def viz_subcortical_points(self, subjects_dir=None, subject=None):
'''
add transparent voxel structures at the subcortical structures
'''
if subjects_dir is None:
subjects_dir = os.environ['SUBJECTS_DIR']
if subject is None:
subject = os.environ['SUBJECT']
structures_list = {
'hippocampus': ([53, 17], (.69, .65, .93)),
'amgydala': ([54, 18], (.8, .5, .29)),
'thalamus': ([49, 10], (.318, 1, .447)),
'caudate': ([50, 11], (1, .855, .67)),
'putamen': ([51, 12], (0, .55, 1)),
'insula': ([55, 19], (1, 1, 1)),
'accumbens': ([58, 26], (1, .44, 1)),
}
asegf = os.path.join(subjects_dir, subject, 'mri', 'aseg.mgz')
aseg = nib.load(asegf)
asegd = aseg.get_data()
for struct in structures_list:
(strucl, strucr), color = structures_list[struct]
for strucu in (strucl, strucr):
strucw = np.where(asegd == strucu)
if np.size(strucw) == 0:
print 'Nonne skippy %s' % struct
continue
import geometry as geo
xfm = geo.get_vox2rasxfm(asegf, stem='vox2ras-tkr')
strucd = np.array(geo.apply_affine(np.transpose(strucw), xfm))
print np.shape(strucd)
src = mlab.pipeline.scalar_scatter(
strucd[:, 0],
strucd[:, 1],
strucd[:, 2],
figure=self.scene.mayavi_scene)
mlab.pipeline.glyph(src,
scale_mode='none',
scale_factor=0.4,
mode='sphere',
opacity=1,
figure=self.scene.mayavi_scene,
color=color)
def get_orig2std(orig):
'''
Given an orig file, get the transformation from the orig to ras2mni.
'''
vox2ras = get_vox2rasxfm(orig)
bx, by, bz = vox2ras[0:3,3]
reorient_orig2std_mat = np.array(((1, 0, 0, bx-128),
(0, 0, -1, by+128),
(0, 1, 0, bz-128),
(0, 0, 0, 1)))
return reorient_orig2std_mat
def load_img(self, imgf, reorient2std=False, image_name=None):
self._finished_plotting = False
img = nib.load(imgf)
aff = np.dot(
get_orig2std(imgf) if reorient2std else np.eye(4),
img.get_affine())
tkr_aff = np.dot(
reorient_orig2std_tkr_mat if reorient2std else np.eye(4),
get_vox2rasxfm(imgf, stem='vox2ras-tkr'))
#from nilearn.image.resampling import reorder_img
#img = reorder_img(uimg, resample='continuous')
xsz, ysz, zsz = img.shape
#print 'image coordinate transform', img.get_affine()
imgd = img.get_data()
if reorient2std:
imgd = np.swapaxes(imgd, 1, 2)[:,:,::-1]
#print 'image size', imgd.shape
if image_name is None:
from utils import gensym
image_name = 'image%s'%gensym()
self.images[image_name] = (imgd, aff, tkr_aff)
self.currently_showing_list.append(
NullInstanceHolder(name=image_name))
self.currently_showing = self.currently_showing_list[-1]
self.pins[image_name] = {}
#self.current_pin = image_name
self.show_image(image_name)
def coronal_slice(elecs, start=None, end=None, outfile=None,
subjects_dir=None,
subject=None, reorient2std=True, dpi=150, size=(200,200),
title=None):
'''
create an image of a coronal slice which serves as a guesstimate of a
depth lead inserted laterally and nonvaryingly in the Y axis
plot the electrodes from the lead overlaid on the slice in the X and Z
directions
Paramaters
----------
elecs : List( Electrode )
list of electrode objects forming this depth lead
start : Electrode
Electrode object at one end of the depth lead
end : Electrode
Electrode object at the other end of the depth lead
outfile : Str
Filename to save the image to
subjects_dir : Str | None
The freesurfer subjects_dir. If this is None, it is assumed to be the
$SUBJECTS_DIR environment variable. If this folder is not writable,
the program will crash.
subject : Str | None
The freesurfer subject. If this is None, it is assumed to be the
$SUBJECT environment variable.
reorient2std : Bool
Apply a matrix to rotate orig.mgz to the standard MNI orientation
emulating fslreorient2std. Pretty much always true here.
dpi : Int
Dots per inch of output image
size : Tuple
Specify a 2-tuple to control the image size, default is (200,200)
title : Str
Specify a matplotlib title
'''
print 'creating coronal slice with start electrodes %s' % str(start)
subjdir_subj = get_subjects_dir( subjects_dir=subjects_dir,
subject=subject )
orig = os.path.join(subjdir_subj, 'mri', 'orig.mgz')
x_size, y_size, z_size = nib.load(orig).shape
# vox2ras and ras2vox shouldnt have different procedures for
# getting the different dimensions. the matrix showing those
# dimensions has the correct dimensions by inversion beforehand
# in the complex 3-way case
vox2ras = get_vox2rasxfm(orig, stem='vox2ras')
ras2vox = np.linalg.inv(vox2ras)
ras2vox[0:3,3] = (x_size/2, y_size/2, z_size/2)
rd, ad, sd = get_std_orientation(ras2vox)
# rd, = np.where(np.abs(ras2vox[:,0]) == np.max(np.abs(ras2vox[:,0])))
# ad, = np.where(np.abs(ras2vox[:,1]) == np.max(np.abs(ras2vox[:,1])))
# sd, = np.where(np.abs(ras2vox[:,2]) == np.max(np.abs(ras2vox[:,2])))
r_size = [x_size, y_size, z_size][rd]
a_size = [x_size, y_size, z_size][ad]
s_size = [x_size, y_size, z_size][sd]
#starty = pd.map_cursor( start.asras(), pd.current_affine, invert=True)[1]
#endy = pd.map_cursor( end.asras(), pd.current_affine, invert=True )[1]
#midy = (starty+endy)/2
#pd.move_cursor(128, midy, 128)
electrodes = np.squeeze([apply_affine([e.asras()], ras2vox)
for e in elecs])
#electrodes = np.array([pd.map_cursor(e.asras(), ras2vox,
# invert=True) for e in elecs])
vol = np.transpose( nib.load(orig).get_data(), (rd, ad, sd) )
if start is not None and end is not None:
start_coord = np.squeeze(apply_affine([start.asras()], ras2vox))
end_coord = np.squeeze(apply_affine([end.asras()], ras2vox))
if start_coord[rd] == end_coord[rd]:
raise ValueError('This lead has no variation in the X axis. It shouldnt be displayed coronally')
slice = np.zeros((s_size, r_size))
m = (start_coord[ad]-end_coord[ad])/(start_coord[rd]-end_coord[rd])
b = start_coord[ad]-m*start_coord[rd]
rnew = np.arange(r_size)
anew = m*rnew+b
alower = np.floor(anew)
afrac = np.mod(anew, 1)
try:
for rvox in rnew:
slice[:, rvox] = (vol[rvox, alower[rvox], :] *
(1-afrac[rvox])+vol[rvox, alower[rvox]+1, :] *
afrac[rvox])
except IndexError:
raise ValueError('This lead has minimal variation in the X axis. It shouldnt be displayed coronally')
else:
slice_nr = np.mean(electrodes[:,ad])
slice = vol[:, slice_nr, :].T
vox2pix = np.zeros((2,4))
vox2pix[0, rd] = 1
vox2pix[1, sd] = 1
ras2pix = np.dot(vox2pix, ras2vox)
pix = np.dot(ras2pix,
np.transpose([np.append(e.asras(), 1) for e in elecs]))
#add data to coronal plane
import pylab as pl
fig = pl.figure()
pl.imshow(slice, cmap='gray')
pl.scatter(pix[0,:], pix[1,:], s=10, c='red', edgecolor='yellow',
linewidths=0.4)
if title is not None:
pl.title(title)
pl.axis('off')
#pl.show()
if outfile is not None:
pl.savefig(outfile, dpi=dpi)
return fig
