# 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
_, roifname = os.path.split(roifile)
outf = os.path.join(root,
'roivalues_%s_%s_%s' % (tracer, cleantime, roifname))
fid = open(outf, 'w+')
fid.write('SUBID,')
rois = sorted(meand.keys())
roiss = ','.join(rois)
fid.write(roiss)
fid.write(',\n')
for subid in sorted(alld.keys()):
fid.write('%s,' % (subid))
for r in rois:
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)
alld[subid] = meand
###write to file
_, roifname = os.path.split(roifile)
outf = os.path.join(
userhome,
'roivalues_strokemasked_%s_%s_%s' % (tracer, cleantime, roifname))
fid = open(outf, 'w+')
fid.write('SUBID,')
rois = sorted(meand.keys())
roiss = ','.join(rois)
fid.write(roiss)
fid.write(',\n')
for subid in sorted(alld.keys()):
fid.write('%s,' % (subid))
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))
continue
dvr_data = pp.nibabel.load(dvr).get_data()
meand = pp.mean_from_labels(roid, raparc, dvr_data)
#csvfile = os.path.join(dvrdir, 'PIBINDEX_%s_%s.csv'%(subid,cleantime))
#pp.meand_to_file(meand, csvfile)
alld[subid] = meand
###write to file
fid =open('pvc_metzler_OLD_PIBINDEX_%s'%(cleantime), 'w+')
fid.write('SUBID,')
rois = sorted(meand.keys())
roiss = ','.join(rois)
fid.write(roiss)
fid.write(',\n')
for subid in sorted(alld.keys()):
fid.write('%s,'%(subid))
for r in rois:
fid.write('%f,'%(alld[subid][r][0]))
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)
raparc = transform_vol(caparc, xfm, dat)
data = pp.nibabel.load(dat).get_data()
meand = pp.mean_from_labels(roid, raparc, data, othermask=stroke_mask)
alld[subid] = meand
###write to file
_, roifname = os.path.split(roifile)
outf = os.path.join(userhome, 'roivalues_strokemasked_%s_%s_%s'%(tracer,
cleantime,
roifname))
fid =open(outf, 'w+')
fid.write('SUBID,')
rois = sorted(meand.keys())
roiss = ','.join(rois)
fid.write(roiss)
fid.write(',\n')
for subid in sorted(alld.keys()):
fid.write('%s,'%(subid))
