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Solved some issues to run img_pipe on the ICBM MNI 152 NLIN ASYM 2009b #41

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Solved some issues to run img_pipe on the ICBM MNI 152 NLIN ASYM 2009b #41

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15 changes: 11 additions & 4 deletions img_pipe/img_pipe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1172,8 +1172,7 @@ def label_elecs(self, elecfile_prefix='TDT_elecs_all', atlas_surf='desikan-killi
label_name = label.split('.')[1]
print('Loading label %s'%label_name)
fid = open(label,'r')
d = np.genfromtxt(fid, delimiter=' ', \
skip_header=2)
d = np.genfromtxt(fid, delimiter=' ', skip_header=2)
vertnum, x, y, z, junk=d[~np.isnan(d)].reshape((-1,5)).T
for v in vertnum:
vert_label[np.int(v)] = label_name.strip()
Expand Down Expand Up @@ -1502,6 +1501,14 @@ def get_surface_warp(self, basename='TDT_elecs_all', template='cvs_avg35_inMNI15
elecmatrix = scipy.io.loadmat(os.path.join(self.elecs_dir, basename + '.mat'))['elecmatrix']
anatomy = scipy.io.loadmat(os.path.join(self.elecs_dir, basename + '.mat'))['anatomy']
labelpath = os.path.join(self.subj_dir, self.subj, 'label')

if anatomy is not None:
surface_indices = np.array(
list(set(np.where(anatomy[:, 2] != 'depth')[0]) & set(np.where(np.all(~np.isnan(elecmatrix), axis=1))[0])),
dtype='int64')
anatomy = anatomy[surface_indices]
elecmatrix = elecmatrix[surface_indices,:]

elecs_warped = self.compute_surface_warp(elecmatrix, anatomy, labelpath, basename, template)

scipy.io.savemat(elecfile, {'elecmatrix': np.array(elecs_warped), 'anatomy': anatomy})
Expand Down Expand Up @@ -1755,7 +1762,7 @@ def plot_elec(self, orig_coords, warped_coords, subj_dat, cvs_dat, elec_num,pdf)
cmap = matplotlib.colors.ListedColormap(np.load(fs_lut)[:cvs_dat.max()+1,:])

lookupTable = os.path.join(self.img_pipe_dir, 'SupplementalFiles', 'FreeSurferLookupTable')
lookup_dict = pickle.load(open(lookupTable,'r'))
lookup_dict = pickle.load(open(lookupTable,'rb'))
fig = plt.figure(figsize=((30,17)))
nonzero_indices = np.where(cvs_dat>0)
offset = 35 #this is how much you want to trim the mri by, there is a lot of empty space
Expand Down Expand Up @@ -2404,12 +2411,12 @@ def plot_recon_anatomy_compare_warped(self, template='cvs_avg35_inMNI152', elecf
subj_mesh.actor.property.opacity = opacity
template_mesh.actor.property.opacity = opacity

arr = mlab.screenshot(antialiased=True)
if screenshot:
plt.figure(figsize=(20,10))
plt.imshow(arr, aspect='equal')
plt.axis('off')
plt.show()
arr = mlab.screenshot(antialiased=True)
if showfig:
mlab.show()
return subj_mesh, template_mesh, mlab
Expand Down