allrealigned = crg_out.outputs.coregistered_files + \ rlgnout.outputs.realigned_files # make new mean files(s) based on fully realigned files # 1. first 20 mins for coreg (frames 1-23) # 2. 40-60 mins for possible SUVR (frames 28-31) mean_20min = pp.make_mean_20min(allrealigned) mean_40_60min = pp.make_mean_40_60(allrealigned) # clean up # remove copied unrealigned frames bg.remove_files(newnifti) # QA # make 4d for QA qadir, exists = qa.make_qa_dir(realigndir, name='data_QA') data4d = qa.make_4d_nibabel(allrealigned, outdir=qadir) #snrimg = qa.gen_sig2noise_img(data4d,qadir) #artout = qa.run_artdetect(data4d,tmpparameterfile) #qa.screen_data_dirnme(data4d, qadir) qa.plot_movement(tmpparameterfile, subid) qa.calc_robust_median_diff(data4d) qa.screen_pet(data4d) # Coregister cerebellum, brainmask and aparc_aseg to pet space # 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
# 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) # remove tmpfiles bg.remove_files(no_nanfiles) bg.remove_files(newnifti) # coreg pons to pet # find PONS pons_searchstr = "%s/ref_region/pons_tu.nii*" % tracerdir pons = pp.find_single_file(pons_searchstr)
rlgnout.outputs.realigned_files # make new mean files(s) based on fully realigned files # 1. first 20 mins for coreg (frames 1-23) # 2. 40-60 mins for possible SUVR (frames 28-31) mean_20min = pp.make_mean_20min(allrealigned) mean_40_60min = pp.make_mean_40_60(allrealigned) # clean up # remove copied unrealigned frames bg.remove_files(newnifti) # QA # make 4d for QA qadir, exists = qa.make_qa_dir(realigndir, name='data_QA') data4d = qa.make_4d_nibabel(allrealigned, outdir=qadir) #snrimg = qa.gen_sig2noise_img(data4d,qadir) #artout = qa.run_artdetect(data4d,tmpparameterfile) #qa.screen_data_dirnme(data4d, qadir) qa.plot_movement(tmpparameterfile, subid) qa.calc_robust_median_diff(data4d) qa.screen_pet(data4d) # Coregister cerebellum, brainmask and aparc_aseg to pet space # 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
# 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) #remove tmpfiles bg.remove_files(no_nanfiles) bg.remove_files(newnifti) # coreg pons to pet # find PONS pons_searchstr = '%s/ref_region/pons_tu.nii*' % tracerdir pons = pp.find_single_file(pons_searchstr)