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
# warp brainmask to template, apply to dvr
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rdvr)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s'%subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s'%subid)
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
# warp brainmask to template, apply to pnfdg
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rpnfdg)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s'%subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s'%subid)
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
# warp brainmask to template, apply to pnfdg
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rpnfdg)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s' % subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s' % subid)
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
# warp brainmask to template, apply to dvr
logging.info('Run warp')
wout = pp.simple_warp(template, cbm, other=rdvr)
if not wout.runtime.returncode == 0:
logging.error('warp to template failed %s' % subid)
shutil.rmtree(warpdir)
continue
logging.info('Finished warping %s' % subid)
