def plot_surf(img_dir, freesurfer_dir, info, surface):
fs = Freesurfer(freesurfer_dir / info['subject'])
surf = getattr(fs.read_brain(surface), info['hemi'])
surf_img = nload(str(info['surf']))
surf_val = surf_img.get_data()[:, 0, 0].astype('float64')
v = Viz3()
v.add_surf(surf, values=surf_val, limits_c=(-6, 6), colorbar=True)
v.save(img_dir / (info['surf'].stem + '.png'))
v.close()
def read_surf(filename, right_or_left):
fs = Freesurfer(filename)
ras_shift = fs.surface_ras_shift
if right_or_left > 0.5:
hemi = 'rh'
else:
hemi = 'lh'
pial = getattr(fs.read_brain(), hemi)
if 'som' not in filename.name:
pial.vert[:, 0] += ras_shift[0]
pial.vert[:, 1] += ras_shift[1]
pial.vert[:, 2] += ras_shift[2]
return pial
def plot_surface(parameters, frequency_band, subject, surf):
elec_file = get_path(parameters, 'elec', subject=subject)
ieeg_file = get_path(parameters,
'ieeg_tsv',
frequency_band=frequency_band,
subject=subject)
fmri_file = get_path(parameters, 'fmri_nii', subject=subject)
if elec_file is None or ieeg_file is None or fmri_file is None:
return
freesurfer_dir = parameters['paths'][
'freesurfer_subjects_dir'] / f'sub-{subject}'
compare_ieeg = read_tsv(ieeg_file)
fs = Freesurfer(freesurfer_dir)
electrodes = Electrodes(elec_file)
elec = electrodes.electrodes.tsv
all_elec = []
labels = []
for chan in compare_ieeg:
i_chan = where(elec['name'] == chan['channel'])[0]
all_elec.append(elec[i_chan])
labels.append(f"{chan['channel']} = {chan['measure']:0.3f}")
elec = concatenate(all_elec)
if mean(elec['x']) > 0:
right_or_left = 1
hemi = 'rh'
else:
right_or_left = -1
hemi = 'lh'
fs = Freesurfer(freesurfer_dir)
pial = getattr(fs.read_brain(), hemi)
vert = pial.vert + fs.surface_ras_shift
if subject in surf:
fmri_vals = surf[subject]
else:
print(f'Computing surf for {subject}')
fmri_vals = project_mri_to_surf(
fmri_file, vert, parameters['plot']['surface']['kernel'])
surf[subject] = fmri_vals
colorscale = 'balance'
traces = [
go.Scatter3d(
x=elec['x'],
y=elec['y'],
z=elec['z'],
text=labels,
mode='markers',
hoverinfo='text',
marker=dict(
size=5,
color=compare_ieeg['measure'],
colorscale=colorscale,
showscale=True,
cmid=0,
colorbar=dict(
title='electrodes',
titleside="top",
ticks="outside",
ticklabelposition="outside",
x=0,
),
),
),
go.Mesh3d(
x=vert[:, 0],
y=vert[:, 1],
z=vert[:, 2],
i=pial.tri[:, 0],
j=pial.tri[:, 1],
k=pial.tri[:, 2],
intensity=fmri_vals,
cmid=0,
colorscale='Balance',
hoverinfo='skip',
flatshading=False,
colorbar=dict(
title='fmri',
titleside="top",
ticks="outside",
ticklabelposition="outside",
x=1,
),
lighting=dict(
ambient=0.18,
diffuse=1,
fresnel=0.1,
specular=1,
roughness=0.1,
),
lightposition=dict(
x=0,
y=0,
z=-1,
),
),
]
fig = go.Figure(
data=traces,
layout=go.Layout(scene=dict(
xaxis=AXIS,
yaxis=AXIS,
zaxis=AXIS,
camera=dict(
eye=dict(
x=right_or_left,
y=0,
z=0,
),
projection=dict(type='orthographic', ),
),
), ),
)
return to_div(fig)
def paper_plot_surf_bold(parameters, subject):
elec_file = get_path(parameters, 'elec', subject=subject)
fmri_file = get_path(parameters, 'fmri_nii', subject=subject)
freesurfer_dir = parameters['paths']['freesurfer_subjects_dir'] / f'sub-{subject}'
fs = Freesurfer(freesurfer_dir)
electrodes = Electrodes(elec_file)
elec = electrodes.electrodes.tsv
if mean(elec['x']) > 0:
right_or_left = 1
hemi = 'rh'
else:
right_or_left = -1
hemi = 'lh'
fs = Freesurfer(freesurfer_dir)
pial = getattr(fs.read_brain(), hemi)
vert = pial.vert + fs.surface_ras_shift
fmri_vals = project_mri_to_surf(fmri_file, vert, parameters['plot']['surface']['kernel'])
colorscale = 'balance'
traces = [
go.Scatter3d(
x=elec['x'] + right_or_left,
y=elec['y'],
z=elec['z'] + 1,
mode='markers',
hoverinfo='text',
marker=dict(
size=5,
color='black',
),
),
go.Mesh3d(
x=vert[:, 0],
y=vert[:, 1],
z=vert[:, 2],
i=pial.tri[:, 0],
j=pial.tri[:, 1],
k=pial.tri[:, 2],
intensity=fmri_vals,
cmax=4,
cmin=-4,
colorscale=colorscale,
hoverinfo='skip',
flatshading=False,
showscale=False,
lighting=dict(
ambient=0.18,
diffuse=1,
fresnel=0.1,
specular=1,
roughness=0.1,
),
lightposition=dict(
x=0,
y=0,
z=-1,
),
),
]
fig = go.Figure(
data=traces,
layout=go.Layout(
scene=dict(
xaxis=AXIS,
yaxis=AXIS,
zaxis=AXIS,
camera=dict(
eye=dict(
x=right_or_left,
y=0,
z=1,
),
projection=dict(
type='orthographic',
),
),
),
),
)
return fig