示例#1
0
        ## 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)
示例#2
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        ## 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)
示例#3
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        ## 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)
示例#4
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        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)