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)