
outdirs.update(dict(rawdatadir=[rawdatadir, exists]))
rawtracer, exists = bg.make_dir(rawdatadir, dirname = tracer)
outdirs.update(dict(rawtracer=[rawtracer, exists]))
anatomydir, exists = bg.make_dir(subdir,dirname='anatomy')
outdirs.update(dict(anatomydir=[anatomydir, exists]))
refdir, exists = bg.make_rec_dir(tracerdir,dirname='ref_region')
outdirs.update(dict(refdir=[refdir, exists]))
#print 'directories created for %s' % subid
logging.info('directories created for %s'%(subid))
for k, v in sorted(outdirs.values()):
logging.info('%s : previously existed = %s'%(k,v))
return outdirs
def setup_dir(root, subid, tracer):
""" check for and Make Subjects Target Directories
Returns Dict of final directories and if they exist"""
outdirs = {}
subdir, exists = bg.make_dir(root, dirname=subid)
outdirs.update(dict(subdir=[subdir, exists]))
tracerdir, exists = bg.make_dir(subdir, dirname='%s' % (tracer.lower()))
outdirs.update(dict(tracerdir=[tracerdir, exists]))
rawdatadir, exists = bg.make_dir(subdir, dirname='raw')
outdirs.update(dict(rawdatadir=[rawdatadir, exists]))
rawtracer, exists = bg.make_dir(rawdatadir, dirname=tracer)
outdirs.update(dict(rawtracer=[rawtracer, exists]))
anatomydir, exists = bg.make_dir(subdir, dirname='anatomy')
outdirs.update(dict(anatomydir=[anatomydir, exists]))
refdir, exists = bg.make_rec_dir(tracerdir, dirname='ref_region')
outdirs.update(dict(refdir=[refdir, exists]))
#print 'directories created for %s' % subid
logging.info('directories created for %s' % (subid))
for k, v in sorted(outdirs.values()):
logging.info('%s : previously existed = %s' % (k, v))
return outdirs
def realigntoframe17(niftilist):
"""given list of nifti files
copies/creates realign_QA
removes first 5 frames
realignes rest to the 17th frame
"""
startdir = os.getcwd()
niftilist.sort()
basepth, _ = os.path.split(niftilist[0])
tmpdir, exists = bg.make_dir(basepth, 'realign_QA')
if exists:
return None, None
# copy files to tmp dir
copiednifti = []
for f in niftilist:
newf = bg.copy_file(f, tmpdir)
copiednifti.append(str(newf))
# put files in correct order
os.chdir(tmpdir)
alteredlist = [x for x in copiednifti]
frame17 = alteredlist[16]
alteredlist.remove(frame17)
alteredlist = alteredlist[5:]
alteredlist.insert(0, frame17)
#print 'alteredlist', alteredlist
# realign
rlgn = spm.Realign(matlab_cmd='matlab-spm8')
rlgn.inputs.in_files = alteredlist
rlgn.inputs.ignore_exception = True
#rlgn.inputs.write_which = [2,0]
#rlgn.register_to_mean = True
rlgnout = rlgn.run()
os.chdir(startdir)
return rlgnout, copiednifti
def realigntoframe1(niftilist):
"""given list of nifti files
copies relevent files to realign_QA
realigns to the 1st frame
"""
startdir = os.getcwd()
niftilist.sort()
basepth, _ = os.path.split(niftilist[0])
tmpdir, exists = bg.make_dir(basepth, 'realign_QA')
if exists:
return None, None
# copy files to tmp dir
copiednifti = []
for f in niftilist:
newf = bg.copy_file(f, tmpdir)
copiednifti.append(str(newf))
print 'copied nifti', copiednifti
# realign to frame1
os.chdir(tmpdir)
rlgn = spm.Realign()
rlgn.inputs.matlab_cmd = 'matlab-spm8'
rlgn.inputs.in_files = copiednifti
rlgn.inputs.ignore_exception = True
#print rlgn.mlab.cmdline
rlgnout = rlgn.run()
os.chdir(startdir)
return rlgnout, copiednifti
def realigntoframe1(niftilist):
"""given list of nifti files
copies relevent files to realign_QA
realigns to the 1st frame
"""
startdir = os.getcwd()
niftilist.sort()
basepth, _ = os.path.split(niftilist[0])
tmpdir, exists = bg.make_dir(basepth, 'realign_QA')
if exists:
return None, None
# copy files to tmp dir
copiednifti = []
for f in niftilist:
newf = bg.copy_file(f, tmpdir)
copiednifti.append(str(newf))
print 'copied nifti', copiednifti
# realign to frame1
os.chdir(tmpdir)
rlgn = spm.Realign()
rlgn.inputs.matlab_cmd = 'matlab-spm8'
rlgn.inputs.in_files = copiednifti
rlgn.inputs.ignore_exception = True
#print rlgn.mlab.cmdline
rlgnout = rlgn.run()
os.chdir(startdir)
return rlgnout, copiednifti
def realigntoframe17(niftilist):
"""given list of nifti files
copies/creates realign_QA
removes first 5 frames
realignes rest to the 17th frame
"""
startdir = os.getcwd()
niftilist.sort()
basepth, _ = os.path.split(niftilist[0])
tmpdir, exists = bg.make_dir(basepth, 'realign_QA')
if exists:
return None, None
# copy files to tmp dir
copiednifti = []
for f in niftilist:
newf = bg.copy_file(f, tmpdir)
copiednifti.append(str(newf))
# put files in correct order
os.chdir(tmpdir)
alteredlist =[x for x in copiednifti]
frame17 = alteredlist[16]
alteredlist.remove(frame17)
alteredlist = alteredlist[5:]
alteredlist.insert(0, frame17)
#print 'alteredlist', alteredlist
# realign
rlgn = spm.Realign(matlab_cmd='matlab-spm8')
rlgn.inputs.in_files = alteredlist
rlgn.inputs.ignore_exception = True
#rlgn.inputs.write_which = [2,0]
#rlgn.register_to_mean = True
rlgnout = rlgn.run()
os.chdir(startdir)
return rlgnout, copiednifti
def rousset_labellist(labeldir, hemi, outdir='rousset_labels'):
rousset_labels = {'frontal':['frontalpole','lateralorbitofrontal'],
'temporal' : ['temporalpole'],
'parietal' : ['inferiorparietal'],
'precuneus' : ['precuneus'],
'cingulate' : ['posteriorcingulate', 'isthmuscingulate']
}
pth, _ = os.path.split(labeldir)
outdir, exists = bg.make_dir(pth, outdir)
# for each rousset label make or copy
labelfiles = []
for label, regions in rousset_labels.items():
outlabel = os.path.join(outdir, '%s.rousset_%s.label'%(hemi, label))
tmpregions = [os.path.join(labeldir,
'%s.%s.label'%(hemi, x)) for x in regions]
if len(regions) == 1:
bg.copy_file(tmpregions[0], outlabel)
else:
generate_roilabels(tmpregions, outlabel)
labelfiles.append(outlabel)
return labelfiles
def rousset_labellist(labeldir, hemi, outdir='rousset_labels'):
rousset_labels = {
'frontal': ['frontalpole', 'lateralorbitofrontal'],
'temporal': ['temporalpole'],
'parietal': ['inferiorparietal'],
'precuneus': ['precuneus'],
'cingulate': ['posteriorcingulate', 'isthmuscingulate']
}
pth, _ = os.path.split(labeldir)
outdir, exists = bg.make_dir(pth, outdir)
# for each rousset label make or copy
labelfiles = []
for label, regions in rousset_labels.items():
outlabel = os.path.join(outdir, '%s.rousset_%s.label' % (hemi, label))
tmpregions = [
os.path.join(labeldir, '%s.%s.label' % (hemi, x)) for x in regions
]
if len(regions) == 1:
bg.copy_file(tmpregions[0], outlabel)
else:
generate_roilabels(tmpregions, outlabel)
labelfiles.append(outlabel)
return labelfiles
# QA
# make 4d for QA
qadir, exists = qa.make_qa_dir(realigndir, name='data_QA')
data4d = qa.make_4d_nibabel(allrealigned, outdir=qadir)
#snrimg = qa.gen_sig2noise_img(data4d,qadir)
#artout = qa.run_artdetect(data4d,tmpparameterfile)
#qa.screen_data_dirnme(data4d, qadir)
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
for sub in subs:
_, fullsubid = os.path.split(sub)
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())
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_metzler')
if exists:
logging.error('%s exists, remove to re-run' % (pvcdir))
continue
# get dvr
globstr = '%s/DVR-%s*nii*' % (dvrdir, subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error('%s missing, skipping' % (globstr))
continue
# copy dvr to pvc directory
cdvr = bg.copy_file(dvr, pvcdir)
# get raparc
corgdir = os.path.join(pth, 'coreg')
globstr = '%s/rB*aparc_aseg.nii' % (corgdir)
raparc = pp.find_single_file(globstr)
for sub in subs:
_, fullsubid = os.path.split(sub)
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())
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_metzler")
if exists:
logging.error("%s exists, remove to re-run" % (pvcdir))
continue
# get dvr
globstr = "%s/DVR-%s*nii*" % (dvrdir, subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error("%s missing, skipping" % (globstr))
continue
# copy dvr to pvc directory
cdvr = bg.copy_file(dvr, pvcdir)
# get raparc
corgdir = os.path.join(pth, "coreg")
globstr = "%s/rB*aparc_aseg.nii" % (corgdir)
raparc = pp.find_single_file(globstr)
if '_v2' in sub:
logging.info('skipping visit2 %s' % (sub))
continue
_, fullsubid = os.path.split(sub)
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)
# 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 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:
logging.warning('%s not found' % (searchstring))
continue
aparc = bg.unzip_file(aparc)
# find PET
pet = movedmean # use previously made summed image
# copy files to tmp dir
logging.info('coreg ref region to %s' % pet)
coreg_dir, exists = bg.make_dir(tracerdir, dirname='coreg_mri2fdg')
if exists:
logging.warning('existing dir %s remove to re-run' % (coreg_dir))
continue
cmri = bg.copy_file(mri, coreg_dir)
cpons = bg.copy_file(pons, coreg_dir)
cpet = bg.copy_file(pet, coreg_dir)
caparc = bg.copy_file(aparc, coreg_dir)
xfm_file = pp.make_transform_name(cpet, cmri)
logging.info('coreg %s' % (subid))
corg_out = pp.invert_coreg(cmri, cpet, xfm_file)
if not corg_out.runtime.returncode == 0:
logging.warning(corg_out.runtime.stderr)
continue
apply_out = pp.apply_transform_onefile(xfm_file, cpons)
if not apply_out.runtime.returncode == 0:
bg.remove_files([aparc])
# make cerebellum
refdir, _ = outdirs['refdir']
cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
if os.path.isfile(cerebellum):
logging.warning('cerebellum %s exists, skipping' % (cerebellum))
else:
# copy aseg+aparc to refdir
try:
caparcnii = bg.copy_file(aparcnii, refdir)
bg.make_cerebellum_nibabel(caparcnii)
bg.remove_files([caparcnii])
except:
logging.warning('Fail: unable to make %s' % (cerebellum))
rawtracer, exists = outdirs['rawtracer']
os.system('rm %s' % rawtracer)
tracerdir, _ = outdirs['tracerdir']
newname = '%s_%s' % (subid, tracer)
niftis = bg.biograph_dicom_convert(tgz[0], tracerdir, subid, tracer)
## center new nifti files
orig_dir, _ = bg.make_dir(tracerdir, dirname='orig')
copied_orig = bg.copy_files(niftis, orig_dir)
bg.remove_files(niftis)
for f, nf in zip(copied_orig, niftis):
print f, nf
nicm.CMTransform(f).fix(new_file=nf)
logging.info('biograph dicoms converted for %s ' % (subid))
for sub in subs:
_, fullsubid = os.path.split(sub)
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)
# make filepath to tracer dir
pth = os.path.join(sub, tracer.lower())
if not os.path.exists(pth):
logging.error('SKIP: missing %s'%pth)
continue
pvcdir, exists = bg.make_dir(pth, 'pvc_metzler')
if exists:
logging.error('%s exists, remove to re-run'%(pvcdir))
continue
# get ponsnormd
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)
tracer = "PIB"
user = os.environ["USER"]
logging.info("###START Setup Directory :::")
logging.info("###TRACER Setup %s :::" % (tracer))
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)
for sub in subs:
if '_v2' in sub:
logging.info('skipping visit2 %s' % (sub))
continue
_, subid = os.path.split(sub)
logging.info('%s' % subid)
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:
if subid is None:
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
# 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:
_, tname, _ = pp.split_filename(template)
for sub in subs:
_, subid = os.path.split(sub)
logging.info('%s'%subid)
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:
if subid is None:
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
# 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
continue
_, fullsubid = os.path.split(sub)
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())
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 exists:
logging.error("%s exists, remove to re-run" % (pvcdir))
continue
# get dvr
globstr = "%s/DVR-%s*nii*" % (dvrdir, subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error("%s missing, skipping" % (globstr))
continue
# copy dvr to pvc directory
cdvr = bg.copy_file(dvr, pvcdir)
# get raparc
corgdir = os.path.join(pth, "coreg")
globstr = "%s/rB*aparc_aseg.nii" % (corgdir)
raparc = pp.find_single_file(globstr)
# QA
# make 4d for QA
qadir, exists = qa.make_qa_dir(realigndir, name='data_QA')
data4d = qa.make_4d_nibabel(allrealigned, outdir=qadir)
#snrimg = qa.gen_sig2noise_img(data4d,qadir)
#artout = qa.run_artdetect(data4d,tmpparameterfile)
#qa.screen_data_dirnme(data4d, qadir)
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
for sub in subs:
_, fullsubid = os.path.split(sub)
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)
# make filepath to tracer dir
pth = os.path.join(sub, tracer.lower())
if not os.path.exists(pth):
logging.error('SKIP: missing %s' % pth)
continue
pvcdir, exists = bg.make_dir(pth, 'pvc_metzler')
if exists:
logging.error('%s exists, remove to re-run' % (pvcdir))
continue
# get ponsnormd
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 subid is None:
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
# 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
for sub in subs:
if '_v2' in sub:
logging.info('skipping visit2 %s'%(sub))
continue
_, subid = os.path.split(sub)
logging.info('%s'%subid)
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:
tracer = 'FDG'
user = os.environ['USER']
logging.info('###START Setup Directory :::')
logging.info('###TRACER Setup %s :::'%(tracer))
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
logging.info('Skipping visit 2 %s'%(sub))
continue
_, fullsubid = os.path.split(sub)
try:
m = pp.re.search('B[0-9]{2}-[0-9]{3}_v[0-9]',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())
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_metzler')
if not exists:
logging.error('%s missing, skipping'%(pvcdir))
continue
# get pvc dvr
globstr = '%s/pvcfs_DVR-%s*nii*'%(pvcdir,subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error('%s missing, skipping'%(globstr))
continue
# get raparc
corgdir = os.path.join(pth, 'coreg')
globstr = '%s/rB*aparc_aseg.nii'%(corgdir)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('%s missing, skipping '%(globstr))
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:
logging.error('%s missing, skipping' % (globstr))
continue
cstrokem = bg.copy_file(strokem, roidir)
globstr = '%s/coreg/*.mat*' % pth
xfm = pp.find_single_file(globstr)
if xfm is None:
# make cerebellum
refdir,_ = outdirs['refdir']
cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
if os.path.isfile(cerebellum):
logging.warning('cerebellum %s exists, skipping'%(cerebellum))
else:
# copy aseg+aparc to refdir
try:
caparcnii = bg.copy_file(aparcnii, refdir)
bg.make_cerebellum_nibabel(caparcnii)
bg.remove_files([caparcnii])
except:
logging.warning('Fail: unable to make %s'%(cerebellum))
rawtracer, exists = outdirs['rawtracer']
os.system('rm %s'%rawtracer)
tracerdir, _ = outdirs['tracerdir']
newname = '%s_%s' % (subid, tracer)
niftis = bg.biograph_dicom_convert(tgz[0], tracerdir, subid, tracer)
## center new nifti files
orig_dir, _ = bg.make_dir(tracerdir, dirname='orig')
copied_orig = bg.copy_files(niftis, orig_dir)
bg.remove_files(niftis)
for f,nf in zip(copied_orig, niftis):
print f, nf
nicm.CMTransform(f).fix(new_file = nf)
logging.info('biograph dicoms converted for %s ' % (subid))
template = str(template[0])
_, tname, _ = pp.split_filename(template)
for sub in subs:
_, subid = os.path.split(sub)
logging.info('%s' % subid)
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:
for sub in subs:
_, fullsubid = os.path.split(sub)
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())
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
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:
logging.warning("%s not found" % (searchstring))
continue
aparc = bg.unzip_file(aparc)
# find PET
pet = movedmean # use previously made summed image
# copy files to tmp dir
logging.info("coreg ref region to %s" % pet)
coreg_dir, exists = bg.make_dir(tracerdir, dirname="coreg_mri2fdg")
if exists:
logging.warning("existing dir %s remove to re-run" % (coreg_dir))
continue
cmri = bg.copy_file(mri, coreg_dir)
cpons = bg.copy_file(pons, coreg_dir)
cpet = bg.copy_file(pet, coreg_dir)
caparc = bg.copy_file(aparc, coreg_dir)
xfm_file = pp.make_transform_name(cpet, cmri)
logging.info("coreg %s" % (subid))
corg_out = pp.invert_coreg(cmri, cpet, xfm_file)
if not corg_out.runtime.returncode == 0:
logging.warning(corg_out.runtime.stderr)
continue
apply_out = pp.apply_transform_onefile(xfm_file, cpons)
if not apply_out.runtime.returncode == 0:
tracer = 'FDG'
user = os.environ['USER']
logging.info('###START Setup Directory :::')
logging.info('###TRACER Setup %s :::' % (tracer))
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
tracer = 'PIB'
user = os.environ['USER']
logging.info('###START Setup Directory :::')
logging.info('###TRACER Setup %s :::' % (tracer))
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)