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 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
def main(infile, param_file, param_source, thresh, outdir=None):
if len(infile) > 1:
# input is list, need to merge
if outdir is None:
outdir, _ = os.path.split(infile[0])
qadir, exists = make_qa_dir(outdir)
if exists:
print '%s exists, remove to re-run'%qadir
return None
merged = make_4d_nibabel(infile,outdir=qadir)
else:
merged = infile[0]
if outdir is None:
outdir, _ = os.path.split(merged)
qadir, exists = make_qa_dir(outdir)
if exists:
print '%s exists, remove to re-run'%qadir
return None
param_file = bg.copy_file(param_file, qadir)
artout = run_artdetect(merged, param_file, thresh, param_source)
vox_outliers = artout.outputs.outlier_files
statd = json.load(open(artout.outputs.statistic_files))
mot = statd[1]['motion_outliers']
intensity = statd[1]['intensity_outliers']
if mot > 0:
try:
tmp = np.loadtxt(artout.outputs.outlier_files)[:mot]
except:
tmp = np.loadtxt(artout.outputs.outlier_files)
tmp.tofile(os.path.join(qadir,'bad_movement_frames.txt'),
sep='\n')
np.array([mot,intensity]).tofile(os.path.join(qadir,
'motion_intensity_outliers'),
sep = '\n')
print 'QA written to %s'%(qadir)
def main(infile, param_file, param_source, thresh, outdir=None):
if len(infile) > 1:
# input is list, need to merge
if outdir is None:
outdir, _ = os.path.split(infile[0])
qadir, exists = make_qa_dir(outdir)
if exists:
print '%s exists, remove to re-run' % qadir
return None
merged = make_4d_nibabel(infile, outdir=qadir)
else:
merged = infile[0]
if outdir is None:
outdir, _ = os.path.split(merged)
qadir, exists = make_qa_dir(outdir)
if exists:
print '%s exists, remove to re-run' % qadir
return None
param_file = bg.copy_file(param_file, qadir)
artout = run_artdetect(merged, param_file, thresh, param_source)
vox_outliers = artout.outputs.outlier_files
statd = json.load(open(artout.outputs.statistic_files))
mot = statd[1]['motion_outliers']
intensity = statd[1]['intensity_outliers']
if mot > 0:
try:
tmp = np.loadtxt(artout.outputs.outlier_files)[:mot]
except:
tmp = np.loadtxt(artout.outputs.outlier_files)
tmp.tofile(os.path.join(qadir, 'bad_movement_frames.txt'), sep='\n')
np.array([mot,
intensity]).tofile(os.path.join(qadir,
'motion_intensity_outliers'),
sep='\n')
print 'QA written to %s' % (qadir)
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)
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
wm, gm, pibi = rousset.generate_pibindex_rois_fs(craparc)
wmf = pp.fname_presuffix(craparc, prefix="wm_")
gmf = pp.fname_presuffix(craparc, prefix="gm_")
pibif = pp.fname_presuffix(craparc, prefix="pibindex_")
aff = rousset.ni.load(craparc).get_affine()
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
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
#
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)
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 raparc is None:
logging.error('%s missing, skipping ' % (globstr))
continue
#copy raparc_aseg to pvd dir
craparc = bg.copy_file(raparc, pvcdir)
# make brainamsk
bmask = metzler.make_aseg_brainmask(craparc)
os.unlink(craparc)
smooth_bmask = pp.fname_presuffix(bmask, prefix='s')
_ = metzler.smooth_mask_nipy(bmask, smooth_bmask)
ero_bmask = metzler.fsl_erode2d(bmask)
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
# qa.save_qa_img(img4d)
qa.plot_movement(tmpparameterfile, subid)
qa.calc_robust_median_diff(img4d)
qa.screen_pet(img4d)
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
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
#
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)
### 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'))
if os.path.isfile(aparcnii):
logging.warning('%s has existing anatomy,'\
'skipping'%(aparcnii))
elif aparc is None:
logging.error('NO APARC ASEG: %s' % aparc)
else:
aparc = bg.copy_file(aparc, outdirs['anatomydir'][0])
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))
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)
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
#qa.save_qa_img(img4d)
qa.plot_movement(tmpparameterfile, subid)
qa.calc_robust_median_diff(img4d)
qa.screen_pet(img4d)
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:
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)
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
xfm = pp.find_single_file(globstr)
if xfm is None:
logging.error('NO transform for %s'%globstr)
continue
stroke_mask = transform_vol(cstrokem, xfm, dat)
# 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*'%(roidir)
raparc = pp.find_single_file(globstr)
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
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
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
wm, gm, pibi = rousset.generate_pibindex_rois_fs(craparc)
wmf = pp.fname_presuffix(craparc, prefix='wm_')
gmf = pp.fname_presuffix(craparc, prefix='gm_')
pibif = pp.fname_presuffix(craparc, prefix='pibindex_')
aff = rousset.ni.load(craparc).get_affine()
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
wm,gm,pibi = rousset.generate_pibindex_rois_fs(craparc)
wmf = pp.fname_presuffix(craparc, prefix='wm_')
gmf = pp.fname_presuffix(craparc, prefix='gm_')
pibif = pp.fname_presuffix(craparc, prefix='pibindex_')
aff = rousset.ni.load(craparc).get_affine()
# 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:
logging.error('NO transform for %s'%globstr)
continue
stroke_mask = transform_vol(cstrokem, xfm, dat)
# 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,
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
xfm = pp.find_single_file(globstr)
if xfm is None:
logging.error('NO transform for %s' % globstr)
continue
stroke_mask = transform_vol(cstrokem, xfm, dat)
# 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*' % (roidir)
raparc = pp.find_single_file(globstr)
#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
globstr = '%s/anatomy/*aparc_aseg.nii*'%sub
aparc = glob(globstr)
if not len(aparc)>0:
logging.error('NO aparcaseg for %s'%globstr)
continue
aparc = aparc[0]
caparc = bg.copy_file(aparc, roidir)
caparc = bg.unzip_file(caparc)# in case zipped
globstr = '%s/coreg_mri2fdg/*.mat*'%pth
xfm = pp.find_single_file(globstr)
if xfm is None:
logging.error('NO transform for %s'%globstr)
continue
cxfm = bg.copy_file(xfm, roidir)
cxfm = bg.unzip_file(cxfm)# in case zipped
pp.apply_transform_onefile(cxfm, caparc)
pp.reslice(dat, caparc)
raparc = pp.prefix_filename(caparc, prefix='r')
data = pp.nibabel.load(dat).get_data()
meand = pp.mean_from_labels(roid, raparc, data)
#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
globstr = '%s/anatomy/*aparc_aseg.nii*' % sub
aparc = glob(globstr)
if not len(aparc) > 0:
logging.error('NO aparcaseg for %s' % globstr)
continue
aparc = aparc[0]
caparc = bg.copy_file(aparc, roidir)
caparc = bg.unzip_file(caparc) # in case zipped
globstr = '%s/coreg_mri2fdg/*.mat*' % pth
xfm = pp.find_single_file(globstr)
if xfm is None:
logging.error('NO transform for %s' % globstr)
continue
cxfm = bg.copy_file(xfm, roidir)
cxfm = bg.unzip_file(cxfm) # in case zipped
pp.apply_transform_onefile(cxfm, caparc)
pp.reslice(dat, caparc)
raparc = pp.prefix_filename(caparc, prefix='r')
data = pp.nibabel.load(dat).get_data()
meand = pp.mean_from_labels(roid, raparc, data)
alld[subid] = meand
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:
logging.error('NO transform for %s' % globstr)
continue
stroke_mask = transform_vol(cstrokem, xfm, dat)
# 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, othermask=stroke_mask)
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.error("%s NO APARC ASEG: %s" % (subid, aparc))
else:
aparc = bg.copy_file(aparc, outdirs["anatomydir"][0])
aparcnii = bg.convert(aparc, aparcnii)
bg.remove_files([aparc])
# make pons
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
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
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))
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)
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:
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)
