def plot_epi_T1_corregistration(mean_epi_file, anat_edge, figsize=(11.7, 8.3)):
fig = plt.figure(figsize=figsize)
func = nb.load(mean_epi_file).get_data()
func_affine = nb.load(mean_epi_file).get_affine()
anat = nb.load(anat_edge).get_data()
anat_affine = nb.load(anat_edge).get_affine()
slicer = viz.plot_anat(
np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
cut_coords=(-6, 3, 28),
figure=fig,
draw_cross=False)
slicer.contour_map(np.asarray(anat),
np.asarray(anat_affine),
levels=[.51],
colors=[
'r',
])
return fig
def warp_report(in_file):
"""Plot the registration summary using nipy contours"""
mni_file = op.join(os.environ["FSL_DIR"],
"data/standard/MNI152_T1_1mm_brain.nii.gz")
mni_img = nib.load(mni_file)
mni_data, mni_aff = mni_img.get_data(), mni_img.get_affine()
sub_img = nib.load(in_file)
sub_data, sub_aff = sub_img.get_data(), sub_img.get_affine()
sub_data[sub_data < 1] = 0
kwargs = dict(draw_cross=False, annotate=False)
cut_coords = dict(x=(-45, -12, 12, 45),
y=(-55, -25, 5, 45),
z=(-30, -5, 20, 40))
colors = sns.color_palette("bright")
im_data = dict()
for axis in ["x", "y", "z"]:
f = plt.figure(figsize=(10, 2.5))
coords = cut_coords[axis]
slicer = viz.plot_anat(sub_data, sub_aff, slicer=axis,
cut_coords=coords, figure=f, **kwargs)
slicer.contour_map(mni_data, mni_aff, colors=colors)
fname = "slices_%s.png" % axis
f.savefig(fname, facecolor="k", edgecolor="k")
im_data[axis] = mplimg.imread(fname)
concat_data = [im_data[axis] for axis in ["x", "y", "z"]]
concat_data = np.concatenate(concat_data, axis=0)
mplimg.imsave("warp_report.png", concat_data)
return op.abspath("warp_report.png")
def contour_image(contour, mean, mask, title=''):
import nibabel as nib
import numpy as np
import nipy.labs.viz as viz
import os
import matplotlib.pyplot as plt
def get_data(imfile):
img = nib.load(imfile)
data, affine = img.get_data(), img.get_affine()
return data, affine
bold_data, nat_aff = get_data(mean)
wm_data, _ = get_data(contour)
brain_mask, _ = get_data(mask)
f = plt.figure(figsize=(12, 6))
kwargs = dict(figure=f, draw_cross=False, annotate=False, slicer="y")
for cut_coords, ax_pos in zip(
np.linspace(-50, 70, 8).reshape(2, 4), [(0, 0, 1, .5),
(0, .5, 1, .5)]):
slicer = viz.plot_anat(bold_data,
nat_aff,
cut_coords=cut_coords,
axes=ax_pos,
**kwargs)
slicer.contour_map(wm_data, nat_aff, colors="palegreen")
slicer.contour_map(brain_mask, nat_aff, colors="tomato")
plt.gca().set_title("%s" % title, size=14)
outfile = os.path.abspath('%s_contour.png' % title)
plt.savefig(outfile)
return outfile
def plot_T1_brainmask(T1, brainmask, figsize=(11.7, 8.3)):
fig = plt.figure(figsize=figsize)
ax = plt.subplot(1, 1, 1)
T1_data = nb.load(T1).get_data()
T1_affine = nb.load(T1).get_affine()
brain_nii = nb.load(brainmask)
brain_data = brain_nii.get_data()
#brain_data[wm_data > 1] = 1
brain_affine = brain_nii.get_affine()
slicer = viz.plot_anat(
np.asarray(T1_data),
np.asarray(T1_affine),
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
figure=fig,
axes=ax,
draw_cross=False)
slicer.contour_map(np.asarray(brain_data),
np.asarray(brain_affine),
linewidths=[0.1],
colors=[
'r',
])
fig.suptitle('FS brain extraction', fontsize='14')
return fig
plt.show(fig)
def plot_hipp_subfields(brain_file, subfield_file, figsize=(40.7, 20.3)):
fig = plt.figure(figsize=figsize)
ax = plt.subplot(1, 1, 1)
print "hello"
brain = nb.load(brain_file).get_data()
brain_affine = nb.load(brain_file).get_affine()
subfield = nb.load(subfield_file).get_data()
subfield_affine = nb.load(subfield_file).get_affine()
plt.histogram(subfield[:])
#
#plt.imshow(subfield[:,:,175], cmap="gray", origin="lower")
#plt.show()
subfield[subfield > 1] = 1
slicer = viz.plot_anat(
np.asarray(brain),
np.asarray(brain_affine),
cut_coords=np.arange(-238, -220, 2), #None, #[0,50,100,150,200,250],
slicer='z',
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
figure=fig,
axes=ax,
draw_cross=False)
slicer.edge_map(np.asarray(subfield),
np.asarray(subfield_affine),
color='r')
#
# fig.suptitle('subfields', fontsize='14')
plt.show()
return fig
def plot_epi_T1_corregistration(mean_epi_file, wm_file, subject_id, similarity_distribution=None, figsize=(11.7,8.3),):
fig = plt.figure(figsize=figsize)
if similarity_distribution:
ax = plt.subplot(2,1,1)
sns.distplot(similarity_distribution.values(), ax=ax)
ax.set_xlabel("EPI-T1 mincost function (over all subjects)")
cur_similarity = similarity_distribution[subject_id]
label = "mincost function = %g"%cur_similarity
plot_vline(cur_similarity, label, ax=ax)
ax = plt.subplot(2,1,2)
else:
ax = plt.subplot(1,1,0)
func = nb.load(mean_epi_file).get_data()
func_affine = nb.load(mean_epi_file).get_affine()
wm_data = nb.load(wm_file).get_data()
wm_affine = nb.load(wm_file).get_affine()
slicer = viz.plot_anat(np.asarray(func), np.asarray(func_affine), black_bg=True,
cmap = cm.Greys_r, # @UndefinedVariable
figure = fig,
axes = ax,
draw_cross = False)
slicer.contour_map(np.asarray(wm_data), np.asarray(wm_affine), linewidths=[0.1], colors=['r',])
fig.suptitle('coregistration', fontsize='14')
return fig
def plot_epi_to_t1_coregistration(epi_file, reg_file, ribbon, fssubjects_dir):
import pylab as plt
from nipy.labs import viz
import nibabel as nb
import numpy as np
import os
import nipype.interfaces.freesurfer as fs
anat = nb.load(ribbon).get_data()
anat[anat > 1] = 1
anat_affine = nb.load(ribbon).get_affine()
func = nb.load(epi_file).get_data()
func_affine = nb.load(epi_file).get_affine()
fig = plt.figure(figsize=(8, 6), edgecolor="k", facecolor="k")
slicer = viz.plot_anat(
np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=plt.cm.spectral,
cut_coords=(-6, 3, 12),
figure=fig,
axes=[0, 0.50, 1, 0.33],
)
slicer.contour_map(np.asarray(anat), np.asarray(anat_affine), levels=[0.51], colors=["r"])
slicer.title(
"Mean EPI with cortical surface contour overlay (before registration)", size=12, color="w", alpha=0
)
res = fs.ApplyVolTransform(
source_file=epi_file, reg_file=reg_file, fs_target=True, subjects_dir=fssubjects_dir
).run()
func = nb.load(res.outputs.transformed_file).get_data()
func_affine = nb.load(res.outputs.transformed_file).get_affine()
slicer = viz.plot_anat(
np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=plt.cm.spectral,
cut_coords=(-6, 3, 12),
figure=fig,
axes=[0, 0, 1, 0.33],
)
slicer.contour_map(np.asarray(anat), np.asarray(anat_affine), levels=[0.51], colors=["r"])
slicer.title("Mean EPI with cortical surface contour overlay (after registration)", size=12, color="w", alpha=0)
plt.savefig("reg_plot.png", facecolor=fig.get_facecolor(), edgecolor="none")
return os.path.abspath("reg_plot.png")
def plot_epi_T1_corregistration(
mean_epi_file,
reg_file,
fssubjects_dir,
subject_id,
similarity_distribution=None,
figsize=(11.7, 8.3),
):
fig = plt.figure(figsize=figsize)
if similarity_distribution:
ax = plt.subplot(2, 1, 1)
sns.distplot(similarity_distribution.values(), ax=ax)
ax.set_xlabel(
"EPI-T1 similarity after coregistration (over all subjects)")
cur_similarity = similarity_distribution[subject_id]
label = "similarity = %g" % cur_similarity
plot_vline(cur_similarity, label, ax=ax)
ax = plt.subplot(2, 1, 0)
else:
ax = plt.subplot(1, 1, 0)
res = ApplyVolTransform(source_file=mean_epi_file,
reg_file=reg_file,
fs_target=True,
subjects_dir=fssubjects_dir,
terminal_output="none").run()
func = nb.load(res.outputs.transformed_file).get_data()
func_affine = nb.load(res.outputs.transformed_file).get_affine()
ribbon_file = "%s/%s/mri/ribbon.mgz" % (fssubjects_dir, subject_id)
ribbon_nii = nb.load(ribbon_file)
ribbon_data = ribbon_nii.get_data()
ribbon_data[ribbon_data > 1] = 1
ribbon_affine = ribbon_nii.get_affine()
slicer = viz.plot_anat(
np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
cut_coords=(-6, 3, 32),
figure=fig,
axes=ax,
draw_cross=False)
slicer.contour_map(np.asarray(ribbon_data),
np.asarray(ribbon_affine),
levels=[.51],
colors=[
'r',
])
return fig
def plot_unwarping(
mean_epi,
mean_epi_uncorrected,
figsize=(11.7, 8.3),
):
fig = plt.figure(figsize=figsize)
ax = plt.subplot(2, 1, 1)
before_unwarp_data = nb.load(mean_epi_uncorrected).get_data()
before_unwarp_affine = nb.load(mean_epi_uncorrected).get_affine()
slicer = viz.plot_anat(
np.asarray(before_unwarp_data),
np.asarray(before_unwarp_affine),
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
cut_coords=(-8, 0, 8),
slicer='x',
figure=fig,
axes=ax,
draw_cross=False)
ax = plt.subplot(2, 1, 2)
unwarped_data = nb.load(mean_epi).get_data()
unwarped_affine = nb.load(mean_epi).get_affine()
slicer = viz.plot_anat(
np.asarray(unwarped_data),
np.asarray(unwarped_affine),
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
cut_coords=(-8, 0, 8),
slicer='x',
figure=fig,
axes=ax,
draw_cross=False)
fig.suptitle('fieldmap correction', fontsize='14')
return fig
def plot_anat(brain):
import os.path
import pylab as pl
from nibabel import load
from nipy.labs import viz
import numpy as np
img = load(brain)
data = img.get_data()
data[np.isnan(data)] = 0
affine = img.get_affine()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='x')
x_view = os.path.abspath('x_view.png')
y_view = os.path.abspath('y_view.png')
z_view = os.path.abspath('z_view.png')
pl.savefig(x_view,bbox_inches='tight')
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='y')
pl.savefig(y_view,bbox_inches='tight')
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='z')
pl.savefig(z_view,bbox_inches='tight')
images = [x_view, y_view, z_view]
pl.close()
return images
def plot_ribbon(Brain):
import os.path
import pylab as pl
from nibabel import load
from nipy.labs import viz
images = []
for brain in Brain:
if os.path.split(brain)[1] == 'ribbon.mgz':
img = load(brain)
data = img.get_data()*100
affine = img.get_affine()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='x', cmap=viz.cm.black_green)
x_view = os.path.abspath('x_view.png')
y_view = os.path.abspath('y_view.png')
z_view = os.path.abspath('z_view.png')
pl.savefig(x_view,bbox_inches='tight')
pl.close()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='y', cmap=viz.cm.black_green)
pl.savefig(y_view,bbox_inches='tight')
pl.close()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='z', cmap=viz.cm.black_green)
pl.savefig(z_view,bbox_inches='tight')
images = [x_view, y_view, z_view]
pl.close()
return images
def plot_anat(brain):
import os.path
import pylab as pl
from nibabel import load
from nipy.labs import viz
import numpy as np
img = load(brain)
data = img.get_data()
data[np.isnan(data)] = 0
affine = img.get_affine()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='x')
x_view = os.path.abspath('x_view.png')
y_view = os.path.abspath('y_view.png')
z_view = os.path.abspath('z_view.png')
pl.savefig(x_view,bbox_inches='tight')
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='y')
pl.savefig(y_view,bbox_inches='tight')
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='z')
pl.savefig(z_view,bbox_inches='tight')
images = [x_view, y_view, z_view]
pl.close()
return images
def plot_ribbon(Brain):
import os.path
import pylab as pl
from nibabel import load
from nipy.labs import viz
images = []
for brain in Brain:
if os.path.split(brain)[1] == 'ribbon.mgz':
img = load(brain)
data = img.get_data()*100
affine = img.get_affine()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='x', cmap=viz.cm.black_green)
x_view = os.path.abspath('x_view.png')
y_view = os.path.abspath('y_view.png')
z_view = os.path.abspath('z_view.png')
pl.savefig(x_view,bbox_inches='tight')
pl.close()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='y', cmap=viz.cm.black_green)
pl.savefig(y_view,bbox_inches='tight')
pl.close()
viz.plot_anat(anat=data, anat_affine=affine, draw_cross=False, slicer='z', cmap=viz.cm.black_green)
pl.savefig(z_view,bbox_inches='tight')
images = [x_view, y_view, z_view]
pl.close()
return images
def plot_epi_T1_corregistration(mean_epi_file,
wm_file,
reg_file,
fssubjects_dir,
subject_id,
figsize=(11.7, 8.3)):
fig = plt.figure(figsize=figsize)
ax = plt.subplot(1, 1, 1)
print ax
res = ApplyVolTransform(source_file=mean_epi_file,
reg_file=reg_file,
fs_target=True,
subjects_dir=fssubjects_dir,
terminal_output="none").run()
func = nb.load(res.outputs.transformed_file).get_data()
func_affine = nb.load(res.outputs.transformed_file).get_affine()
# ribbon_file = "%s/%s/mri/ribbon.mgz"%(fssubjects_dir, subject_id)
# ribbon_nii = nb.load(ribbon_file)
# ribbon_data = ribbon_nii.get_data()
# ribbon_data[ribbon_data > 1] = 1
# ribbon_affine = ribbon_nii.get_affine()
wm_nii = nb.load(wm_file)
wm_data = wm_nii.get_data()
wm_data[wm_data > 1] = 1
wm_affine = wm_nii.get_affine()
slicer = viz.plot_anat(
np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
figure=fig,
axes=ax,
draw_cross=False)
slicer.contour_map(np.asarray(wm_data),
np.asarray(wm_affine),
linewidths=[0.1],
colors=[
'r',
])
fig.suptitle('coregistration', fontsize='14')
return fig
plt.show(fig)
def plot_epi_T1_corregistration(
mean_epi_file,
wm_file,
subject_id,
similarity_distribution=None,
figsize=(11.7, 8.3),
):
fig = plt.figure(figsize=figsize)
if similarity_distribution:
ax = plt.subplot(2, 1, 1)
sns.distplot(similarity_distribution.values(), ax=ax)
ax.set_xlabel("EPI-T1 mincost function (over all subjects)")
cur_similarity = similarity_distribution[subject_id]
label = "mincost function = %g" % cur_similarity
plot_vline(cur_similarity, label, ax=ax)
ax = plt.subplot(2, 1, 2)
else:
ax = plt.subplot(1, 1, 0)
func = nb.load(mean_epi_file).get_data()
func_affine = nb.load(mean_epi_file).get_affine()
wm_data = nb.load(wm_file).get_data()
wm_affine = nb.load(wm_file).get_affine()
slicer = viz.plot_anat(
np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=cm.Greys_r, # @UndefinedVariable
figure=fig,
axes=ax,
draw_cross=False)
slicer.contour_map(np.asarray(wm_data),
np.asarray(wm_affine),
linewidths=[0.1],
colors=[
'r',
])
fig.suptitle('coregistration', fontsize='14')
return fig
def plot_epi_T1_corregistration(mean_epi_file, reg_file, fssubjects_dir, subject_id, similarity_distribution=None, figsize=(11.7,8.3),):
fig = plt.figure(figsize=figsize)
if similarity_distribution:
ax = plt.subplot(2,1,1)
sns.distplot(similarity_distribution.values(), ax=ax)
ax.set_xlabel("EPI-T1 similarity after coregistration (over all subjects)")
cur_similarity = similarity_distribution[subject_id]
label = "similarity = %g"%cur_similarity
plot_vline(cur_similarity, label, ax=ax)
ax = plt.subplot(2,1,0)
else:
ax = plt.subplot(1,1,0)
res = ApplyVolTransform(source_file = mean_epi_file,
reg_file = reg_file,
fs_target = True,
subjects_dir = fssubjects_dir,
terminal_output = "none").run()
func = nb.load(res.outputs.transformed_file).get_data()
func_affine = nb.load(res.outputs.transformed_file).get_affine()
ribbon_file = "%s/%s/mri/ribbon.mgz"%(fssubjects_dir, subject_id)
ribbon_nii = nb.load(ribbon_file)
ribbon_data = ribbon_nii.get_data()
ribbon_data[ribbon_data > 1] = 1
ribbon_affine = ribbon_nii.get_affine()
slicer = viz.plot_anat(np.asarray(func), np.asarray(func_affine), black_bg=True,
cmap = cm.Greys_r, # @UndefinedVariable
cut_coords = (-6,3,32),
figure = fig,
axes = ax,
draw_cross = False)
slicer.contour_map(np.asarray(ribbon_data), np.asarray(ribbon_affine), levels=[.51], colors=['r',])
return fig
def contour_image(contour,mean,mask,title=''):
import nibabel as nib
import numpy as np
import nipy.labs.viz as viz
import os
import matplotlib.pyplot as plt
def get_data(imfile):
img = nib.load(imfile)
data, affine = img.get_data(), img.get_affine()
return data,affine
bold_data, nat_aff = get_data(mean)
wm_data, _ = get_data(contour)
brain_mask, _ = get_data(mask)
f = plt.figure(figsize=(12, 6))
kwargs = dict(figure=f, draw_cross=False, annotate=False, slicer="y")
for cut_coords, ax_pos in zip(np.linspace(-50, 70, 8).reshape(2, 4), [(0, 0, 1, .5), (0, .5, 1, .5)]):
slicer = viz.plot_anat(bold_data, nat_aff, cut_coords=cut_coords, axes=ax_pos, **kwargs)
slicer.contour_map(wm_data, nat_aff, colors="palegreen")
slicer.contour_map(brain_mask, nat_aff, colors="tomato")
plt.gca().set_title("%s"%title, size=14)
outfile = os.path.abspath('%s_contour.png'%title)
plt.savefig(outfile)
return outfile
def plot_epi_to_t1_coregistration(epi_file, reg_file, ribbon,
fssubjects_dir):
import pylab as plt
from nipy.labs import viz
import nibabel as nb
import numpy as np
import os
import nipype.interfaces.freesurfer as fs
anat = nb.load(ribbon).get_data()
anat[anat > 1] = 1
anat_affine = nb.load(ribbon).get_affine()
func = nb.load(epi_file).get_data()
func_affine = nb.load(epi_file).get_affine()
fig = plt.figure(figsize=(8, 6), edgecolor='k', facecolor='k')
slicer = viz.plot_anat(np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=plt.cm.spectral,
cut_coords=(-6, 3, 12),
figure=fig,
axes=[0, .50, 1, .33])
slicer.contour_map(np.asarray(anat),
np.asarray(anat_affine),
levels=[.51],
colors=[
'r',
])
slicer.title(
"Mean EPI with cortical surface contour overlay (before registration)",
size=12,
color='w',
alpha=0)
res = fs.ApplyVolTransform(source_file=epi_file,
reg_file=reg_file,
fs_target=True,
subjects_dir=fssubjects_dir).run()
func = nb.load(res.outputs.transformed_file).get_data()
func_affine = nb.load(res.outputs.transformed_file).get_affine()
slicer = viz.plot_anat(np.asarray(func),
np.asarray(func_affine),
black_bg=True,
cmap=plt.cm.spectral,
cut_coords=(-6, 3, 12),
figure=fig,
axes=[0, 0, 1, .33])
slicer.contour_map(np.asarray(anat),
np.asarray(anat_affine),
levels=[.51],
colors=[
'r',
])
slicer.title(
"Mean EPI with cortical surface contour overlay (after registration)",
size=12,
color='w',
alpha=0)
plt.savefig("reg_plot.png",
facecolor=fig.get_facecolor(),
edgecolor='none')
return os.path.abspath("reg_plot.png")
cmaps_list = (cmaps['Yl'], cmaps['Gr'], cmaps['Rd'], cmaps['Ma'],
cmaps['Or'], cmaps['Bl'], cmaps['Cy'], cmaps['Pu'])
###############################################################################
atlas_name = atlas_file.replace('.nii.gz', '')
if os.path.exists(atlas_name):
shutil.rmtree(atlas_name, ignore_errors=True)
os.mkdir(atlas_name)
fnames = list()
for axis, cut in cuts:
slicer = viz.plot_anat(slicer=axis, cut_coords=(cut, ),)
for level in (1, 2, 3):
level_labels = np.trunc(atlas / 1000. * 10 ** (level - 1))
level_labels = level_labels.astype(np.int)
for label in np.unique(level_labels):
if label == 0:
continue
slicer.contour_map(level_labels == label, affine,
levels=[.5], colors='k',
linewidths=linewidths[level])
for label in range(1, 9):
this_altas = atlas.copy()
this_altas[atlas >= 1000 * (label + 1)] = 0
slicer.plot_map(atlas, affine,
cmap=cmaps_list[label - 1],
threshold=1000 * label - 2,
The idea is to represent the anatomical image to be checked with an overlay of
the edges of the reference image. This idea is borrowed from FSL.
Needs the *templates* data package.
Needs matplotlib.
"""
print(__doc__)
try:
import matplotlib.pyplot as plt
except ImportError:
raise RuntimeError("This script needs the matplotlib library")
from nipy.labs import viz
from nipy.labs.viz_tools import anat_cache
# Get the data. Here we are using the reference T1 image
anat, affine, _ = anat_cache._AnatCache.get_anat()
# Here we use the same image as a reference. As a result it is perfectly
# aligned.
reference = anat
reference_affine = affine
slicer = viz.plot_anat(anat, affine, dim=.2, black_bg=True)
slicer.edge_map(reference, reference_affine)
plt.show()
def plot_segmentation(img, gm_filename, wm_filename=None,
csf_filename=None,
output_filename=None, cut_coords=None,
slicer='ortho',
cmap=None,
title='GM + WM + CSF segmentation'):
"""
Plot a contour mapping of the GM, WM, and CSF of a subject's anatomical.
Parameters
----------
img_filename: string or image object
path of file containing image data, or image object simply
gm_filename: string
path of file containing Grey Matter template
wm_filename: string (optional)
path of file containing White Matter template
csf_filename: string (optional)
path of file containing Cerebro-Spinal Fluid template
"""
# sanity
if cmap is None:
cmap = pl.cm.gray
if cut_coords is None:
cut_coords = (-10, -28, 17)
if slicer in ['x', 'y', 'z']:
cut_coords = (cut_coords['xyz'.index(slicer)],)
# plot img
if hasattr(img, '__len__'):
img = compute_mean_3D_image(img)
# XXX else i'm assuming a nifi object ;)
anat = img.get_data()
anat_affine = img.get_affine()
_slicer = viz.plot_anat(
anat, anat_affine, cut_coords=cut_coords,
slicer=slicer,
cmap=cmap,
# black_bg=True,
)
# draw a GM contour map
gm = nibabel.load(gm_filename)
gm_template = gm.get_data()
gm_affine = gm.get_affine()
_slicer.contour_map(gm_template, gm_affine, levels=[.51], colors=["r"])
# draw a WM contour map
if not wm_filename is None:
wm = nibabel.load(wm_filename)
wm_template = wm.get_data()
wm_affine = wm.get_affine()
_slicer.contour_map(wm_template, wm_affine, levels=[.51], colors=["g"])
# draw a CSF contour map
if not csf_filename is None:
csf = nibabel.load(csf_filename)
csf_template = csf.get_data()
csf_affine = csf.get_affine()
_slicer.contour_map(
csf_template, csf_affine, levels=[.51], colors=['b'])
# misc
_slicer.title("%s (cmap: %s)" % (title, cmap.name), size=12, color='w',
alpha=0)
# pl.legend(("WM", "CSF", "GM"), loc="lower left", ncol=len(cut_coords))
if not output_filename is None:
pl.savefig(output_filename, bbox_inches='tight', dpi=200,
facecolor="k",
edgecolor="k")
def plot_registration(reference_img, coregistered_img,
title="untitled coregistration!",
cut_coords=None,
slicer='ortho',
cmap=None,
output_filename=None):
"""Plots a coregistered source as bg/contrast for the reference image
Parameters
----------
reference_img: string
path to reference (background) image
coregistered_img: string
path to other image (to be compared with reference)
slicer: string (optional, defaults to 'ortho')
slicer param to pass to the nipy.labs.viz.plot_??? APIs
cmap: matplotlib colormap object (optional, defaults to spectral)
colormap to user for plots
output_filename: string (optional)
path where plot will be stored
"""
# sanity
if cmap is None:
cmap = pl.cm.gray # registration QA always gray cmap!
if cut_coords is None:
cut_coords = (-10, -28, 17)
if slicer in ['x', 'y', 'z']:
cut_coords = (cut_coords['xyz'.index(slicer)],)
# plot the coregistered image
if hasattr(coregistered_img, '__len__'):
coregistered_img = compute_mean_3D_image(coregistered_img)
# XXX else i'm assuming a nifi object ;)
coregistered_data = coregistered_img.get_data()
coregistered_affine = coregistered_img.get_affine()
_slicer = viz.plot_anat(
anat=coregistered_data,
anat_affine=coregistered_affine,
cmap=cmap,
cut_coords=cut_coords,
slicer=slicer,
# black_bg=True,
)
# overlap the reference image
if hasattr(reference_img, '__len__'):
reference_img = compute_mean_3D_image(reference_img)
# XXX else i'm assuming a nifi object ;)
reference_data = reference_img.get_data()
reference_affine = reference_img.get_affine()
_slicer.edge_map(reference_data, reference_affine)
# misc
_slicer.title("%s (cmap: %s)" % (title, cmap.name), size=12, color='w',
alpha=0)
if not output_filename is None:
try:
pl.savefig(output_filename, dpi=200, bbox_inches='tight',
facecolor="k",
edgecolor="k")
except AttributeError:
# XXX TODO: handy this case!!
pass
The idea is to represent the anatomical image to be checked with an overlay of
the edges of the reference image. This idea is borrowed from FSL.
Needs the *templates* data package.
Needs matplotlib.
"""
print(__doc__)
try:
import matplotlib.pyplot as plt
except ImportError:
raise RuntimeError("This script needs the matplotlib library")
from nipy.labs import viz
from nipy.labs.viz_tools import anat_cache
# Get the data. Here we are using the reference T1 image
anat, affine, _ = anat_cache._AnatCache.get_anat()
# Here we use the same image as a reference. As a result it is perfectly
# aligned.
reference = anat
reference_affine = affine
slicer = viz.plot_anat(anat, affine, dim=.2, black_bg=True)
slicer.edge_map(reference, reference_affine)
plt.show()
