## 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)
continue
xfm = fst.fs_generate_dat(cponsnormed, t1, subid)
outfiles = fst.pet_2_surf(cponsnormed, xfm, mridir)
## 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)
continue
xfm = fst.fs_generate_dat(cponsnormed, t1, subid)
outfiles = fst.pet_2_surf(cponsnormed, xfm, mridir)
## 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)
outfiles = fst.pet_2_surf(cdvr, xfm, mridir)
# zip files in coregdir
allf = glob("%s/*" % coregdir)
bg.zip_files(allf)
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)
outfiles = fst.pet_2_surf(cdvr, xfm, mridir)
# zip files in coregdir
allf = glob('%s/*' % coregdir)
bg.zip_files(allf)