def surface_images(out_dir, subj):
"""Plot the white, pial, and inflated surfaces to look for defects."""
for surf in ["white", "pial", "inflated"]:
panels = []
for hemi in ["lh", "rh"]:
try:
b = Brain(subj, hemi, surf, curv=False, background="white")
except TypeError:
# PySurfer <= 0.5
b = Brain(subj,
hemi,
surf,
curv=False,
config_opts=dict(background="white"))
for view in ["lat", "med", "ven"]:
b.show_view(view, distance="auto")
panels.append(crop(b.screenshot()))
b.close()
# Make and save a figure
f = multi_panel_brain_figure(panels)
fname = op.join(out_dir, "{}_surface.png".format(surf))
f.savefig(fname, bbox_inches="tight")
plt.close(f)
def contrast_loop(subj, contrasts, stat_temp, mask_temp, png_temp, args,
z_thresh, sign):
"""Iterate over contrasts and make surface images."""
for contrast in contrasts:
# Calculate where the overlay should saturate
z_max = calculate_sat_point(stat_temp, contrast, sign, subj)
panels = []
for hemi in ["lh", "rh"]:
# Initialize the brain object
b_subj = subj if args.regspace == "epi" else "fsaverage"
try:
b = Brain(b_subj, hemi, args.geometry, background="white")
except TypeError:
# PySurfer <= v0.5
b = Brain(b_subj,
hemi,
args.geometry,
config_opts={"background": "white"})
# Plot the mask
mask_file = mask_temp.format(contrast=contrast,
hemi=hemi,
subj=subj)
add_mask_overlay(b, mask_file)
# Plot the overlay
stat_file = stat_temp.format(contrast=contrast,
hemi=hemi,
subj=subj)
add_stat_overlay(b,
stat_file,
z_thresh,
z_max,
sign,
sig_to_z=args.regspace == "fsaverage")
# Take screenshots
for view in ["lat", "med", "ven"]:
b.show_view(view, distance="auto")
sleep(.1)
panels.append(crop(b.screenshot()))
b.close()
# Make a single figure with all the panels
f = multi_panel_brain_figure(panels)
kwargs = {}
if sign in ["pos", "abs"]:
kwargs["pos_cmap"] = "Reds_r"
if sign in ["neg", "abs"]:
kwargs["neg_cmap"] = "Blues"
add_colorbars(f, z_thresh, z_max, **kwargs)
# Save the figure in both hemisphere outputs
for hemi in ["lh", "rh"]:
png_file = png_temp.format(hemi=hemi, contrast=contrast, subj=subj)
f.savefig(png_file, bbox_inches="tight")
plt.close(f)
def curvature_normalization(data_dir, subj):
"""Normalize the curvature map and plot contour over fsaverage."""
surf_dir = op.join(data_dir, subj, "surf")
snap_dir = op.join(data_dir, subj, "snapshots")
panels = []
for hemi in ["lh", "rh"]:
# Load the curv values and apply registration to fsaverage
curv_fname = op.join(surf_dir, "{}.curv".format(hemi))
curv_vals = nib.freesurfer.read_morph_data(curv_fname)
subj_curv_vals = apply_surface_warp(data_dir, subj, hemi, curv_vals)
subj_curv_binary = (subj_curv_vals > 0)
# Load the template curvature
norm_fname = op.join(data_dir, "fsaverage", "surf",
"{}.curv".format(hemi))
norm_curv_vals = nib.freesurfer.read_morph_data(norm_fname)
norm_curv_binary = (norm_curv_vals > 0)
# Compute the curvature overlap image
curv_overlap = np.zeros_like(norm_curv_binary, np.int)
curv_overlap[norm_curv_binary & subj_curv_binary] = 1
curv_overlap[norm_curv_binary ^ subj_curv_binary] = 2
# Mask out the medial wall
cortex_fname = op.join(data_dir, "fsaverage", "label",
"{}.cortex.label".format(hemi))
cortex = nib.freesurfer.read_label(cortex_fname)
medial_wall = ~np.in1d(np.arange(curv_overlap.size), cortex)
curv_overlap[medial_wall] = 1
# Plot the curvature overlap image
try:
b = Brain("fsaverage", hemi, "inflated", background="white")
except TypeError:
# PySurfer <= 0.5
b = Brain("fsaverage",
hemi,
"inflated",
config_opts=dict(background="white"))
b.add_data(curv_overlap,
min=0,
max=2,
colormap=[".9", ".45", "indianred"],
colorbar=False)
for view in ["lat", "med", "ven"]:
b.show_view(view, distance="auto")
panels.append(crop(b.screenshot()))
b.close()
# Make and save a figure
f = multi_panel_brain_figure(panels)
fname = op.join(snap_dir, "surface_registration.png")
f.savefig(fname, bbox_inches="tight")
plt.close(f)
def curvature_normalization(data_dir, subj):
"""Normalize the curvature map and plot contour over fsaverage."""
surf_dir = op.join(data_dir, subj, "surf")
snap_dir = op.join(data_dir, subj, "snapshots")
panels = []
for hemi in ["lh", "rh"]:
# Load the curv values and apply registration to fsaverage
curv_fname = op.join(surf_dir, "{}.curv".format(hemi))
curv_vals = nib.freesurfer.read_morph_data(curv_fname)
subj_curv_vals = apply_surface_warp(data_dir, subj,
hemi, curv_vals)
subj_curv_binary = (subj_curv_vals > 0)
# Load the template curvature
norm_fname = op.join(data_dir, "fsaverage", "surf",
"{}.curv".format(hemi))
norm_curv_vals = nib.freesurfer.read_morph_data(norm_fname)
norm_curv_binary = (norm_curv_vals > 0)
# Compute the curvature overlap image
curv_overlap = np.zeros_like(norm_curv_binary, np.int)
curv_overlap[norm_curv_binary & subj_curv_binary] = 1
curv_overlap[norm_curv_binary ^ subj_curv_binary] = 2
# Mask out the medial wall
cortex_fname = op.join(data_dir, "fsaverage", "label",
"{}.cortex.label".format(hemi))
cortex = nib.freesurfer.read_label(cortex_fname)
medial_wall = ~np.in1d(np.arange(curv_overlap.size), cortex)
curv_overlap[medial_wall] = 1
# Plot the curvature overlap image
try:
b = Brain("fsaverage", hemi, "inflated", background="white")
except TypeError:
# PySurfer <= 0.5
b = Brain("fsaverage", hemi, "inflated",
config_opts=dict(background="white"))
b.add_data(curv_overlap, min=0, max=2,
colormap=[".9", ".45", "indianred"], colorbar=False)
for view in ["lat", "med", "ven"]:
b.show_view(view, distance="auto")
panels.append(crop(b.screenshot()))
b.close()
# Make and save a figure
f = multi_panel_brain_figure(panels)
fname = op.join(snap_dir, "surface_registration.png")
f.savefig(fname, bbox_inches="tight")
plt.close(f)
def contrast_loop(subj, contrasts, stat_temp, mask_temp, png_temp,
args, z_thresh, sign):
"""Iterate over contrasts and make surface images."""
for contrast in contrasts:
# Calculate where the overlay should saturate
z_max = calculate_sat_point(stat_temp, contrast, sign, subj)
panels = []
for hemi in ["lh", "rh"]:
# Initialize the brain object
b_subj = subj if args.regspace == "epi" else "fsaverage"
try:
b = Brain(b_subj, hemi, args.geometry, background="white")
except TypeError:
# PySurfer <= v0.5
b = Brain(b_subj, hemi, args.geometry,
config_opts={"background": "white"})
# Plot the mask
mask_file = mask_temp.format(contrast=contrast,
hemi=hemi, subj=subj)
add_mask_overlay(b, mask_file)
# Plot the overlay
stat_file = stat_temp.format(contrast=contrast,
hemi=hemi, subj=subj)
add_stat_overlay(b, stat_file, z_thresh, z_max, sign,
sig_to_z=args.regspace == "fsaverage")
# Take screenshots
for view in ["lat", "med", "ven"]:
b.show_view(view, distance="auto")
sleep(.1)
panels.append(crop(b.screenshot()))
b.close()
# Make a single figure with all the panels
f = multi_panel_brain_figure(panels)
kwargs = {}
if sign in ["pos", "abs"]:
kwargs["pos_cmap"] = "Reds_r"
if sign in ["neg", "abs"]:
kwargs["neg_cmap"] = "Blues"
add_colorbars(f, z_thresh, z_max, **kwargs)
# Save the figure in both hemisphere outputs
for hemi in ["lh", "rh"]:
png_file = png_temp.format(hemi=hemi, contrast=contrast, subj=subj)
f.savefig(png_file, bbox_inches="tight")
plt.close(f)
def plot_brains(axes, palette):
lat_ax, med_ax = axes
lat_color, med_color = palette
b = Brain("fsaverage", "lh", "pial",
background="white", size=(1200, 1200))
b.add_morphometry("curv", grayscale=True, min=-.5, max=.5,
colormap="Greys", colorbar=False)
b.add_label("roi_labels/lh.ifs.label", alpha=.9, color="#feb308")
b.add_label("roi_labels/lh.mfc.label", alpha=.9, color="#cf6275")
mlab.view(160, 70)
lat_ax.imshow(crop(b.screenshot()), rasterized=True)
mlab.view(15, 90)
med_ax.imshow(crop(b.screenshot()), rasterized=True)
b.close()
for ax in axes:
ax.set_axis_off()
def plot_brains(subjects, axes):
for subj, subj_axes in zip(subjects, axes):
exp = dict(pc="dots", ti="sticks")[subj[:2]]
data_fname = "roi_cache/{}_{}_ifs.npz".format(subj, exp)
with np.load(data_fname) as dobj:
vox_ijk = dobj["vox_ijk"]
res_fname = "decoding_analysis/{}_{}_ifs.pkz".format(subj, exp)
res = moss.load_pkl(res_fname)
prefs = res.prefs
surf_vals = roi_to_surf(exp, subj, prefs, vox_ijk)
lut = get_colormap(exp, False)
for hemi, ax in zip(["lh", "rh"], subj_axes):
b = Brain(subj,
hemi,
"inflated",
background="white",
cortex=("binary", -4, 8, False),
size=(1000, 600))
b.add_data(surf_vals.ix[hemi].fillna(-11).values,
colormap=lut,
colorbar=False,
thresh=-10,
min=-1.75,
max=1.75)
mlab.view(*get_ifs_view(subj, hemi))
img = crop(b.screenshot())
ax.imshow(img, rasterized=True)
ax.set(xticks=[], yticks=[])
b.close()
def surface_images(out_dir, subj):
"""Plot the white, pial, and inflated surfaces to look for defects."""
for surf in ["white", "pial", "inflated"]:
panels = []
for hemi in ["lh", "rh"]:
try:
b = Brain(subj, hemi, surf, curv=False, background="white")
except TypeError:
# PySurfer <= 0.5
b = Brain(subj, hemi, surf, curv=False,
config_opts=dict(background="white"))
for view in ["lat", "med", "ven"]:
b.show_view(view, distance="auto")
panels.append(crop(b.screenshot()))
b.close()
# Make and save a figure
f = multi_panel_brain_figure(panels)
fname = op.join(out_dir, "{}_surface.png".format(surf))
f.savefig(fname, bbox_inches="tight")
plt.close(f)