In [4]:

    

import gc
import pylab as plt
import nibabel as nb
from matplotlib.backends.backend_pdf import PdfPages
from mriqc.volumes import plot_mosaic, plot_distrbution_of_values
from mriqc.motion import plot_frame_displacement


    

In [13]:

    

output_file = "/tmp/report.pdf"

report = PdfPages(output_file)

epi_nii = nb.load("/Users/filo/krzysztof.gorgolewski@gmail.com/projects/OpenfMRI/datasets/BIDS examples/ds007_partial/sub00001/functional/sub00001_task001_run001_bold.nii.gz")
mean_epi = epi_nii.get_data().mean(axis=3)

fig = plot_mosaic(mean_epi, title="Mean EPI", figsize=(8.3, 11.7))
report.savefig(fig, dpi=300)
fig.clf()

epi_std = epi_nii.get_data().std(axis=3)
epi_tsnr = mean_epi/epi_std
fig = plot_mosaic(epi_tsnr, title="tSNR", figsize=(8.3, 11.7))
report.savefig(fig, dpi=300)
fig.clf()

report.close()
gc.collect()
plt.close()


    

In [10]:

    

epi_nii.shape


    

    
Out[10]:





(64, 64, 33, 182)

In [11]:

    

mean_epi.shape


    

    
Out[11]:





(64, 64, 33)

In [ ]: