def vizify(self):
for hemi in self.hemis:
print "visualize %s" % hemi
# Bring up the beauty (the underlay)
brain = Brain(self.subject_id, hemi, self.surf, \
config_opts=self.config_opts, \
subjects_dir=self.subjects_dir)
surf_data = io.read_scalar_data(self.overlay_surf[hemi])
if (sum(abs(surf_data)) > 0):
# Overlay another hopeful beauty (functional overlay)
brain.add_overlay(self.overlay_surf[hemi], name=self.overlay_name,
min=self.min, max=self.max, sign=self.sign)
# Update colorbar
#brain.overlays[self.overlay_name].pos_bar.lut_mode = self.colorbar
tmp = brain.overlays[self.overlay_name]
lut = tmp.pos_bar.lut.table.to_array()
lut[:,0:3] = self.colorbar
tmp.pos_bar.lut.table = lut
# Refresh
brain.show_view("lat")
brain.hide_colorbar()
# Save the beauts
brain.save_imageset("%s_%s" % (self.outprefix, hemi), self.views,
'jpg', colorbar=None)
# End a great journey, till another life
brain.close()
return
def visMontage(pathToSurface, overlay, outputPath, hemi, type='white'):
brain = Brain(pathToSurface, hemi, type)
brain.add_overlay(overlay, -5, 3)
brain.save_montage(outputPath, ['l', 'm'], orientation='v')
brain.close()
return outputPath
def test_overlay():
"""Test plotting of overlay
"""
mlab.options.backend = 'test'
# basic overlay support
overlay_file = pjoin(data_dir, "lh.sig.nii.gz")
brain = Brain(*std_args)
brain.add_overlay(overlay_file)
brain.overlays["sig"].remove()
brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
sig1 = io.read_scalar_data(pjoin(data_dir, "lh.sig.nii.gz"))
sig2 = io.read_scalar_data(pjoin(data_dir, "lh.alt_sig.nii.gz"))
thresh = 4
sig1[sig1 < thresh] = 0
sig2[sig2 < thresh] = 0
conjunct = np.min(np.vstack((sig1, sig2)), axis=0)
brain.add_overlay(sig1, 4, 30, name="sig1")
brain.overlays["sig1"].pos_bar.lut_mode = "Reds"
brain.overlays["sig1"].pos_bar.visible = False
brain.add_overlay(sig2, 4, 30, name="sig2")
brain.overlays["sig2"].pos_bar.lut_mode = "Blues"
brain.overlays["sig2"].pos_bar.visible = False
brain.add_overlay(conjunct, 4, 30, name="conjunct")
brain.overlays["conjunct"].pos_bar.lut_mode = "Purples"
brain.overlays["conjunct"].pos_bar.visible = False
brain.close()
def load_fmri(subject, input_file, hemi="both"):
brain = Brain(subject, hemi, "pial", curv=False)
brain.toggle_toolbars(True)
if hemi == "both":
for hemi in ["rh", "lh"]:
brain.add_overlay(input_file.format(hemi), hemi=hemi)
else:
brain.add_overlay(input_file.format(hemi), hemi=hemi)
def main(subid, overlay):
_, fname = os.path.split(overlay)
hemi = fname[:2]
brain = Brain(subid, hemi, "pial",
config_opts=dict(cortex="low_contrast"))
brain.add_overlay(overlay, min=0.4, max=4, sign="pos")
brain.show_view('m')
def corr_image(resting_image,fwhm):
"""This function makes correlation image on brain surface"""
import numpy as np
import nibabel as nb
import matplotlib.pyplot as plt
from surfer import Brain, Surface
import os
img = nb.load(resting_image)
corrmat = np.corrcoef(np.squeeze(img.get_data()))
corrmat[np.isnan(corrmat)] = 0
corrmat_npz = os.path.abspath('corrmat.npz')
np.savez(corrmat_npz,corrmat=corrmat)
br = Brain('fsaverage5', 'lh', 'smoothwm')
#br.add_overlay(corrmat[0,:], min=0.2, name=0, visible=True)
lh_aparc_annot_file = os.path.join(os.environ["FREESURFER_HOME"],'/subjects/label/lh.aparc.annot')
values = nb.freesurfer.read_annot(lh_aparc_annot_file)
#br.add_overlay(np.mean(corrmat[values[0]==5,:], axis=0), min=0.8, name='mean', visible=True)
data = img.get_data()
data = np.squeeze(img.get_data())
#
precuneus_signal = np.mean(data[values[0]==np.nonzero(np.array(values[2])=='precuneus')[0][0],:], axis=0)
precuneus = np.corrcoef(precuneus_signal, data)
#precuneus.shape
#br.add_overlay(precuneus[0,1:], min=0.3, sign='pos', name='mean', visible=True)
br.add_overlay(precuneus[0,1:], min=0.2, name='mean')#, visible=True)
#br.add_overlay(precuneus[0,1:], min=0.2, name='mean')#, visible=True)
plt.hist(precuneus[0,1:], 128)
plt.savefig(os.path.abspath("histogram.png"))
plt.close()
corr_image = os.path.abspath("corr_image%s.png"%fwhm)
br.save_montage(corr_image)
ims = br.save_imageset(prefix=os.path.abspath('fwhm_%s'%str(fwhm)),views=['medial','lateral','caudal','rostral','dorsal','ventral'])
br.close()
print ims
#precuneus[np.isnan(precuneus)] = 0
#plt.hist(precuneus[0,1:])
roitable = [['Region','Mean Correlation']]
for i, roi in enumerate(np.unique(values[2])):
roitable.append([roi,np.mean(precuneus[values[0]==np.nonzero(np.array(values[2])==roi)[0][0]])])
#images = [corr_fimage]+ims+[os.path.abspath("histogram.png"), roitable]
roitable=[roitable]
histogram = os.path.abspath("histogram.png")
return corr_image, ims, roitable, histogram, corrmat_npz
def make_brain(subject_id,image_path):
from surfer import Brain
hemi = 'lh'
surface = 'inflated'
brain = Brain(subject_id, hemi, surface)
brain.add_overlay(image_path,min=thr)
outpath = os.path.join(os.getcwd(),os.path.split(image_path)[1]+'_surf.png')
brain.save_montage(outpath)
return outpath
def show_fMRI_using_pysurfer(subject, input_file, hemi='both'):
brain = Brain(subject, hemi, "pial", curv=False, offscreen=False)
brain.toggle_toolbars(True)
if hemi=='both':
for hemi in ['rh', 'lh']:
print('adding {}'.format(input_file.format(hemi=hemi)))
brain.add_overlay(input_file.format(hemi=hemi), hemi=hemi)
else:
print('adding {}'.format(input_file.format(hemi=hemi)))
brain.add_overlay(input_file.format(hemi=hemi), hemi=hemi)
def make_pysurfer_images_lh_rh(folder,suffix='cope1',hemi='lh',threshold=0.9499,coords=(),surface='inflated',fwhm=0,filename='',saveFolder=[],vmax=5.0,bsize=5):
from surfer import Brain, io
TFCEposImg,posImg,TFCEnegImg,negImg=getFileNamesfromFolder(folder,suffix)
pos=image.math_img("np.multiply(img1,img2)",
img1=image.threshold_img(TFCEposImg,threshold=threshold),img2=posImg)
neg=image.math_img("np.multiply(img1,img2)",
img1=image.threshold_img(TFCEnegImg,threshold=threshold),img2=negImg)
fw=image.math_img("img1-img2",img1=pos,img2=neg)
if fwhm==0:
smin=np.min(np.abs(fw.get_data()[fw.get_data()!=0]))
else:
smin=2
mri_file = "%s/thresholded_posneg.nii.gz" % folder
fw.to_filename(mri_file)
"""Bring up the visualization"""
brain = Brain("fsaverage",hemi,surface, offscreen=True , background="white")
"""Project the volume file and return as an array"""
reg_file = os.path.join("/opt/freesurfer","average/mni152.register.dat")
surf_data = io.project_volume_data(mri_file, hemi, reg_file,smooth_fwhm=fwhm)
# surf_data_rh = io.project_volume_data(mri_file, "rh", reg_file,smooth_fwhm=fwhm)
"""
You can pass this array to the add_overlay method for a typical activation
overlay (with thresholding, etc.).
"""
brain.add_overlay(surf_data, min=smin, max=vmax, name="activation", hemi=hemi)
# brain.overlays["activation"]
# brain.add_overlay(surf_data_rh, min=smin, max=5, name="ang_corr_rh", hemi='rh')
if len(coords)>0:
if coords[0]>0:
hemi2='rh'
else:
hemi2='lh'
brain.add_foci(coords, map_surface="pial", color="gold",hemi=hemi2)
if len(saveFolder)>0:
folder=saveFolder
image_out=brain.save_montage('%s/%s-%s.png' % (folder,hemi,filename),order=['l','m'],orientation='h',border_size=bsize,colorbar=None)
else:
image_out=brain.save_image('%s/surfaceplot.jpg' % folder)
brain.close()
return image_out
def plot_rs_surf(in_file, thr_list=[(.2,1)],roi_coords=(), fwhm=0):
# in_file .nii to be projected on surface
# list of tuples defining min and max thr_list=[(.2,1)]
import os
import subprocess
from surfer import Brain, io
arch = subprocess.check_output('arch')
if arch.startswith('x86_'): # set offscrene rendering to avoid intereference on linux
from mayavi import mlab
mlab.options.offscreen = True
out_file_list = []
in_file_name = os.path.basename(in_file)
reg_file = os.path.join(os.environ["FREESURFER_HOME"],"average/mni152.register.dat")
for thr in thr_list:
min_thr = thr[0]
max_thr = thr[1]
print(min_thr)
print(max_thr)
for hemi in ['lh', 'rh']:
brain = Brain("fsaverage", hemi, "inflated", views=['lat', 'med'], config_opts=dict(background="white"))
surf_data = io.project_volume_data(in_file, hemi, reg_file, smooth_fwhm=fwhm)
brain.add_overlay(surf_data, min=min_thr, max=max_thr, name="ang_corr", hemi=hemi)
roi_str = ''
if not(roi_coords == ()):
if roi_coords[0] <0: #lh
hemi_str = 'lh'
else:
hemi_str = 'rh'
roi_str = '_roi_%s.%s.%s' % roi_coords
if hemi_str == hemi:
brain.add_foci(roi_coords, map_surface="white", hemi=hemi_str, color='red', scale_factor=2)
out_filename = os.path.join(os.getcwd(), in_file_name + roi_str + '_thr_%s' % min_thr + '_' + hemi + '.png')
out_file_list += [out_filename]
brain.save_image(out_filename)
brain.close()
return out_file_list
def test_image():
"""Test image saving
"""
tmp_name = mktemp() + '.png'
mlab.options.backend = 'auto'
subject_id, _, surf = std_args
brain = Brain(subject_id, 'both', surf=surf, size=100)
brain.add_overlay(overlay_fname, hemi='lh', min=5, max=20, sign="pos")
brain.save_imageset(tmp_name, ['med', 'lat'], 'jpg')
brain = Brain(*std_args, size=100)
brain.save_image(tmp_name)
brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='v')
brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='h')
brain.save_montage(tmp_name, [['l', 'v'], ['m', 'f']])
brain.screenshot()
brain.close()
def plot_rs_surf_bh(in_file, thr_list=[(.2,1)],roi_coords=(), fwhm=0):
# in_file .nii to be projected on surface
# list of tuples defining min and max thr_list=[(.2,1)]
import os
from surfer import Brain, io
out_file_list = []
in_file_name = os.path.basename(in_file)
reg_file = os.path.join(os.environ["FREESURFER_HOME"],"average/mni152.register.dat")
for thr in thr_list:
min_thr = thr[0]
max_thr = thr[1]
print(min_thr)
print(max_thr)
brain = Brain("fsaverage", "split", "inflated", views=['lat', 'med'], config_opts=dict(background="white"))
surf_data_lh = io.project_volume_data(in_file, "lh", reg_file, smooth_fwhm=fwhm)
surf_data_rh = io.project_volume_data(in_file, "rh", reg_file, smooth_fwhm=fwhm)
brain.add_overlay(surf_data_lh, min=min_thr, max=max_thr, name="ang_corr_lh", hemi='lh')
brain.add_overlay(surf_data_rh, min=min_thr, max=max_thr, name="ang_corr_rh", hemi='rh')
roi_str = ''
if not(roi_coords == ()):
if roi_coords[0] <0: #lh
hemi_str = 'lh'
else:
hemi_str = 'rh'
roi_str = '_roi_%s.%s.%s' % roi_coords
brain.add_foci(roi_coords, map_surface="white", hemi=hemi_str, color='red', scale_factor=2)
out_filename = os.path.join(os.getcwd(), in_file_name + roi_str + '_thr_%s' % min_thr + '.png')
out_file_list += [out_filename]
brain.save_image(out_filename)
brain.close()
return out_file_list
def test_image(tmpdir):
"""Test image saving."""
tmp_name = tmpdir.join('temp.png')
tmp_name = str(tmp_name) # coerce to str to avoid PIL error
_set_backend()
subject_id, _, surf = std_args
brain = Brain(subject_id, 'both', surf=surf, size=100)
brain.add_overlay(overlay_fname, hemi='lh', min=5, max=20, sign="pos")
brain.save_imageset(tmp_name, ['med', 'lat'], 'jpg')
brain.close()
brain = Brain(*std_args, size=100)
brain.save_image(tmp_name)
brain.save_image(tmp_name, 'rgba', True)
brain.screenshot()
if os.getenv('TRAVIS', '') != 'true':
# for some reason these fail on Travis sometimes
brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='v')
brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='h')
brain.save_montage(tmp_name, [['l', 'v'], ['m', 'f']])
brain.close()
def test_image(tmpdir):
"""Test image saving."""
tmp_name = tmpdir.join('temp.png')
tmp_name = str(tmp_name) # coerce to str to avoid PIL error
_set_backend()
subject_id, _, surf = std_args
brain = Brain(subject_id, 'both', surf=surf, size=100)
brain.add_overlay(overlay_fname, hemi='lh', min=5, max=20, sign="pos")
brain.save_imageset(tmp_name, ['med', 'lat'], 'jpg')
brain.close()
brain = Brain(*std_args, size=100)
if sys.platform == 'darwin' and os.getenv('TRAVIS', '') == 'true':
raise SkipTest('image saving on OSX travis is not supported')
brain.save_image(tmp_name)
brain.save_image(tmp_name, 'rgba', True)
brain.screenshot()
if os.getenv('TRAVIS', '') != 'true':
# for some reason these fail on Travis sometimes
brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='v')
brain.save_montage(tmp_name, ['l', 'v', 'm'], orientation='h')
brain.save_montage(tmp_name, [['l', 'v'], ['m', 'f']])
brain.close()
def surface_streamlines_map(subjects_dir, subject_id, hemi, surf, alpha,
coords):
"""
Bring up the visualization.
display a map
"""
brain = Brain(subjects_dir=subjects_dir,
subject_id=subject_id,
hemi=hemi,
surf=surf,
alpha=alpha)
if hemi == 'both':
hemi_both = ['lh', 'rh']
for hemi_index in range(len(['lh', 'rh'])):
brain.add_overlay(
coords[hemi_index],
min=coords[hemi_index][coords[hemi_index] > 0].min(),
max=coords[hemi_index].max(),
sign='pos',
hemi=hemi_both[hemi_index])
elif hemi == 'lh':
brain.add_overlay(coords[0],
min=coords[0][coords[0] > 0].min(),
max=coords[0].max(),
sign='pos',
hemi='lh',
name='lh')
else:
brain.add_overlay(coords[1],
min=coords[1][coords[1] > 0].min(),
max=coords[1].max(),
sign='pos',
hemi='rh',
name='rh')
mlab.show()
import os.path as op
from surfer import Brain
"""
Bring up the visualization
"""
brain = Brain("fsaverage", "lh", "inflated")
"""
Get a path to the overlay file.
"""
overlay_file = op.join("example_data", "lh.sig.nii.gz")
"""
Display the overlay on the surface using the defaults
to control thresholding and colorbar saturation.
These can be set through your config file.
"""
brain.add_overlay(overlay_file)
"""
You can then turn the overlay off.
"""
brain.overlays["sig"].remove()
"""
Now add the overlay again, but this time with set threshold
and showing only the positive activations
"""
brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
## AGE
"""Bring up the visualization"""
brain = Brain("fsaverage_copy", "rh", "iter8_inflated",
config_opts=dict(background="white"),
subjects_dir="/home2/data/PublicProgram/freesurfer")
"""Project the volume file and return as an array"""
cwas_file = path.join(overlap_dir, "surf_rh_fdr_logp_age_thr2.nii.gz")
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(cwas_file, min=1, max=3, name="tmp1")
# Update color bar
## get overlay and color bar
tmp1 = brain.overlays["tmp1"]
lut = tmp1.pos_bar.lut.table.to_array()
## update color scheme
single = [251, 154, 143]
overlap = [227, 26, 28]
lut[0:85,0:3] = single
lut[85:170,0:3] = single
lut[170:256,0:3] = overlap
tmp1.pos_bar.lut.table = lut
from surfer import Brain, io
"""Bring up the visualization"""
brain = Brain("fsaverage", "lh", "inflated",
config_opts=dict(background="white"))
"""Project the volume file and return as an array"""
mri_file = "auto_examples/data/resting_corr.nii.gz"
reg_file = "auto_examples/data/register.dat"
surf_data = io.project_volume_data(mri_file, "lh", reg_file)
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(surf_data, min=.3, max=.7, name="ang_corr")
"""
You can also pass it to add_data for more control
over the visualzation. Here we'll plot the whole
range of correlations
"""
brain.overlays["ang_corr"].remove()
brain.add_data(surf_data, -.7, .7, colormap="jet", alpha=.7)
"""
This overlay represents resting-state correlations with a
seed in left angular gyrus. Let's plot that seed.
"""
seed_coords = (-45, -67, 36)
brain.add_foci(seed_coords, map_surface="white")
## AGE
"""Bring up the visualization"""
brain = Brain("fsaverage_copy", "lh", "iter8_inflated",
config_opts=dict(background="white"),
subjects_dir="/home2/data/PublicProgram/freesurfer")
"""Project the volume file and return as an array"""
cwas_file = path.join(overlap_dir, "surf_lh_fdr_logp_age_thr2.nii.gz")
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(cwas_file, min=1, max=3, name="tmp1")
# Update color bar
## get overlay and color bar
tmp1 = brain.overlays["tmp1"]
lut = tmp1.pos_bar.lut.table.to_array()
## update color scheme
single = [251, 154, 143]
overlap = [227, 26, 28]
lut[0:85,0:3] = single
lut[85:170,0:3] = single
lut[170:256,0:3] = overlap
tmp1.pos_bar.lut.table = lut
export SUBJECTS_DIR='/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/mri'
export QT_API=pyqt
ipython
from surfer import Brain
%gui qt
brain = Brain("fsaverage", "lh", "inflated")
overlay_file = "/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_SPROJ_SJ_lh.mgz"
brain.add_overlay(overlay_file, min=3.10, max=5.80, sign="pos")
brain = Brain("fsaverage", "rh", "inflated")
overlay_file = "/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_SPROJ_SJ_rh.mgz"
brain.add_overlay(overlay_file, min=3.10, max=5.80, sign="pos")
brain = Brain("fsaverage", "rh", "inflated")
overlay_file = "/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_SPROJ_SJ_rh.mgz"
brain.add_overlay(overlay_file, min=2.34, max=5.50, sign="pos")
Get a path to the overlay file.
"""
mri_file = '/Users/jamalw/Desktop/PNI/music_event_structures/data/best_k_map_z' + str(
z) + '.nii.gz'
reg_file = '/Applications/freesurfer/average/mni152.register.dat'
data = nib.load(mri_file)
minval = 0
maxval = np.max(data.get_data())
surf_data_lh = project_volume_data(mri_file, "lh", reg_file)
surf_data_rh = project_volume_data(mri_file, "rh", reg_file)
brain.add_overlay(surf_data_lh,
min=minval,
max=maxval,
name="thirty_sec_lh",
hemi='lh')
brain.add_overlay(surf_data_rh,
min=minval,
max=maxval,
name="thirty_sec_rh",
hemi='rh')
for overlay in brain.overlays_dict["thirty_sec_lh"]:
overlay.remove()
for overlay in brain.overlays_dict["thirty_sec_rh"]:
overlay.remove()
brain.add_data(surf_data_lh,
0,
surf_data = io.project_volume_data(mri_file, "rh", reg_file)
"""Load the output data and get maximum value"""
img = nib.load(mri_file)
data = img.get_data()
data_max = data.max()
if data_max == 0:
data_min = 0
else:
data_min = 1.3
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(surf_data, min=data_min, max=data_max, name="ang_corr")
"""
Save some images
"""
odir = "/home/data/Projects/CWAS/development+motion/viz"
brain.save_imageset(path.join(odir, "zpics_glm_regress_surface_%s_rh" % "only_age"),
['med', 'lat', 'ros', 'caud'], 'jpg')
brain.close()
## Age with motion as covariate
print "age with motion"
def surfer(hemi, overlay, annot='Yeo2011_7Networks_N1000'):
brain = Brain("fsaverage", hemi, "inflated")
brain.add_annotation(annot, borders=False, alpha=0.3)
brain.add_overlay(overlay, min=1.66, max=4)
return brain
"""Project the volume file and return as an array"""
orig_file = path.join(mdmr_dir, "clust_logp_%s.nii.gz" % factor)
"""Load the output data and get maximum value"""
img = nib.load(orig_file)
data = img.get_data()
data_max = data.max()
if data_max == 0:
data_min = 0
else:
data_min = data[data.nonzero()].min()
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(cwas_file,
min=data_min,
max=data_max,
name="%s_rh" % factor)
## get overlay and color bar
tmp1 = brain.overlays["%s_rh" % factor]
lut = tmp1.pos_bar.lut.table.to_array()
## update color scheme
lut[:, 0:3] = cols
tmp1.pos_bar.lut.table = lut
## refresh view
brain.show_view("lat")
brain.hide_colorbar()
"""
Save some images
print __doc__
from surfer import Brain, io
"""Bring up the visualization"""
brain = Brain("fsaverage",
"lh",
"inflated",
config_opts=dict(background="white"))
"""Project the volume file and return as an array"""
mri_file = "example_data/resting_corr.nii.gz"
reg_file = "example_data/register.dat"
surf_data = io.project_volume_data(mri_file, "lh", reg_file)
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(surf_data, min=.3, max=.7, name="ang_corr")
"""
You can also pass it to add_data for more control
over the visualzation. Here we'll plot the whole
range of correlations
"""
brain.overlays["ang_corr"].remove()
brain.add_data(surf_data, -.7, .7, colormap="jet", alpha=.7)
"""
This overlay represents resting-state correlations with a
seed in left angular gyrus. Let's plot that seed.
"""
seed_coords = (-45, -67, 36)
brain.add_foci(seed_coords, map_surface="white")
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 9 13:22:37 2019
@author: kwn500
"""
from surfer import Brain
import os
subject_id = 'fsaverage'
hemi = 'lh'
surf = 'inflated'
cope_filepath = '/scratch/groups/Projects/P1361/fMRI/fsl_output/level3/freesurfer/'
cope_output = cope_filepath + 'output/'
cope_file = 'shape_versus_passive_zstat_lh'
os.environ['SUBJECTS_DIR'] = "/usr/share/freesurfer-data/subjects"
brain = Brain(subject_id, hemi, surf)
brain.add_overlay(cope_filepath + cope_file + '.mgh', 2.3, 8)
brain.save_imageset(
cope_output + cope_file,
['medial', 'lateral', 'rostral', 'caudal', 'dorsal', 'ventral'], 'png',
[1, 2, 3, 4, 5, 6])
brain.close()
def surfer(hemi, overlay, annot='Yeo2011_7Networks_N1000'):
brain = Brain("fsaverage", hemi, "inflated")
brain.add_annotation(annot, borders=False, alpha=0.3)
brain.add_overlay(overlay, min=1.66, max=4)
return brain
sig2[sig2 < thresh] = 0 """ A conjunction is defined as the minimum significance value between the two maps at each vertex. """ conjunct = np.min(np.vstack((sig1, sig2)), axis=0) """ Now load the numpy array as an overlay. Use a high saturation point so that the blob will largely be colored with lower values from the lookup table. """ brain.add_overlay(sig1, 4, 30, name="sig1") """ A pointer to the overlay's color manager gets stored in the overlays dictionary. Change the lookup table to "Reds" and turn the color bar itself off, as otherwise the bars for the three maps will get confusingly stacked. """ brain.overlays["sig1"].pos_bar.lut_mode = "Reds" brain.overlays["sig1"].pos_bar.visible = False """ Now load the other two maps and again change the lookup table and turn off the color bar itself. """
Alternatively, if your data are already in register with the Freesurfer
anatomy, you can provide project_volume_data with the subject ID, avoiding the
need to specify a registration file.
By default, 3mm of smoothing is applied on the surface to clean up the overlay
a bit, although the extent of smoothing can be controlled.
"""
zstat = project_volume_data(volume_file,
"lh",
subject_id="fsaverage",
smooth_fwhm=0.5)
"""
Once you have the statistical data loaded into Python, you can simply pass it
to the `add_overlay` method of the Brain object.
"""
brain.add_overlay(zstat, min=2, max=12)
"""
It can also be a good idea to plot the inverse of the mask that was used in the
analysis, so you can be clear about areas that were not included.
It's good to change some parameters of the sampling to account for the fact
that you are projecting binary (0, 1) data.
"""
mask_file = "example_data/mask.nii.gz"
mask = project_volume_data(mask_file,
"lh",
subject_id="fsaverage",
smooth_fwhm=0,
projsum="max").astype(bool)
mask = ~mask
brain.add_data(mask,
def corr_image(resting_image, fwhm):
"""This function makes correlation image on brain surface"""
import numpy as np
import nibabel as nb
import matplotlib.pyplot as plt
from surfer import Brain, Surface
import os
img = nb.load(resting_image)
corrmat = np.corrcoef(np.squeeze(img.get_data()))
corrmat[np.isnan(corrmat)] = 0
corrmat_npz = os.path.abspath('corrmat.npz')
np.savez(corrmat_npz, corrmat=corrmat)
br = Brain('fsaverage5', 'lh', 'smoothwm')
#br.add_overlay(corrmat[0,:], min=0.2, name=0, visible=True)
values = nb.freesurfer.read_annot(
'/software/Freesurfer/5.1.0/subjects/fsaverage5/label/lh.aparc.annot')
#br.add_overlay(np.mean(corrmat[values[0]==5,:], axis=0), min=0.8, name='mean', visible=True)
data = img.get_data()
data = np.squeeze(img.get_data())
#
precuneus_signal = np.mean(data[values[0] == np.nonzero(
np.array(values[2]) == 'precuneus')[0][0], :],
axis=0)
precuneus = np.corrcoef(precuneus_signal, data)
#precuneus.shape
#br.add_overlay(precuneus[0,1:], min=0.3, sign='pos', name='mean', visible=True)
br.add_overlay(precuneus[0, 1:], min=0.2, name='mean') #, visible=True)
#br.add_overlay(precuneus[0,1:], min=0.2, name='mean')#, visible=True)
plt.hist(precuneus[0, 1:], 128)
plt.savefig(os.path.abspath("histogram.png"))
plt.close()
corr_image = os.path.abspath("corr_image%s.png" % fwhm)
br.save_montage(corr_image)
ims = br.save_imageset(
prefix=os.path.abspath('fwhm_%s' % str(fwhm)),
views=['medial', 'lateral', 'caudal', 'rostral', 'dorsal', 'ventral'])
br.close()
print ims
#precuneus[np.isnan(precuneus)] = 0
#plt.hist(precuneus[0,1:])
roitable = [['Region', 'Mean Correlation']]
for i, roi in enumerate(np.unique(values[2])):
roitable.append([
roi,
np.mean(precuneus[values[0] == np.nonzero(
np.array(values[2]) == roi)[0][0]])
])
#images = [corr_fimage]+ims+[os.path.abspath("histogram.png"), roitable]
roitable = [roitable]
histogram = os.path.abspath("histogram.png")
return corr_image, ims, roitable, histogram, corrmat_npz
mri_file = path.join(mdmr_dir, "mni305_log_fdr_pvals_age.nii.gz")
reg_file = path.join(mdmr_dir, "mni305_log_fdr_pvals_age.nii.gz.reg")
surf_data = io.project_volume_data(mri_file, "lh", reg_file)
"""Load the output data and get maximum value"""
img = nib.load(mri_file)
data = img.get_data()
data_max = data.max()
if data_max == 0:
data_min = 0
else:
data_min = 1.3
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(surf_data, min=data_min, max=data_max, name="ang_corr")
"""
Save some images
"""
odir = "/home/data/Projects/CWAS/development+motion/viz"
brain.save_imageset(
path.join(odir, "zpics_glm_regress_surface_%s_lh" % "only_age"),
['med', 'lat', 'ros', 'caud'], 'jpg')
brain.close()
## Age with motion as covariate
print "age with motion"
mdmr_dir = "/home2/data/Projects/CWAS/development+motion/cwas_regress_motion/rois_random_k3200/age+motion_sex+tr.mdmr"
def test_overlay():
"""Test plotting of overlay."""
_set_backend()
# basic overlay support
overlay_file = pjoin(data_dir, "lh.sig.nii.gz")
brain = Brain(*std_args)
brain.add_overlay(overlay_file)
brain.overlays["sig"].remove()
brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
sig1 = io.read_scalar_data(pjoin(data_dir, "lh.sig.nii.gz"))
sig2 = io.read_scalar_data(pjoin(data_dir, "lh.alt_sig.nii.gz"))
# two-sided overlay
brain.add_overlay(sig1, 4, 30, name="two-sided")
overlay = brain.overlays_dict.pop('two-sided')[0]
assert_array_equal(overlay.pos_bar.data_range, [4, 30])
assert_array_equal(overlay.neg_bar.data_range, [-30, -4])
assert_equal(overlay.pos_bar.reverse_lut, True)
assert_equal(overlay.neg_bar.reverse_lut, False)
overlay.remove()
thresh = 4
sig1[sig1 < thresh] = 0
sig2[sig2 < thresh] = 0
conjunct = np.min(np.vstack((sig1, sig2)), axis=0)
brain.add_overlay(sig1, 4, 30, name="sig1")
brain.overlays["sig1"].pos_bar.lut_mode = "Reds"
brain.overlays["sig1"].pos_bar.visible = False
brain.add_overlay(sig2, 4, 30, name="sig2")
brain.overlays["sig2"].pos_bar.lut_mode = "Blues"
brain.overlays["sig2"].pos_bar.visible = False
brain.add_overlay(conjunct, 4, 30, name="conjunct")
brain.overlays["conjunct"].pos_bar.lut_mode = "Purples"
brain.overlays["conjunct"].pos_bar.visible = False
brain.set_surf('white')
brain.close()
Alternatively, if your data are already in register with the Freesurfer
anatomy, you can provide project_volume_data with the subject ID, avoiding the
need to specify a registration file.
By default, 3mm of smoothing is applied on the surface to clean up the overlay a
bit, although the extent of smoothing can be controlled.
"""
zstat = project_volume_data(volume_file, "lh",
subject_id="fsaverage", smooth_fwhm=0.5)
"""
Once you have the statistical data loaded into Python, you can simply pass it
to the `add_overlay` method of the Brain object.
"""
brain.add_overlay(zstat, min=2, max=12)
"""
It can also be a good idea to plot the inverse of the mask that was used in the
analysis, so you can be clear about areas that were not included.
It's good to change some parameters of the sampling to account for the fact that
you are projecting binary (0, 1) data.
"""
mask_file = "example_data/mask.nii.gz"
mask = project_volume_data(mask_file, "lh", subject_id="fsaverage",
smooth_fwhm=0, projsum="max").astype(bool)
mask = ~mask
brain.add_data(mask, min=0, max=10, thresh=.5,
colormap="bone", alpha=.6, colorbar=False)
time=str(time), subid=subid))
############################################
# Visualize accuracy (for given subject)
############################################
from surfer import Brain, project_volume_data
tr_shift_test_list = [0, 2, 4, 6, 8, 10,
12] # seconds to shift onset forward by
# for subid in subj_info.subid:
subid = 'ap101'
for time in tr_shift_test_list:
brain = Brain(subid,
"split",
"inflated",
views=['lat', 'med', 'ven'],
background="white")
volume_file = '/Volumes/group/awagner/sgagnon/AP/analysis/mvpa_raw/searchlight_test/sourcehit_time{time}_acc_{subid}.nii.gz'.format(
time=str(time), subid=subid)
for hemi in ['lh', 'rh']:
zstat = project_volume_data(volume_file,
hemi,
subject_id=subid,
smooth_fwhm=0.5)
brain.add_overlay(zstat, hemi=hemi, min=.333)
brain.save_image(
'/Volumes/group/awagner/sgagnon/AP/analysis/mvpa_raw/searchlight_test/sourcehit_time{time}_acc_{subid}.png'
.format(time=str(time), subid=subid))
def test_overlay():
"""Test plotting of overlay."""
_set_backend()
# basic overlay support
overlay_file = pjoin(data_dir, "lh.sig.nii.gz")
brain = Brain(*std_args)
brain.add_overlay(overlay_file)
brain.overlays["sig"].remove()
brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
sig1 = io.read_scalar_data(pjoin(data_dir, "lh.sig.nii.gz"))
sig2 = io.read_scalar_data(pjoin(data_dir, "lh.alt_sig.nii.gz"))
# two-sided overlay
brain.add_overlay(sig1, 4, 30, name="two-sided")
overlay = brain.overlays_dict.pop('two-sided')[0]
assert_array_equal(overlay.pos_bar.data_range, [4, 30])
assert_array_equal(overlay.neg_bar.data_range, [-30, -4])
assert_equal(overlay.pos_bar.reverse_lut, True)
assert_equal(overlay.neg_bar.reverse_lut, False)
overlay.remove()
thresh = 4
sig1[sig1 < thresh] = 0
sig2[sig2 < thresh] = 0
conjunct = np.min(np.vstack((sig1, sig2)), axis=0)
brain.add_overlay(sig1, 4, 30, name="sig1")
brain.overlays["sig1"].pos_bar.lut_mode = "Reds"
brain.overlays["sig1"].pos_bar.visible = False
brain.add_overlay(sig2, 4, 30, name="sig2")
brain.overlays["sig2"].pos_bar.lut_mode = "Blues"
brain.overlays["sig2"].pos_bar.visible = False
brain.add_overlay(conjunct, 4, 30, name="conjunct")
brain.overlays["conjunct"].pos_bar.lut_mode = "Purples"
brain.overlays["conjunct"].pos_bar.visible = False
brain.set_surf('white')
brain.close()
import os.path as op
import numpy as np
from surfer import io
########################## TJ - SJ #########################"
brain = Brain("fsaverage", "lh", "pial", config_opts={"cortex":"low_contrast","background":"black"})
sig1 = np.nan_to_num(io.read_scalar_data("/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_TJ-SJ_lh.mgz"))
sig2 = np.nan_to_num(io.read_scalar_data('/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_SJ-TJ_lh.mgz'))
thresh = 1
sig1[sig1 < thresh] = 0
sig2[sig2 < thresh] = 0
conjunct = np.min(np.vstack((sig1, sig2)), axis=0)
brain.add_overlay(sig1, 1, 8, name="sig1")
brain.overlays["sig1"].pos_bar.lut_mode = "Reds"
brain.overlays["sig1"].pos_bar.visible = False
brain.add_overlay(sig2, 1, 8, name="sig2")
brain.overlays["sig2"].pos_bar.lut_mode = "Blues"
brain.overlays["sig2"].pos_bar.visible = False
################### CONJ[TJ-CTRL SJ- CTRL] #####################
################## WHITE #######################################
###################### LH #######################
brain = Brain("fsaverage", "lh", "white", config_opts={"cortex":"low_contrast","background":"black"})
overlay_file = "/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_CONJTASK_lh_projfrac05.mgz"
brain.add_overlay(overlay_file, min=1, max=10, sign="pos")
mayavi.mlab.view(azimuth=-33, elevation=None, distance=None, focalpoint=None,
roll=None, reset_roll=True, figure=None)
mayavi.mlab.savefig("/neurospin/unicog/protocols/IRMf/MentalTravel_Martin_2014/BAPTISTE_FOLDER/PICTURES/MOD40/GROUPlvl_CONJTASK_lh_projfrac05_face1.png", size=None, figure=None, magnification='auto')
"""Bring up the visualization"""
brain = Brain("fsaverage", "split", "inflated",
views=['lat', 'med'], background="white")
"""Project the volume file and return as an array"""
mri_file = "example_data/resting_corr.nii.gz"
reg_file = os.path.join(os.environ["FREESURFER_HOME"],
"average/mni152.register.dat")
surf_data_lh = project_volume_data(mri_file, "lh", reg_file)
surf_data_rh = project_volume_data(mri_file, "rh", reg_file)
"""
You can pass this array to the add_overlay method for a typical activation
overlay (with thresholding, etc.).
"""
brain.add_overlay(surf_data_lh, min=.3, max=.7, name="ang_corr_lh", hemi='lh')
brain.add_overlay(surf_data_rh, min=.3, max=.7, name="ang_corr_rh", hemi='rh')
"""
You can also pass it to add_data for more control
over the visualization. Here we'll plot the whole
range of correlations
"""
for overlay in brain.overlays_dict["ang_corr_lh"]:
overlay.remove()
for overlay in brain.overlays_dict["ang_corr_rh"]:
overlay.remove()
"""
We want to use an appropriate color map for these data: a divergent map that
is centered on 0, which is a meaningful transition-point as it marks the change
def surface_roi_contour(subjects_dir, subject_id, hemi, surf, alpha, coords,
region):
"""
Bring up the visualization.
Add the contour of region.
"""
brain = Brain(subjects_dir=subjects_dir,
subject_id=subject_id,
hemi=hemi,
surf=surf,
alpha=alpha)
if hemi == 'both':
brain.add_contour_overlay(region[0],
min=region[0].min(),
max=region[0].max(),
n_contours=2,
line_width=1.5,
colormap="YlOrRd_r",
hemi='lh',
remove_existing=True,
colorbar=False)
brain.add_overlay(coords[0],
min=coords[0][coords[0] > 0].min(),
max=coords[0].max(),
sign='pos',
hemi='lh',
name='lh')
brain.add_contour_overlay(region[1],
min=region[1].min(),
max=region[1].max(),
n_contours=2,
line_width=1.5,
colormap="YlOrRd_r",
hemi='rh',
remove_existing=False,
colorbar=False)
brain.add_overlay(coords[1],
min=coords[1][coords[1] > 0].min(),
max=coords[1].max(),
sign='pos',
hemi='rh',
name='rh')
elif hemi == 'lh':
brain.add_contour_overlay(region[0],
min=region[0].min(),
max=region[0].max(),
n_contours=2,
line_width=1.5,
colormap="YlOrRd_r",
hemi='lh',
remove_existing=True,
colorbar=False)
brain.add_overlay(coords[0],
min=coords[0][coords[0] > 0].min(),
max=coords[0].max(),
sign='pos',
hemi='lh',
name='lh')
else:
brain.add_contour_overlay(region[1],
min=region[1].min(),
max=region[1].max(),
n_contours=2,
line_width=1.5,
colormap="YlOrRd_r",
hemi='rh',
remove_existing=True,
colorbar=False)
brain.add_overlay(coords[1],
min=coords[1][coords[1] > 0].min(),
max=coords[1].max(),
sign='pos',
hemi='rh',
name='rh')
mlab.show()
data = nib.load(mri_file)
minval = 0.2
maxval = np.max(data.get_data())
surf_data_lh = project_volume_data(mri_file,"lh",reg_file)
surf_data_rh = project_volume_data(mri_file,"rh",reg_file)
qmri_file = '/Users/jamalw/Desktop/PNI/music_event_structures/qstats_map.nii.gz'
qdata_lh = project_volume_data(qmri_file,"lh",reg_file)
surf_data_lh[np.logical_or(qdata_lh>0.005,surf_data_lh<0)] = 0
qdata_rh = project_volume_data(qmri_file,"rh",reg_file)
surf_data_rh[np.logical_or(qdata_rh>0.005, surf_data_rh<0)] = 0
brain.add_overlay(surf_data_lh,min=minval,max=maxval,name="thirty_sec_lh", hemi='lh',sign="pos")
brain.add_overlay(surf_data_rh,min=minval,max=maxval,name="thirty_sec_rh", hemi='rh',sign="pos")
#
#for overlay in brain.overlays_dict["thirty_sec_lh"]:
# overlay.remove()
#for overlay in brain.overlays_dict["thirty_sec_rh"]:
# overlay.remove()
#
#brain.add_data(surf_data_lh, minval,maxval, colormap="CMRmap", alpha=1,
# hemi='lh')
#brain.add_data(surf_data_rh, minval,maxval, colormap="CMRmap", alpha=1,
# hemi='rh')
#
brain.save_image("zstats_human_bounds_srm_k30.png")
#
mlab.show()
projmeth = "frac" # frac' method, projection on a fraction of thickness
projsum = "max" # the max value is projected
projarg = [0, 1, 0.1] # from 0 to 1 thickness fract every 0.1 step
smooth_fwhm = 0 # no smoothing
surf_data = io.project_volume_data(r, hemi,
projmeth=projmeth,
projsum=projsum,
projarg=projarg,
smooth_fwhm = smooth_fwhm,
subject_id='fsaverage')
# nothing to do, if all points in the projection are nul
if surf_data.max()!=0:
name_overlay = '{name_roi}_{hemi}'.format(name_roi=name_roi, hemi=hemi)
brain.add_overlay(surf_data, name=name_overlay, hemi=hemi)
overlay_roi = brain.overlays[name_overlay]
lut = overlay_roi.pos_bar.lut.table.to_array()
lut[0:255, 0:3] = color_list[cpt_color]
overlay_roi.pos_bar.lut.table = lut
# Save in png
#brain.save_imageset(save_png, ['lat'], 'png', colorbar=None)
# Color cpt
cpt_color += 1
# If you just want one roi by one
# Remove for the next roi
# for overlay in brain.overlays_dict[name_overlay]:
# overlay.remove()
mdmr_dir = path.join(
basedir, "%s_rois_random_k3200/age+gender_15k.mdmr" % sample)
"""Bring up the visualization"""
brain = Brain("fsaverage_copy",
"rh",
"iter8_inflated",
config_opts=dict(background="white"),
subjects_dir="/home2/data/PublicProgram/freesurfer")
"""Get the volume => surface file"""
cwas_file = path.join(mdmr_dir, "surf_rh_fdr_logp_%s.nii.gz" % factor)
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(cwas_file,
min=2,
max=max_zvals[i],
name="%s_rh" % factor)
## get overlay and color bar
tmp1 = brain.overlays["%s_rh" % factor]
lut = tmp1.pos_bar.lut.table.to_array()
## update color scheme
lut[:, 0:3] = cols
tmp1.pos_bar.lut.table = lut
## refresh view
brain.show_view("lat")
brain.hide_colorbar()
"""Save Pictures"""
brain.save_imageset(
def visOverlay(pathToSurface, overlay, outputPath, hemi, type='white'):
brain = Brain(pathToSurface, hemi, type)
brain.add_overlay(overlay, -1, 1)
brain.show_view('lateral')
brain.save_imageset(outputPath, ['med', 'lat'], 'png')
brain.close()
config_opts = dict([(k, v) for k, v in argdict.items() if k in confkeys and v])
# Load up the figure and underlying brain object
b = Brain(args.subject_id, args.hemi, args.surf, args.curv,
args.title, config_opts=config_opts)
# Maybe load some morphometry
if args.morphometry is not None:
b.add_morphometry(args.morphometry)
# Maybe load an overlay
if args.overlay is not None:
if args.range is not None:
args.min, args.max = args.range
b.add_overlay(args.overlay, args.min, args.max, args.sign)
# Maybe load an annot
if args.annotation is not None:
if not args.borders:
args.borders = any([args.overlay, args.morphometry])
b.add_annotation(args.annotation, args.borders)
# Maybe load a label
if args.label is not None:
if not args.borders:
args.borders = any([args.overlay, args.morphometry])
b.add_label(args.label, args.borders)
# Also point brain at the Brain() object
brain = b
def load_and_show_npy(subject, npy_file, hemi):
x = np.load(npy_file)
brain = Brain(subject, hemi, "pial", curv=False, offscreen=False)
brain.toggle_toolbars(True)
brain.add_overlay(x[:, 0], hemi=hemi)
def load_and_show_npy(subject, npy_file, hemi):
x = np.load(npy_file)
brain = Brain(subject, hemi, "pial", curv=False, offscreen=False)
brain.toggle_toolbars(True)
brain.add_overlay(x[:, 0], hemi=hemi)
projsum = "max" # the max value is projected
projarg = [0, 1, 0.1] # from 0 to 1 thickness fract every 0.1 step
smooth_fwhm = 0 # no smoothing
surf_data = io.project_volume_data(r,
hemi,
projmeth=projmeth,
projsum=projsum,
projarg=projarg,
smooth_fwhm=smooth_fwhm,
subject_id='fsaverage')
# nothing to do, if all points in the projection are nul
if surf_data.max() != 0:
name_overlay = '{name_roi}_{hemi}'.format(name_roi=name_roi,
hemi=hemi)
brain.add_overlay(surf_data, name=name_overlay, hemi=hemi)
overlay_roi = brain.overlays[name_overlay]
lut = overlay_roi.pos_bar.lut.table.to_array()
lut[0:255, 0:3] = color_list[cpt_color]
overlay_roi.pos_bar.lut.table = lut
# Save in png
#brain.save_imageset(save_png, ['lat'], 'png', colorbar=None)
# Color cpt
cpt_color += 1
# If you just want one roi by one
# Remove for the next roi
# for overlay in brain.overlays_dict[name_overlay]:
# overlay.remove()
brain = Brain("fsaverage", hemi, surf,
views=views, background="white")
"""Project the volume file and return as an array"""
mri_file = "example_data/resting_corr.nii.gz"
reg_file = os.path.join(os.environ["FREESURFER_HOME"],
"average/mni152.register.dat")
surf_data_lh = project_volume_data(mri_file, "lh", reg_file)
surf_data_rh = project_volume_data(mri_file, "rh", reg_file)
"""
You can pass this array to the add_overlay method for a typical activation
overlay (with thresholding, etc.).
"""
brain.add_overlay(surf_data_lh, min=.3, max=.7, name="ang_corr_lh", hemi='lh')
brain.add_overlay(surf_data_rh, min=.3, max=.7, name="ang_corr_rh", hemi='rh')
"""
You can also pass it to add_data for more control
over the visualization. Here we'll plot the whole
range of correlations
"""
for overlay in brain.overlays_dict["ang_corr_lh"]:
overlay.remove()
for overlay in brain.overlays_dict["ang_corr_rh"]:
overlay.remove()
"""
We want to use an appropriate color map for these data: a divergent map that
is centered on 0, which is a meaningful transition-point as it marks the change
from surfer import Brain, io
"""Bring up the visualization"""
brain = Brain("fsaverage", "split", "inflated", views=["lat", "med"], config_opts=dict(background="white"))
"""Project the volume file and return as an array"""
mri_file = "example_data/resting_corr.nii.gz"
reg_file = "example_data/register.dat"
surf_data_lh = io.project_volume_data(mri_file, "lh", reg_file)
surf_data_rh = io.project_volume_data(mri_file, "rh", reg_file)
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(surf_data_lh, min=0.3, max=0.7, name="ang_corr_lh", hemi="lh")
brain.add_overlay(surf_data_rh, min=0.3, max=0.7, name="ang_corr_rh", hemi="rh")
"""
You can also pass it to add_data for more control
over the visualzation. Here we'll plot the whole
range of correlations
"""
for overlay in brain.overlays_dict["ang_corr_lh"]:
overlay.remove()
for overlay in brain.overlays_dict["ang_corr_rh"]:
overlay.remove()
brain.add_data(surf_data_lh, -0.7, 0.7, colormap="jet", alpha=0.7, hemi="lh")
brain.add_data(surf_data_rh, -0.7, 0.7, colormap="jet", alpha=0.7, hemi="rh")
"""
orig_file = path.join(mdmr_dir, "clust_logp_%s.nii.gz" % factor)
"""Load the output data and get maximum value"""
img = nib.load(orig_file)
data = img.get_data()
data_max = data.max()
if data_max == 0:
data_min = 0
else:
data_min = data[data.nonzero()].min()
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(cwas_file, min=data_min, max=data_max, name="%s_rh" % factor)
## get overlay and color bar
tmp1 = brain.overlays["%s_rh" % factor]
lut = tmp1.pos_bar.lut.table.to_array()
## update color scheme
lut[:,0:3] = cols
tmp1.pos_bar.lut.table = lut
## refresh view
brain.show_view("lat")
brain.hide_colorbar()
"""
Save some images
from mayavi import mlab
from surfer import Brain, io
subject = 'fsaverage' # SAD_017
surface = 'pial'
br1 = Brain(subject, 'rh', surface, title='lgroup')
l_surf_data = io.project_volume_data('/mindhive/scratch/satra/sadfigures/nipype_mem/nipype-interfaces-spm-model-EstimateContrast/cf535c8b3e6380c2c8512307f3c294ad/spmT_0001.img',
'rh', subject_id='fsaverage',
target_subject=subject)
br1.add_overlay(l_surf_data, min=2, max=3.7, sign='pos', name='lgroup')
br2 = Brain(subject, 'rh', surface, title='hgroup')
h_surf_data = io.project_volume_data('/mindhive/scratch/satra/sadfigures/nipype_mem/nipype-interfaces-spm-model-EstimateContrast/d1fbe9c9d24038d7d1e16b16936f52ed/spmT_0001.img',
'rh', subject_id='fsaverage',
target_subject=subject)
br2.add_overlay(h_surf_data, min=2, max=3.7, sign='pos', name='hgroup')
mlab.sync_camera(br1._f, br2._f)
mlab.sync_camera(br2._f, br1._f)
"""
br1.save_image('lgroup.png')
br2.save_image('hgroup.png')
"""
mdmr_dir = path.join(basedir, "%s_rois_random_k3200/age+gender_15k.mdmr" % sample)
"""Bring up the visualization"""
brain = Brain("fsaverage_copy", "lh", "iter8_inflated",
config_opts=dict(background="white"),
subjects_dir="/home2/data/PublicProgram/freesurfer")
"""Get the volume => surface file"""
cwas_file = path.join(mdmr_dir, "surf_lh_fdr_logp_%s.nii.gz" % factor)
"""
You can pass this array to the add_overlay method for
a typical activation overlay (with thresholding, etc.)
"""
brain.add_overlay(cwas_file, min=2, max=max_zvals[i], name="%s_lh" % factor)
## get overlay and color bar
tmp1 = brain.overlays["%s_lh" % factor]
lut = tmp1.pos_bar.lut.table.to_array()
## update color scheme
lut[:,0:3] = cols
tmp1.pos_bar.lut.table = lut
## refresh view
brain.show_view("lat")
brain.hide_colorbar()
"""Save Pictures"""
brain.save_imageset(path.join(odir, "zpics_%s_%s_surface_lh" % (sample, factor)),
#%gui qt
%gui wx
from surfer import Brain
import mayavi
from numpy import array
import os.path as op
import numpy as np
from surfer import io
################### TJ-CTRL #####################
###################### LH #######################
brain = Brain("fsaverage", "lh", "inflated", config_opts={"cortex":"low_contrast","background":"black"})
overlay_file = "/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_TJ_CTRL_tT_extT_lh_projfrac05.mgz"
brain.add_overlay(overlay_file, min=3.11, max=10, sign="pos")
mayavi.mlab.view(azimuth=315, elevation=None, distance=None, focalpoint=None,
roll=None, reset_roll=True, figure=None)
mayavi.mlab.savefig("/neurospin/unicog/protocols/IRMf/BENOIT_MT/BAPTISTE_FOLDER/PICTURES/MOD30-2/GROUPlvl_TJ_CTRL_tT_extT_lh_projfrac05_face1.png", size=None, figure=None, magnification='auto')
mayavi.mlab.view(azimuth=135, elevation=None, distance=None, focalpoint=None,
roll=None, reset_roll=True, figure=None)
mayavi.mlab.savefig("/neurospin/unicog/protocols/IRMf/BENOIT_MT/BAPTISTE_FOLDER/PICTURES/MOD30-2/GROUPlvl_TJ_CTRL_tT_extT_lh_projfrac05_face2.png", size=None, figure=None, magnification='auto')
mayavi.mlab.view(azimuth=225, elevation=None, distance=None, focalpoint=None,
roll=None, reset_roll=True, figure=None)
mayavi.mlab.savefig("/neurospin/unicog/protocols/IRMf/BENOIT_MT/BAPTISTE_FOLDER/PICTURES/MOD30-2/GROUPlvl_TJ_CTRL_tT_extT_lh_projfrac05_face3.png", size=None, figure=None, magnification='auto')
###################### RH #######################
brain = Brain("fsaverage", "rh", "inflated", config_opts={"cortex":"low_contrast","background":"black"})
overlay_file = "/neurospin/meg/meg_tmp/MTT_MEG_Baptiste/MEG/GROUP/fMRI/GROUPlvl_TJ_CTRL_tT_extT_rh_projfrac05.mgz"
brain.add_overlay(overlay_file, min=3.11, max=10, sign="pos")
mayavi.mlab.view(azimuth=225, elevation=None, distance=None, focalpoint=None,
roll=None, reset_roll=True, figure=None)