Esempi in Python per compute_perfusion

Esempio n. 1

File: plot_group_cbf.py Progetto: process-asl/process-asl

        target=out_average.outputs.mean_image,
        source=out_get_m0.outputs.m0_file,
        write_interp=3,
        jobtype='estwrite')

    # Smooth M0
    smooth_m0 = mem.cache(spm.Smooth)
    out_smooth_m0 = smooth_m0(
        in_files=out_coregister_m0.outputs.coregistered_source,
        fwhm=[5., 5., 5.])

    # Compute perfusion
    n_scans = preprocessing.get_scans_number(
        out_realign.outputs.realigned_files)
    perfusion_file = quantification.compute_perfusion(
        out_realign.outputs.realigned_files,
        ctl_scans=range(1, n_scans, 2),
        tag_scans=range(0, n_scans, 2))

    # Compute CBF
    quantify = mem.cache(quantification.QuantifyCBF)
    out_quantify = quantify(
        perfusion_file=perfusion_file,
        m0_file=out_smooth_m0.outputs.smoothed_files,
        tr=2500.,
        t1_gm=1331.)

    # Compute brain mask
    brain_mask_file = preprocessing.compute_brain_mask(
        out_coregister_anat.outputs.coregistered_source, frac=.2)
    brain_mask_file = preprocessing.compute_brain_mask(
        out_average.outputs.mean_image, frac=.5)

Esempio n. 2

File: multiple_subjects.py Progetto: ainafp/process-asl

        write_interp=3,
        jobtype='estwrite')

    # Smooth M0
    smooth_m0 = mem.cache(spm.Smooth)
    out_smooth_m0 = smooth_m0(
        in_files=out_coregister_m0.outputs.coregistered_source,
        fwhm=[5., 5., 5.])

    # Compute perfusion
    n_scans = preprocessing.get_scans_number(
        out_realign.outputs.realigned_files)
    ctl_scans = range(1, n_scans, 2)
    tag_scans = range(0, n_scans, 2)
    perfusion_file = quantification.compute_perfusion(
        out_realign.outputs.realigned_files,
        ctl_scans=ctl_scans,
        tag_scans=tag_scans)

    # Compute CBF
    quantify = mem.cache(quantification.QuantifyCBF)
    out_quantify = quantify(
        perfusion_file=perfusion_file,
        m0_file=out_smooth_m0.outputs.smoothed_files,
        tr=2500.,
        t1_gm=1331.)

    # Compute brain mask
    brain_mask_file = preprocessing.compute_brain_mask(
        out_coregister_anat.outputs.coregistered_source, frac=.2)

    # Normalize CBF

Esempio n. 3

                                  source=out_get_m0.outputs.m0_file,
                                  write_interp=3,
                                  jobtype='estwrite')

# Smooth M0
smooth_m0 = mem.cache(spm.Smooth)
out_smooth_m0 = smooth_m0(
    in_files=out_coregister_m0.outputs.coregistered_source, fwhm=[5., 5., 5.])

# Compute perfusion
from procasl import preprocessing, quantification
n_scans = preprocessing.get_scans_number(out_realign.outputs.realigned_files)
ctl_scans = range(1, n_scans, 2)
tag_scans = range(0, n_scans, 2)
perfusion_file = quantification.compute_perfusion(
    out_realign.outputs.realigned_files,
    ctl_scans=ctl_scans,
    tag_scans=tag_scans)

# Compute CBF
quantify = mem.cache(quantification.QuantifyCBF)
out_quantify = quantify(perfusion_file=perfusion_file,
                        m0_file=out_smooth_m0.outputs.smoothed_files,
                        tr=2500.,
                        t1_gm=1331.)

# Mask CBF map with brain mask
brain_mask_file = preprocessing.compute_brain_mask(
    out_coregister_anat.outputs.coregistered_source, frac=.2)
cbf_map = preprocessing.apply_mask(out_quantify.outputs.cbf_file,
                                   brain_mask_file)