else:
            aparc = bg.copy_file(aparc, outdirs["anatomydir"][0])
            aparcnii = bg.convert(aparc, aparcnii)
            bg.remove_files([aparc])
        # make pons
        refdir, _ = outdirs["refdir"]
        brainstem = os.path.join(refdir, "brainstem.nii.gz")
        if os.path.isfile(brainstem):
            logging.warning("brainstem %s exists, skipping" % (brainstem))

        else:
            # copy aseg+aparc to refdir
            try:
                caparcnii = bg.copy_file(aparcnii, refdir)
                bg.make_brainstem(caparcnii)
                brainstem = bg.unzip_file(brainstem)
                bg.remove_files([caparcnii.replace(".gz", "")])
            except:
                logging.warning("Check  %s" % (brainstem))

        rawtracer, exists = outdirs["rawtracer"]
        rawtracer_base, _ = os.path.split(rawtracer)
        os.system("rm -rf %s" % rawtracer_base)
        tracerdir, _ = outdirs["tracerdir"]

        newname = "%s_%s" % (subid, tracer)
        copied_ecats = bg.copy_files(ecats, tracerdir)
        bg.convertallecat(copied_ecats, newname)

        logging.info("ecats converted for %s " % (subid))
示例#2
0
            logging.error('%s NO APARC ASEG: %s' % (subid, aparc))

        else:
            aparc = bg.copy_file(aparc, outdirs['anatomydir'][0])
            aparcnii = bg.convert(aparc, aparcnii)
            bg.remove_files([aparc])
        # make cerebellum
        refdir, _ = outdirs['refdir']
        cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
        if os.path.isfile(cerebellum):
            logging.warning('cerebellum %s exists, skipping' % (cerebellum))

        else:
            # copy aseg+aparc to refdir
            try:
                caparcnii = bg.copy_file(aparcnii, refdir)
                bg.make_cerebellum_nibabel(caparcnii)
                bg.remove_files([caparcnii])
            except:
                logging.warning('Fail: unable to make %s' % (cerebellum))

        rawtracer, exists = outdirs['rawtracer']
        os.system('rm %s' % rawtracer)
        tracerdir, _ = outdirs['tracerdir']

        newname = '%s_%s' % (subid, tracer)
        copied_ecats = bg.copy_files(ecats, tracerdir)
        bg.convertallecat(copied_ecats, newname)

        logging.info('ecats converted for %s ' % (subid))
        # make cerebellum
        refdir,_ = outdirs['refdir']
        cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
        if os.path.isfile(cerebellum):
            logging.warning('cerebellum %s exists, skipping'%(cerebellum))
            
        else:
            # copy aseg+aparc to refdir
            try:
                caparcnii = bg.copy_file(aparcnii, refdir)                        
                bg.make_cerebellum_nibabel(caparcnii)
                bg.remove_files([caparcnii])
            except:
                logging.warning('Fail: unable to make %s'%(cerebellum))
        
        rawtracer, exists = outdirs['rawtracer']
        os.system('rm %s'%rawtracer)
        tracerdir, _ = outdirs['tracerdir']
        
        newname = '%s_%s' % (subid, tracer)
        niftis = bg.biograph_dicom_convert(tgz[0], tracerdir, subid, tracer)
        ## center new nifti files
        orig_dir, _ = bg.make_dir(tracerdir, dirname='orig')
        copied_orig = bg.copy_files(niftis, orig_dir)
        bg.remove_files(niftis)
        for f,nf  in zip(copied_orig, niftis):
            print f, nf
            nicm.CMTransform(f).fix(new_file = nf)
        logging.info('biograph dicoms converted for %s ' % (subid))                
            
示例#4
0
            bg.remove_files([aparc])
        # make cerebellum
        refdir, _ = outdirs['refdir']
        cerebellum = os.path.join(refdir, 'grey_cerebellum.nii')
        if os.path.isfile(cerebellum):
            logging.warning('cerebellum %s exists, skipping' % (cerebellum))

        else:
            # copy aseg+aparc to refdir
            try:
                caparcnii = bg.copy_file(aparcnii, refdir)
                bg.make_cerebellum_nibabel(caparcnii)
                bg.remove_files([caparcnii])
            except:
                logging.warning('Fail: unable to make %s' % (cerebellum))

        rawtracer, exists = outdirs['rawtracer']
        os.system('rm %s' % rawtracer)
        tracerdir, _ = outdirs['tracerdir']

        newname = '%s_%s' % (subid, tracer)
        niftis = bg.biograph_dicom_convert(tgz[0], tracerdir, subid, tracer)
        ## center new nifti files
        orig_dir, _ = bg.make_dir(tracerdir, dirname='orig')
        copied_orig = bg.copy_files(niftis, orig_dir)
        bg.remove_files(niftis)
        for f, nf in zip(copied_orig, niftis):
            print f, nf
            nicm.CMTransform(f).fix(new_file=nf)
        logging.info('biograph dicoms converted for %s ' % (subid))