Create a snapshot from FreeSurfer results

plot_freesurfer.py

from nisnap import snap
from nisnap.utils import aseg
import sys
aparc_fp, bg, snap_fp = sys.argv[1:]

filepaths = aseg.__preproc_aseg__(aparc_fp, bg)

axes = 'x'
figsize = {'x': (23, 15)}
rowsize = {'x': 8}
n_slices = {'x': 48}
labels = aseg.basal_ganglia_labels
step = 1
threshold = 75

def __select_slices__(filepaths, axes, rowsize, figsize, step=1, threshold=0):
    import numpy as np
    import nibabel as nib
    from nisnap.utils import slices
    data = np.asarray(nib.load(filepaths).dataobj)

    rowsize = slices._fix_rowsize_(axes, rowsize)
    figsize = slices._fix_figsize_(axes, figsize)
    sl = slices.cut_slices(data, axes, rowsize, slices=None, step=step,
                           threshold=threshold)
    sl = {a: [item for sublist in sl[a] for item in sublist] for a in axes}
    return sl

sl = __select_slices__(filepaths, axes, rowsize,
                       figsize, step=step,
                       threshold=threshold)
slices = {}
for a in axes:
    margin = int((len(sl[a]) - n_slices[a]) / 2.0)
    sx = sl[a][margin:len(sl[a]) - margin - 1]
    slices[a] = sx

# Create snapshot with proper options

snap.plot_segment(filepaths, axes=axes, bg=bg, opacity=70,
                  slices=slices, animated=False, savefig=snap_fp,
                  figsize=figsize, rowsize=rowsize,
                  contours=True, samebox=True,
                  labels=labels)