From 1716aabd4633c1c1bd2da5c6a6e0000dfb45167f Mon Sep 17 00:00:00 2001
From: Cristi Donos <cristidonos@yahoo.com>
Date: Sat, 30 Jun 2018 21:42:02 -0500
Subject: [PATCH 01/46] - Brain.add_foci can now map values using foci color
 and size. - added Brain.add_text3d for labeling foci in 3d

---
 surfer/viz.py | 97 ++++++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 88 insertions(+), 9 deletions(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index ad00748..5083c6c 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -1570,7 +1570,7 @@ def add_morphometry(self, measure, grayscale=False, hemi=None,
 
     def add_foci(self, coords, coords_as_verts=False, map_surface=None,
                  scale_factor=1, color="white", alpha=1, name=None,
-                 hemi=None):
+                 hemi=None, allow_data=False, data=None):
         """Add spherical foci, possibly mapping to displayed surf.
 
         The foci spheres can be displayed at the coordinates given, or
@@ -1588,8 +1588,8 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             whether the coords parameter should be interpreted as vertex ids
         map_surface : Freesurfer surf or None
             surface to map coordinates through, or None to use raw coords
-        scale_factor : float
-            Controls the size of the foci spheres (relative to 1cm).
+        scale_factor : int
+            controls the size of the foci spheres
         color : matplotlib color code
             HTML name, RBG tuple, or hex code
         alpha : float in [0, 1]
@@ -1600,6 +1600,14 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             If None, it is assumed to belong to the hemipshere being
             shown. If two hemispheres are being shown, an error will
             be thrown.
+        allow_data : bool | False
+            If True, will plot foci using quiver3d instead of points3d to allow
+            mapping data to spheres.
+        data : numpy array
+            1D array the same size as the number of foci. Spheres will be
+            colorcoded acording to data values, whereas spheres' sizes will be
+            coded using the absolute values of data.
+
         """
         from matplotlib.colors import colorConverter
         hemi = self._check_hemi(hemi)
@@ -1614,8 +1622,7 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             foci_coords = np.atleast_2d(coords)
         else:
             foci_surf = Surface(self.subject_id, hemi, map_surface,
-                                subjects_dir=self.subjects_dir,
-                                units=self._units)
+                                subjects_dir=self.subjects_dir)
             foci_surf.load_geometry()
             foci_vtxs = utils.find_closest_vertices(foci_surf.coords, coords)
             foci_coords = self.geo[hemi].coords[foci_vtxs]
@@ -1630,12 +1637,16 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
 
         views = self._toggle_render(False)
         fl = []
-        if self._units == 'm':
-            scale_factor = scale_factor / 1000.
         for brain in self._brain_list:
             if brain['hemi'] == hemi:
-                fl.append(brain['brain'].add_foci(foci_coords, scale_factor,
-                                                  color, alpha, name))
+                if allow_data:
+                    vtxs = utils.find_closest_vertices(self.geo[hemi].coords, foci_coords)
+                    fl.append(brain['brain'].add_foci_data(foci_coords,
+                                                           scale_factor, color, alpha, name, data,
+                                                           self.geo[hemi].nn[vtxs, :]))
+                else:
+                    fl.append(brain['brain'].add_foci(foci_coords,
+                                                      scale_factor, color, alpha, name))
         self.foci_dict[name] = fl
         self._toggle_render(True, views)
 
@@ -1737,6 +1748,45 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0,
         if justification is not None:
             text.property.justification = justification
 
+    def add_text3d(self, x, y, z, text, name, color=None, opacity=1.0,
+                 row=-1, col=-1, font_size=None, justification=None):
+        """ Add a text to the visualization
+
+        Parameters
+        ----------
+        x : Float
+            x coordinate
+        y : Float
+            y coordinate
+        z : Float
+            z coordinate
+        text : str
+            Text to add
+        name : str
+            Name of the text (text label can be updated using update_text())
+        color : Tuple
+            Color of the text. Default is the foreground color set during
+            initialization (default is black or white depending on the
+            background color).
+        opacity : Float
+            Opacity of the text. Default: 1.0
+        row : int
+            Row index of which brain to use
+        col : int
+            Column index of which brain to use
+        """
+        if name in self.texts_dict:
+            self.texts_dict[name]['text'].remove()
+        text = self.brain_matrix[row, col].add_text3d(x, y, z, text,
+                                                    name, color, opacity)
+        self.texts_dict[name] = dict(row=row, col=col, text=text)
+        if font_size is not None:
+            text.property.font_size = font_size
+            text.actor.text_scale_mode = 'viewport'
+        if justification is not None:
+            text.property.justification = justification
+
+
     def update_text(self, text, name, row=-1, col=-1):
         """Update text label
 
@@ -3290,6 +3340,27 @@ def add_foci(self, foci_coords, scale_factor, color, alpha, name):
                 scale_factor=(10. * scale_factor), color=color, opacity=alpha)
         return points
 
+    def add_foci_data(self, foci_coords, scale_factor, color, alpha, name,data, normals):
+        """Add spherical foci with attached data, possibly mapping to displayed surf"""
+        # Create the visualization
+        hemi = self.hemi
+        if data == None:
+            u = np.array(normals[:,0])
+            v = np.array(normals[:,1])
+            w = np.array(normals[:,2])
+        else:
+            u = self.geo[hemi].nn[:,0] * np.abs(data)
+            v = self.geo[hemi].nn[:,1] * np.abs(data)
+            w = self.geo[hemi].nn[:,2] * np.abs(data)
+        with warnings.catch_warnings(record=True):  # traits
+            points = mlab.quiver3d(foci_coords[:, 0],foci_coords[:, 1],foci_coords[:, 2],
+                u,v,w, scalars = data, colormap='coolwarm', mode='sphere',
+                name=name, figure=self._f, scale_factor=(10. * scale_factor),
+                color=color, opacity=alpha)
+            points.glyph.color_mode = 'color_by_scalar'
+            points.glyph.glyph_source.glyph_source.center = [0, 0, 0]
+        return points
+
     def add_contour_overlay(self, scalar_data, min=None, max=None,
                             n_contours=7, line_width=1.5, lut=None,
                             colorbar=True):
@@ -3325,6 +3396,14 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0):
                              opacity=opacity, figure=self._f)
             return text
 
+    def add_text3d(self, x, y, z, text, name, color=None, opacity=1.0):
+        """ Add a text in 3D to the visualization"""
+        color = self._fg_color if color is None else color
+        with warnings.catch_warnings(record=True):
+            text = mlab.text3d(x, y, z, text, name=name, color=color,
+                             opacity=opacity, figure=self._f)
+            return text
+
     def remove_data(self, layer_id):
         """Remove data shown with .add_data()"""
         data = self.data.pop(layer_id)

From 9fbd69f91aa130e0d5a5c3820c40811df3e3c3d7 Mon Sep 17 00:00:00 2001
From: Cristi Donos <cristidonos@yahoo.com>
Date: Tue, 23 Oct 2018 13:42:00 +0300
Subject: [PATCH 02/46] re-organized add_foci function to allow data mapping
 and extended plot_foci example

---
 examples/plot_foci.py | 31 ++++++++++++++++++-
 surfer/viz.py         | 69 ++++++++++++++++++++-----------------------
 2 files changed, 62 insertions(+), 38 deletions(-)

diff --git a/examples/plot_foci.py b/examples/plot_foci.py
index 0d0c364..639b7c9 100644
--- a/examples/plot_foci.py
+++ b/examples/plot_foci.py
@@ -9,10 +9,11 @@
 """
 import os
 import os.path as op
-from numpy import arange
+from numpy import arange, linspace
 from numpy.random import permutation
 import nibabel as nib
 from surfer import Brain
+from mayavi import mlab
 
 print(__doc__)
 
@@ -78,3 +79,31 @@
 """
 brain.add_foci(coords, coords_as_verts=True,
                scale_factor=scale_factor, color="#A52A2A")
+
+"""
+Now we demonstrate plotting some data with a set of randomly
+choosen vertices from within the middle temporal sulcus.
+"""
+verts = arange(0, len(ids))
+coords = permutation(verts[ids == 26])[:10]
+
+"""
+Generate a dataset with some values in the [-1, 1] range
+"""
+dataset_name ='some_data'
+data = linspace(start=-1, stop=1, num=10)
+
+"""
+Now we plot the foci colorcoded acording to data values, whereas foci sizes will be
+coded using the absolute values of data.
+Using the 'name' argument we can reference newly added foci to create a colorbar using mayavi.
+"""
+brain.add_foci(coords, coords_as_verts=True, name=dataset_name,
+               scale_factor=1, data=data, colormap='cool')
+
+""" 
+Sometimes a qualitative representation is not enough, and we need to plot the colorbar as well. 
+This can be done using the 'name' argument in add_foci, by referencing the newly added foci to 
+create a colorbar with mayavi.
+"""
+mlab.colorbar(brain.foci[dataset_name], nb_labels=5, label_fmt='  %.2f  ')
\ No newline at end of file
diff --git a/surfer/viz.py b/surfer/viz.py
index 5083c6c..6c2204b 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -1570,7 +1570,7 @@ def add_morphometry(self, measure, grayscale=False, hemi=None,
 
     def add_foci(self, coords, coords_as_verts=False, map_surface=None,
                  scale_factor=1, color="white", alpha=1, name=None,
-                 hemi=None, allow_data=False, data=None):
+                 hemi=None, data=None, colormap=None):
         """Add spherical foci, possibly mapping to displayed surf.
 
         The foci spheres can be displayed at the coordinates given, or
@@ -1588,7 +1588,7 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             whether the coords parameter should be interpreted as vertex ids
         map_surface : Freesurfer surf or None
             surface to map coordinates through, or None to use raw coords
-        scale_factor : int
+        scale_factor : float
             controls the size of the foci spheres
         color : matplotlib color code
             HTML name, RBG tuple, or hex code
@@ -1600,13 +1600,14 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             If None, it is assumed to belong to the hemipshere being
             shown. If two hemispheres are being shown, an error will
             be thrown.
-        allow_data : bool | False
-            If True, will plot foci using quiver3d instead of points3d to allow
-            mapping data to spheres.
         data : numpy array
-            1D array the same size as the number of foci. Spheres will be
-            colorcoded acording to data values, whereas spheres' sizes will be
-            coded using the absolute values of data.
+            None or 1D array the same size as the number of foci (n,).
+            Spheres sizes will be coded using the absolute values of data.
+            If data is None, all spheres will have the same size.
+        colormap : str
+            Mayavi colormap name. Default is None, which means all foci will
+            have the same color given by the 'color' argument. If colormap is
+            not None, foci will be colorcoded acording to data values.
 
         """
         from matplotlib.colors import colorConverter
@@ -1639,14 +1640,12 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
         fl = []
         for brain in self._brain_list:
             if brain['hemi'] == hemi:
-                if allow_data:
-                    vtxs = utils.find_closest_vertices(self.geo[hemi].coords, foci_coords)
-                    fl.append(brain['brain'].add_foci_data(foci_coords,
-                                                           scale_factor, color, alpha, name, data,
-                                                           self.geo[hemi].nn[vtxs, :]))
-                else:
-                    fl.append(brain['brain'].add_foci(foci_coords,
-                                                      scale_factor, color, alpha, name))
+                vtxs = utils.find_closest_vertices(self.geo[hemi].coords,
+                                                   foci_coords)
+                fl.append(brain['brain'].add_foci(foci_coords, scale_factor,
+                                                  color, alpha, name, data,
+                                                  self.geo[hemi].nn[vtxs, :],
+                                                  colormap))
         self.foci_dict[name] = fl
         self._toggle_render(True, views)
 
@@ -1736,6 +1735,7 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0,
             Row index of which brain to use
         col : int
             Column index of which brain to use
+        font_size :
         """
         if name in self.texts_dict:
             self.texts_dict[name]['text'].remove()
@@ -3330,34 +3330,29 @@ def add_morphometry(self, morph_data, colormap, measure,
         return dict(surface=surf, colorbar=bar, measure=measure, brain=self,
                     array_id=array_id)
 
-    def add_foci(self, foci_coords, scale_factor, color, alpha, name):
-        """Add spherical foci, possibly mapping to displayed surf"""
-        # Create the visualization
-        with warnings.catch_warnings(record=True):  # traits
-            points = mlab.points3d(
-                foci_coords[:, 0], foci_coords[:, 1], foci_coords[:, 2],
-                np.ones(foci_coords.shape[0]), name=name, figure=self._f,
-                scale_factor=(10. * scale_factor), color=color, opacity=alpha)
-        return points
-
-    def add_foci_data(self, foci_coords, scale_factor, color, alpha, name,data, normals):
+    def add_foci(self, foci_coords, scale_factor, color, alpha, name, data, normals, colormap):
         """Add spherical foci with attached data, possibly mapping to displayed surf"""
         # Create the visualization
-        hemi = self.hemi
-        if data == None:
+        if data is None:
             u = np.array(normals[:,0])
             v = np.array(normals[:,1])
             w = np.array(normals[:,2])
         else:
-            u = self.geo[hemi].nn[:,0] * np.abs(data)
-            v = self.geo[hemi].nn[:,1] * np.abs(data)
-            w = self.geo[hemi].nn[:,2] * np.abs(data)
+            u = normals[:,0] * np.abs(data)
+            v = normals[:,1] * np.abs(data)
+            w = normals[:,2] * np.abs(data)
         with warnings.catch_warnings(record=True):  # traits
-            points = mlab.quiver3d(foci_coords[:, 0],foci_coords[:, 1],foci_coords[:, 2],
-                u,v,w, scalars = data, colormap='coolwarm', mode='sphere',
-                name=name, figure=self._f, scale_factor=(10. * scale_factor),
-                color=color, opacity=alpha)
-            points.glyph.color_mode = 'color_by_scalar'
+            if colormap is None:
+                points = mlab.quiver3d(foci_coords[:, 0],foci_coords[:, 1],foci_coords[:, 2],
+                    u,v,w, scalars = data, mode='sphere',
+                    name=name, figure=self._f, scale_factor=(10. * scale_factor),
+                    color=color, opacity=alpha)
+            else:
+                points = mlab.quiver3d(foci_coords[:, 0],foci_coords[:, 1],foci_coords[:, 2],
+                    u,v,w, scalars = data, colormap=colormap, mode='sphere',
+                    name=name, figure=self._f, scale_factor=(10. * scale_factor),
+                    color=color, opacity=alpha)
+                points.glyph.color_mode = 'color_by_scalar'
             points.glyph.glyph_source.glyph_source.center = [0, 0, 0]
         return points
 

From 16e5ed218a9ca8e0fbcece964027e3803de52003 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 26 Oct 2018 08:27:01 -0400
Subject: [PATCH 03/46] MRG: Fix scale_data_colormap and add FXAA (#261)

* FIX: Render tweaks

* FIX: Use correct data_dict

* FIX: test backend

* FIX: Better check

* FIX: Old VTK
---
 surfer/viz.py | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index cb76a1c..75eab52 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -229,6 +229,11 @@ def _make_viewer(figure, n_row, n_col, title, scene_size, offscreen,
                     for f in figure:
                         f.scene.interactor.interactor_style = \
                             tvtk.InteractorStyleTerrain()
+            for figure in figures:
+                for f in figure:
+                    # on a non-testing backend, and using modern VTK/Mayavi
+                    if hasattr(getattr(f.scene, 'renderer', None), 'use_fxaa'):
+                        f.scene.renderer.use_fxaa = True
     else:
         if isinstance(figure, int):  # use figure with specified id
             figure = [mlab.figure(figure, size=scene_size)]
@@ -387,6 +392,7 @@ class Brain(object):
     texts : dict
         The text objects.
     """
+
     def __init__(self, subject_id, hemi, surf, title=None,
                  cortex="classic", alpha=1.0, size=800, background="black",
                  foreground=None, figure=None, subjects_dir=None,
@@ -1182,7 +1188,8 @@ def time_label(x):
 
         self._data_dicts[hemi].append(data)
 
-        self.scale_data_colormap(min, mid, max, transparent, center, alpha)
+        self.scale_data_colormap(min, mid, max, transparent, center, alpha,
+                                 data)
 
         if initial_time_index is not None:
             self.set_data_time_index(initial_time_index)
@@ -1903,7 +1910,7 @@ def _brain_color(self):
 
     @verbose
     def scale_data_colormap(self, fmin, fmid, fmax, transparent,
-                            center=None, alpha=1.0, verbose=None):
+                            center=None, alpha=1.0, data=None, verbose=None):
         """Scale the data colormap.
 
         The colormap may be sequential or divergent. When the colormap is
@@ -1942,17 +1949,22 @@ def scale_data_colormap(self, fmin, fmid, fmax, transparent,
             center of the (divergent) colormap
         alpha : float
             sets the overall opacity of colors, maintains transparent regions
+        data : dict | None
+            The data entry for which to scale the colormap.
+            If None, will use the data dict from either the left or right
+            hemisphere (in that order).
         verbose : bool, str, int, or None
             If not None, override default verbose level (see surfer.verbose).
         """
         divergent = center is not None
 
         # Get the original colormap
-        for h in ['lh', 'rh']:
-            data = self.data_dict[h]
-            if data is not None:
-                table = data["orig_ctable"].copy()
-                break
+        if data is None:
+            for h in ['lh', 'rh']:
+                data = self.data_dict[h]
+                if data is not None:
+                    break
+        table = data["orig_ctable"].copy()
 
         lut = _scale_mayavi_lut(table, fmin, fmid, fmax, transparent,
                                 center, alpha)
@@ -2957,6 +2969,7 @@ def _scale_mayavi_lut(lut_table, fmin, fmid, fmax, transparent,
 
 class _Hemisphere(object):
     """Object for visualizing one hemisphere with mlab"""
+
     def __init__(self, subject_id, hemi, figure, geo, geo_curv,
                  geo_kwargs, geo_reverse, subjects_dir, bg_color, backend,
                  fg_color):
@@ -3139,7 +3152,7 @@ def _add_vector_data(self, vectors, vector_values, fmin, fmid, fmax,
                 vmax=fmax, figure=self._f, opacity=vector_alpha)
 
         # Enable backface culling
-        quiver.actor.property.backface_culling = False
+        quiver.actor.property.backface_culling = True
         quiver.mlab_source.update()
 
         # Compute scaling for the glyphs

From df6852705bcbb055e171e94cf77825ba8564475b Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 22 Mar 2019 19:24:03 +1100
Subject: [PATCH 04/46] MRG: width/height in offscreen mode (#265)

* FIX: width/height in offscreen mode

* MAINT: Sisyphus

* BUG: Modernize labels

* FIX: Circle

* FIX: Stretch

* FIX: More

* MAINT: Push the rock

* FIX: Skip for 3
---
 .circleci/config.yml       | 95 ++++++++++++++++++++++++++------------
 .travis.yml                |  7 +--
 appveyor.yml               |  3 +-
 setup.cfg                  |  5 +-
 surfer/tests/test_utils.py |  4 +-
 surfer/tests/test_viz.py   | 48 ++++++++++---------
 surfer/utils.py            |  7 +++
 surfer/viz.py              |  2 +-
 8 files changed, 107 insertions(+), 64 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 849d72a..bbb755d 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,48 +1,66 @@
 version: 2
 jobs:
-    build:
+    build_docs:
       docker:
-        - image: circleci/python:3.6-jessie
+        - image: circleci/python:3.7-stretch
       steps:
-        # Get our data and merge with upstream
         - checkout
-        - run: echo $(git log -1 --pretty=%B) | tee gitlog.txt
-        - run: echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
         - run:
-           command: |
-             if [[ $(cat merge.txt) != "" ]]; then
-               echo "Merging $(cat merge.txt)";
-               git pull --ff-only origin "refs/pull/$(cat merge.txt)/merge";
-             fi
+            name: Set BASH_ENV
+            command: |
+              echo "set -e" >> $BASH_ENV;
+              echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV;
+              echo "export DISPLAY=:99" >> $BASH_ENV;
+              echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV;
+              echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV;
+        - run:
+            name: Merge with upstream
+            command: |
+              echo $(git log -1 --pretty=%B) | tee gitlog.txt
+              echo ${CI_PULL_REQUEST//*pull\//} | tee merge.txt
+              if [[ $(cat merge.txt) != "" ]]; then
+                echo "Merging $(cat merge.txt)";
+                git remote add upstream git://github.com/nipy/PySurfer.git;
+                git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
+                git fetch upstream master;
+              fi
 
         # Load our data
         - restore_cache:
             keys:
-              - data-cache
+              - data-cache-0
               - pip-cache
 
-        # Fix libgcc_s.so.1 pthread_cancel bug:
+        - run:
+            name: Spin up Xvfb
+            command: |
+              /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+
         # https://github.com/ContinuumIO/anaconda-issues/issues/9190#issuecomment-386508136
         # https://github.com/golemfactory/golem/issues/1019
-        - run: sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6 qt5-default
-        - run: echo "export SUBJECTS_DIR=~/subjects" >> $BASH_ENV
-        - run: echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV
-        - run: echo "export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0.4200.1" >> $BASH_ENV
-        # Spin up Xvfb
-        - run: echo "export DISPLAY=:99" >> $BASH_ENV
-        - run: /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
-        # Python env
-        - run: pip install -U --user --progress-bar off numpy scipy matplotlib vtk PyQt5 sip PyQt5-sip nibabel sphinx numpydoc pillow imageio https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master
-        - run: pip install -U --user --progress-bar off mayavi
+        - run:
+            name: Fix libgcc_s.so.1 pthread_cancel bug
+            command: |
+              sudo apt-get install qt5-default
+
+        - run:
+            name: Get Python running
+            command: |
+              pip install --user -q --upgrade pip numpy
+              pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master mayavi
         - save_cache:
             key: pip-cache
             paths:
-              - "~/.cache/pip"
-        - run: python setup.py develop --user
-        # Check libs
-        - run: LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
-        - run: echo $SUBJECTS_DIR
+              - ~/.cache/pip
+
+        # Look at what we have and fail early if there is some library conflict
+        - run:
+            name: Check installation
+            command: |
+              LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
+              echo $SUBJECTS_DIR
         - run:
+            name: Get data
             command: |
               if [ ! -d $SUBJECTS_DIR ]; then
                 mkdir $SUBJECTS_DIR;
@@ -51,14 +69,31 @@ jobs:
                 unzip fsaverage_min.zip;
                 rm fsaverage_min.zip;
               fi;
-        - run: ls $SUBJECTS_DIR
-        - run: cd doc && sphinx-build -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_morphometry\|plot_label\.py\|plot_probabilistic_label\|plot_resting_correlations\|plot_transparent_brain\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html
+              ls $SUBJECTS_DIR
+        - run:
+            name: Install PySurfer
+            command: |
+              python setup.py develop --user
+
+        - run:
+            name: Build docs
+            command: |
+              cd doc
+              sphinx-build -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_morphometry\|plot_label\.py\|plot_probabilistic_label\|plot_resting_correlations\|plot_transparent_brain\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html
 
         - store_artifacts:
             path: doc/_build/html/
             destination: html
 
         - save_cache:
-            key: data-cache
+            key: data-cache-0
             paths:
               - "~/subjects"
+
+workflows:
+  version: 2
+
+  default:
+    jobs:
+      - build_docs
+
diff --git a/.travis.yml b/.travis.yml
index f44bb7c..ed5c16c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,9 +2,9 @@ language: c
 sudo: false
 
 env:
-    global: PYTHON_VERSION=3.6
+    global: PYTHON_VERSION=3.7
             CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt>=5.9 coverage pytest pytest-cov flake8 pygments traits traitsui pyface"
-            PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio"
+            PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio imageio-ffmpeg"
             DISPLAY=:99.0
 
 matrix:
@@ -57,9 +57,6 @@ before_script:
     - unzip ../fsaverage_min.zip
     - cd ..
     - export SUBJECTS_DIR="${PWD}/subjects"
-    - if [[ $PIP_DEPENDENCIES == *"imageio"* ]] || [ ! -z "$CONDA_ENVIRONMENT" ]; then
-        python -c "import imageio; imageio.plugins.ffmpeg.download()";
-      fi
 
 script:
     - cd ${SRC_DIR}
diff --git a/appveyor.yml b/appveyor.yml
index 4a79ae0..39520c5 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -6,9 +6,8 @@ environment:
 install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
   - "python --version"
-  - "pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio codecov pyqt5==5.9"
+  - "pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9"
   - "pip install traits traitsui pyface vtk mayavi nibabel"
-  - "python -c \"import imageio; imageio.plugins.ffmpeg.download()\""
   - "powershell make/get_fsaverage.ps1"
   - "python setup.py develop"
   - "SET SUBJECTS_DIR=%CD%\\subjects"
diff --git a/setup.cfg b/setup.cfg
index 133852e..d9bfc29 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -8,4 +8,7 @@ filterwarnings =
     ignore:can't resolve package from __spec__ or __package__, falling back on __name__ and __path__:ImportWarning
     ignore:The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead:DeprecationWarning
     ignore:elementwise == comparison failed:DeprecationWarning
-    ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning
\ No newline at end of file
+    ignore:Importing from numpy:DeprecationWarning
+    ignore:.*ufunc size changed.*:RuntimeWarning
+    ignore:Using or importing the ABCs:DeprecationWarning
+    ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning
diff --git a/surfer/tests/test_utils.py b/surfer/tests/test_utils.py
index 8d71382..d9a6d72 100644
--- a/surfer/tests/test_utils.py
+++ b/surfer/tests/test_utils.py
@@ -32,12 +32,12 @@ def _slow_compute_normals(rr, tris):
 @utils.requires_fsaverage()
 def test_surface():
     """Test IO for Surface class"""
-    subj_dir = utils._get_subjects_dir()
+    extra, subj_dir = utils._get_extra()
     for subjects_dir in [None, subj_dir]:
         surface = utils.Surface('fsaverage', 'lh', 'inflated',
                                 subjects_dir=subjects_dir)
         surface.load_geometry()
-        surface.load_label('BA1')
+        surface.load_label('BA1' + extra)
         surface.load_curvature()
         xfm = np.eye(4)
         xfm[:3, -1] += 2  # translation
diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 5d534a2..158518d 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -13,7 +13,8 @@
 from unittest import SkipTest
 
 from surfer import Brain, io, utils
-from surfer.utils import requires_fsaverage, requires_imageio, requires_fs
+from surfer.utils import (requires_fsaverage, requires_imageio, requires_fs,
+                          _get_extra)
 
 warnings.simplefilter('always')
 
@@ -247,30 +248,30 @@ def test_label():
     brain = Brain(subject_id, hemi, surf)
     view = get_view(brain)
 
-    brain.add_label("BA1")
+    extra, subj_dir = _get_extra()
+    brain.add_label("BA1" + extra)
     check_view(brain, view)
-    brain.add_label("BA1", color="blue", scalar_thresh=.5)
-    subj_dir = utils._get_subjects_dir()
+    brain.add_label("BA1" + extra, color="blue", scalar_thresh=.5)
     label_file = pjoin(subj_dir, subject_id,
-                       "label", "%s.MT.label" % hemi)
+                       "label", "%s.MT%s.label" % (hemi, extra))
     brain.add_label(label_file)
-    brain.add_label("BA44", borders=True)
-    brain.add_label("BA6", alpha=.7)
+    brain.add_label("BA44" + extra, borders=True)
+    brain.add_label("BA6" + extra, alpha=.7)
     brain.show_view("medial")
-    brain.add_label("V1", color="steelblue", alpha=.6)
-    brain.add_label("V2", color="#FF6347", alpha=.6)
-    brain.add_label("entorhinal", color=(.2, 1, .5), alpha=.6)
+    brain.add_label("V1" + extra, color="steelblue", alpha=.6)
+    brain.add_label("V2" + extra, color="#FF6347", alpha=.6)
+    brain.add_label("entorhinal" + extra, color=(.2, 1, .5), alpha=.6)
     brain.set_surf('white')
     brain.show_view(dict(elevation=40, distance=430), distance=430)
     with pytest.raises(ValueError, match='!='):
         brain.show_view(dict(elevation=40, distance=430), distance=431)
 
     # remove labels
-    brain.remove_labels('V1')
-    assert 'V2' in brain.labels_dict
-    assert 'V1' not in brain.labels_dict
+    brain.remove_labels('V1' + extra)
+    assert 'V2' + extra in brain.labels_dict
+    assert 'V1' + extra not in brain.labels_dict
     brain.remove_labels()
-    assert 'V2' not in brain.labels_dict
+    assert 'V2' + extra not in brain.labels_dict
 
     brain.close()
 
@@ -354,7 +355,8 @@ def test_morphometry():
 def test_movie(tmpdir):
     """Test saving a movie of an MEG inverse solution."""
     import imageio
-
+    if sys.version_info < (3,):
+        raise SkipTest('imageio ffmpeg requires Python 3')
     # create and setup the Brain instance
     _set_backend()
     brain = Brain(*std_args)
@@ -432,15 +434,15 @@ def test_probabilistic_labels():
     brain = Brain("fsaverage", "lh", "inflated",
                   cortex="low_contrast")
 
-    brain.add_label("BA1", color="darkblue")
-
-    brain.add_label("BA1", color="dodgerblue", scalar_thresh=.5)
+    extra, subj_dir = _get_extra()
+    brain.add_label("BA1" + extra, color="darkblue")
+    brain.add_label("BA1" + extra, color="dodgerblue", scalar_thresh=.5)
+    brain.add_label("BA45" + extra, color="firebrick", borders=True)
+    brain.add_label("BA45" + extra, color="salmon", borders=True,
+                    scalar_thresh=.5)
 
-    brain.add_label("BA45", color="firebrick", borders=True)
-    brain.add_label("BA45", color="salmon", borders=True, scalar_thresh=.5)
-
-    subj_dir = utils._get_subjects_dir()
-    label_file = pjoin(subj_dir, "fsaverage", "label", "lh.BA6.label")
+    label_file = pjoin(subj_dir, "fsaverage", "label",
+                       "lh.BA6%s.label" % (extra,))
     prob_field = np.zeros_like(brain.geo['lh'].x)
     ids, probs = nib.freesurfer.read_label(label_file, read_scalars=True)
     prob_field[ids] = probs
diff --git a/surfer/utils.py b/surfer/utils.py
index cd2b9f3..8e3e22c 100644
--- a/surfer/utils.py
+++ b/surfer/utils.py
@@ -745,3 +745,10 @@ def requires_fs():
     has = ('FREESURFER_HOME' in os.environ)
     return pytest.mark.skipif(
         not has, reason='Requires FreeSurfer command line tools')
+
+
+def _get_extra():
+    # Get extra label for newer freesurfer
+    subj_dir = _get_subjects_dir()
+    fname = op.join(subj_dir, 'fsaverage', 'label', 'lh.BA1.label')
+    return '_exvivo' if not op.isfile(fname) else '', subj_dir
diff --git a/surfer/viz.py b/surfer/viz.py
index 75eab52..4fcde5d 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -208,7 +208,7 @@ def _make_viewer(figure, n_row, n_col, title, scene_size, offscreen,
             try:
                 mlab.options.offscreen = True
                 with warnings.catch_warnings(record=True):  # traits
-                    figures = [[mlab.figure(size=(h / n_row, w / n_col))
+                    figures = [[mlab.figure(size=(w / n_col, h / n_row))
                                 for _ in range(n_col)] for __ in range(n_row)]
             finally:
                 mlab.options.offscreen = orig_val

From 8b0d631d93b2e7074a33a51148bbd034410171de Mon Sep 17 00:00:00 2001
From: Marijn van Vliet <w.m.vanvliet@gmail.com>
Date: Wed, 22 May 2019 17:22:50 +0300
Subject: [PATCH 05/46] Integrate better with Jupyter notebook (#268)

* Integrate better with Jupyuter notebook

Mayavi can render things inside a jupyter notebook as either PNG or X3D.
This functionality can be enabled with `mlab.init_notebook()`.

This PR adds an `_ipython_display_` hook to the `Brain` class that
renders the brain accordgin to the Mayavi notebook integration settings.

* Add note on Jupyter notebook integration to docs

* Fix links in doc
---
 doc/install.rst | 11 +++++++++++
 surfer/viz.py   | 17 +++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/doc/install.rst b/doc/install.rst
index bb6c441..91b5691 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -77,6 +77,17 @@ notebook), you have to activate the correct GUI backend, which is probably qt::
 This will allow you to have an open PySurfer window while still being able to
 execute code in the console/notebook.
 
+It is also possible to embed the PySurfer visualization into a Jupyter notebook.
+This is achieved by leveraging `Mayavi's notebook integration
+<https://docs.enthought.com/mayavi/mayavi/tips.html#using-mayavi-in-jupyter-notebooks>`_::
+
+    from mayavi import mlab
+    mlab.init_notebook(backend='png')
+
+The ``backend`` parameter can either be ``'png'`` to render the visualization
+as a static PNG image, or ``'x3d'`` to render it using
+`X3D <https://www.x3dom.org>`_ (still experimental).
+
 If you are having trouble getting started using PySurfer, please describe the problem on the `nipy mailing list`_.
 
 .. include:: links_names.txt
diff --git a/surfer/viz.py b/surfer/viz.py
index 4fcde5d..14b921c 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2776,6 +2776,23 @@ def animate(self, views, n_steps=180., fname=None, use_cache=False,
             if ret:
                 print("\n\nError occured when exporting movie\n\n")
 
+    def __repr__(self):
+        return ('<Brain subject_id="%s", hemi="%s", surf="%s">' %
+                (self.subject_id, self._hemi, self.surf))
+
+    def _ipython_display_(self):
+        """Called by Jupyter notebook to display a brain."""
+        from IPython.display import display as idisplay
+
+        if mlab.options.offscreen:
+            # Render the mayavi scenes to the notebook
+            for figure in self._figures:
+                for scene in figure:
+                    idisplay(scene.scene)
+        else:
+            # Render string representation
+            print(repr(self))
+
 
 def _scale_sequential_lut(lut_table, fmin, fmid, fmax):
     """Scale a sequential colormap."""

From 27f54c652aa1d4999d8cd8d3d7e42fe3938cda31 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Jun 2019 07:43:12 -0400
Subject: [PATCH 06/46] MAINT: Update fsaverage (#270)

* MAINT: Update fsaverage

* FIX: Bump to 3.5

* ENH: Run more on CircleCI

* MAINT: CI

* MAINT: CI

* MAINT: CI

* MAINT: Circle

* FIX: Pattern

* FIX: Circle

* FIX: Try again

* FIX: Better

* FIX: One more
---
 .circleci/config.yml                 | 41 ++++++++++++++--------------
 .travis.yml                          | 36 +++++++++---------------
 doc/Makefile                         |  4 +--
 doc/conf.py                          | 26 +++++++-----------
 doc/documentation/command_line.rst   |  3 --
 examples/plot_label.py               | 16 +++++------
 examples/plot_probabilistic_label.py | 10 +++----
 7 files changed, 58 insertions(+), 78 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index bbb755d..dd7ca25 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -13,6 +13,7 @@ jobs:
               echo "export DISPLAY=:99" >> $BASH_ENV;
               echo "export OPENBLAS_NUM_THREADS=4" >> $BASH_ENV;
               echo "export PATH=~/.local/bin:$PATH" >> $BASH_ENV;
+              echo "export PATTERN=\"plot_\(?\!fmri_activation_volume\|resting_correlations\)\"" >> $BASH_ENV;
         - run:
             name: Merge with upstream
             command: |
@@ -25,12 +26,6 @@ jobs:
                 git fetch upstream master;
               fi
 
-        # Load our data
-        - restore_cache:
-            keys:
-              - data-cache-0
-              - pip-cache
-
         - run:
             name: Spin up Xvfb
             command: |
@@ -43,11 +38,18 @@ jobs:
             command: |
               sudo apt-get install qt5-default
 
+        # Load our data
+        - restore_cache:
+            keys:
+              - data-cache-0
+              - pip-cache
+
         - run:
             name: Get Python running
             command: |
               pip install --user -q --upgrade pip numpy
-              pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master mayavi
+              pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg sphinx-gallery
+              pip install --user -q --upgrade mayavi "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
         - save_cache:
             key: pip-cache
             paths:
@@ -58,18 +60,19 @@ jobs:
             name: Check installation
             command: |
               LIBGL_DEBUG=verbose python -c "from mayavi import mlab; import matplotlib.pyplot as plt; mlab.figure(); plt.figure()"
-              echo $SUBJECTS_DIR
+
         - run:
             name: Get data
             command: |
-              if [ ! -d $SUBJECTS_DIR ]; then
-                mkdir $SUBJECTS_DIR;
-                cd $SUBJECTS_DIR;
-                wget http://faculty.washington.edu/larsoner/fsaverage_min.zip;
-                unzip fsaverage_min.zip;
-                rm fsaverage_min.zip;
-              fi;
+              echo $SUBJECTS_DIR
+              mkdir -p $SUBJECTS_DIR
+              python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)"
               ls $SUBJECTS_DIR
+        - save_cache:
+            key: data-cache-0
+            paths:
+              - "~/subjects"
+
         - run:
             name: Install PySurfer
             command: |
@@ -79,16 +82,13 @@ jobs:
             name: Build docs
             command: |
               cd doc
-              sphinx-build -D plot_gallery=1 -D sphinx_gallery_conf.filename_pattern=^\(\(?\!plot_fmri_activation_volume\|plot_morphometry\|plot_label\.py\|plot_probabilistic_label\|plot_resting_correlations\|plot_transparent_brain\|rotate_animation\|save_movie\|save_views\).\)*\$ -b html -d _build/doctrees . _build/html
+              echo $PATTERN
+              make html_dev-pattern
 
         - store_artifacts:
             path: doc/_build/html/
             destination: html
 
-        - save_cache:
-            key: data-cache-0
-            paths:
-              - "~/subjects"
 
 workflows:
   version: 2
@@ -96,4 +96,3 @@ workflows:
   default:
     jobs:
       - build_docs
-
diff --git a/.travis.yml b/.travis.yml
index ed5c16c..523612e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,11 +1,14 @@
 language: c
 sudo: false
-
+dist: xenial
+services:
+    - xvfb
 env:
     global: PYTHON_VERSION=3.7
             CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt>=5.9 coverage pytest pytest-cov flake8 pygments traits traitsui pyface"
             PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio imageio-ffmpeg"
             DISPLAY=:99.0
+            SUBJECTS_DIR=~/subjects
 
 matrix:
     include:
@@ -16,11 +19,11 @@ matrix:
               packages:
                 - mencoder
 
-        # 2.7, no mencoder
+        # 3.5, no mencoder
         - os: linux
-          env: PYTHON_VERSION=2.7
-               CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8 mayavi"
-               PIP_DEPENDENCIES="codecov pytest-sugar faulthandler pytest-faulthandler nibabel imageio"
+          env: PYTHON_VERSION=3.5
+               CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8"
+               PIP_DEPENDENCIES="codecov pytest-sugar nibabel imageio imageio-ffmpeg"
 
         # OSX
         - os: osx
@@ -32,32 +35,19 @@ before_install:
     - if [ "${TRAVIS_OS_NAME}" == "osx" ]; then
         unset -f cd;
       fi;
-    - if [ "${TRAVIS_OS_NAME}" == "linux" ]; then
-        echo "Starting Xvfb...";
-        /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render;
-      fi;
     - git clone https://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda.sh
-    - if [ "$PYTHON_VERSION" != "2.7" ]; then
-        pip install vtk;
-        pip install mayavi;
-      fi;
+    - pip install vtk
+    - pip install mayavi
+    - mkdir -p $SUBJECTS_DIR
+    - pip install "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
+    - python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)"
 
 install:
     - python setup.py build
     - python setup.py install
     - SRC_DIR=$(pwd)
 
-before_script:
-    # Let's create a (fake) display on Travis, and let's use a funny resolution
-    - cd ~
-    - wget --quiet http://faculty.washington.edu/larsoner/fsaverage_min.zip
-    - mkdir subjects
-    - cd subjects
-    - unzip ../fsaverage_min.zip
-    - cd ..
-    - export SUBJECTS_DIR="${PWD}/subjects"
-
 script:
     - cd ${SRC_DIR}
     - pytest surfer --cov=surfer -v
diff --git a/doc/Makefile b/doc/Makefile
index 96649d1..77929cb 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -2,9 +2,9 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -nWT --keep-going
 SPHINXBUILD   = sphinx-build
-PAPER         =
+GPAPER         =
 BUILDDIR      = _build
 
 # Internal variables.
diff --git a/doc/conf.py b/doc/conf.py
index 5e60d4c..83feed8 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -51,7 +51,7 @@
 ]
 
 autosummary_generate = True
-autodoc_default_flags = ['inherited-members']
+autodoc_default_options = {'inherited-members': None}
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -250,10 +250,10 @@
     # 'python': ('http://docs.python.org/', None),
     # 'numpy': ('http://docs.scipy.org/doc/numpy-dev/', None),
     # 'scipy': ('http://scipy.github.io/devdocs/', None),
-    'matplotlib': ('http://matplotlib.org', None),
-    'imageio': ('http://imageio.readthedocs.io/en/latest', None),
-    'mayavi': ('http://docs.enthought.com/mayavi/mayavi', None),
-    'nibabel': ('http://nipy.org/nibabel', None),
+    'matplotlib': ('https://matplotlib.org', None),
+    'imageio': ('https://imageio.readthedocs.io/en/latest', None),
+    'mayavi': ('https://docs.enthought.com/mayavi/mayavi', None),
+    'nibabel': ('https://nipy.org/nibabel', None),
 }
 
 # One entry per manual page. List of tuples
@@ -268,31 +268,25 @@
 
 try:
     from mayavi import mlab
-    find_mayavi_figures = True
     # Do not pop up any mayavi windows while running the
     # examples. These are very annoying since they steal the focus.
     mlab.options.offscreen = True
+    scrapers = ('matplotlib', 'mayavi')
 except Exception:
-    find_mayavi_figures = False
+    scrapers = ('matplotlib',)
 
 sphinx_gallery_conf = {
     'doc_module': ('surfer',),
-    'reference_url': {
-        'surfer': None,
-        'matplotlib': 'http://matplotlib.org',
-        'numpy': 'http://docs.scipy.org/doc/numpy',
-        'scipy': 'http://docs.scipy.org/doc/scipy/reference',
-        'mayavi': 'http://docs.enthought.com/mayavi/mayavi',
-        },
+    'reference_url': {'surfer': None},
     'examples_dirs': examples_dirs,
     'gallery_dirs': gallery_dirs,
     'within_subsection_order': FileNameSortKey,
-    'find_mayavi_figures': find_mayavi_figures,
+    'image_scrapers': scrapers,
     'default_thumb_file': os.path.join('_static', 'pysurfer_logo_small.png'),
     'backreferences_dir': 'generated',
     'download_section_examples': False,
     'thumbnail_size': (250, 250),
-    }
+}
 
 numpydoc_class_members_toctree = False
 numpydoc_show_inherited_class_members = False
diff --git a/doc/documentation/command_line.rst b/doc/documentation/command_line.rst
index cd21a64..6015a13 100644
--- a/doc/documentation/command_line.rst
+++ b/doc/documentation/command_line.rst
@@ -50,6 +50,3 @@ Other command-line options
 As in tksurfer, most aspects of the visualization can be initialized
 from the command-line. To get a full documentation of the command-line
 interface, simply type ``pysurfer`` at a terminal prompt and hit enter.
-For convenience, this usage message is reproduced below.
-
-.. literalinclude:: pysurfer_usage.txt
diff --git a/examples/plot_label.py b/examples/plot_label.py
index 8083347..8b602d7 100644
--- a/examples/plot_label.py
+++ b/examples/plot_label.py
@@ -18,31 +18,31 @@
 
 # If the label lives in the normal place in the subjects directory,
 # you can plot it by just using the name
-brain.add_label("BA1_exvivo")
+brain.add_label("BA1")
 
 # Some labels have an associated scalar value at each ID in the label.
 # For example, they may be probabilistically defined. You can threshold
 # what vertices show up in the label using this scalar data
-brain.add_label("BA1_exvivo", color="blue", scalar_thresh=.5)
+brain.add_label("BA1", color="blue", scalar_thresh=.5)
 
 # Or you can give a path to a label in an arbitrary location
 subj_dir = brain.subjects_dir
 label_file = os.path.join(subj_dir, subject_id,
-                          "label", "%s.MT_exvivo.label" % hemi)
+                          "label", "%s.MT.label" % hemi)
 brain.add_label(label_file)
 
 # By default the label is 'filled-in', but you can
 # plot just the label boundaries
-brain.add_label("BA44_exvivo", borders=True)
+brain.add_label("BA44", borders=True)
 
 # You can also control the opacity of the label color
-brain.add_label("BA6_exvivo", alpha=.7)
+brain.add_label("BA6", alpha=.7)
 
 # Finally, you can plot the label in any color you want.
 brain.show_view(dict(azimuth=-42, elevation=105, distance=225,
                      focalpoint=[-30, -20, 15]))
 
 # Use any valid matplotlib color.
-brain.add_label("V1_exvivo", color="steelblue", alpha=.6)
-brain.add_label("V2_exvivo", color="#FF6347", alpha=.6)
-brain.add_label("entorhinal_exvivo", color=(.2, 1, .5), alpha=.6)
+brain.add_label("V1", color="steelblue", alpha=.6)
+brain.add_label("V2", color="#FF6347", alpha=.6)
+brain.add_label("entorhinal", color=(.2, 1, .5), alpha=.6)
diff --git a/examples/plot_probabilistic_label.py b/examples/plot_probabilistic_label.py
index 30ba576..213445b 100644
--- a/examples/plot_probabilistic_label.py
+++ b/examples/plot_probabilistic_label.py
@@ -28,27 +28,27 @@
 The easiest way to label any vertex that could be in the region is with
 add_label.
 """
-brain.add_label("BA1_exvivo", color="#A6BDDB")
+brain.add_label("BA1", color="#A6BDDB")
 
 """
 You can also threshold based on the probability of that region being at each
 vertex.
 """
-brain.add_label("BA1_exvivo", color="#2B8CBE", scalar_thresh=.5)
+brain.add_label("BA1", color="#2B8CBE", scalar_thresh=.5)
 
 """
 It's also possible to plot just the label boundary, in case you wanted to
 overlay the label on an activation plot to asses whether it falls within that
 region.
 """
-brain.add_label("BA45_exvivo", color="#F0F8FF", borders=3, scalar_thresh=.5)
-brain.add_label("BA45_exvivo", color="#F0F8FF", alpha=.3, scalar_thresh=.5)
+brain.add_label("BA45", color="#F0F8FF", borders=3, scalar_thresh=.5)
+brain.add_label("BA45", color="#F0F8FF", alpha=.3, scalar_thresh=.5)
 
 """
 Finally, with a few tricks, you can display the whole probabilistic map.
 """
 subjects_dir = environ["SUBJECTS_DIR"]
-label_file = join(subjects_dir, "fsaverage", "label", "lh.BA6_exvivo.label")
+label_file = join(subjects_dir, "fsaverage", "label", "lh.BA6.label")
 
 prob_field = np.zeros_like(brain.geo['lh'].x)
 ids, probs = read_label(label_file, read_scalars=True)

From b9a7dd6060e9228023482764b1bc5c576a6989c4 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Tue, 30 Jul 2019 14:23:49 -0400
Subject: [PATCH 07/46] MAINT: Fix ignores for CIs (#272)

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index d9bfc29..9bc24df 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -11,4 +11,5 @@ filterwarnings =
     ignore:Importing from numpy:DeprecationWarning
     ignore:.*ufunc size changed.*:RuntimeWarning
     ignore:Using or importing the ABCs:DeprecationWarning
+    ignore:the imp module is deprecated in favour of importlib:DeprecationWarning
     ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning

From b2474cfa1f3f31c748f6fba30b4cd0e95528043c Mon Sep 17 00:00:00 2001
From: Michael Waskom <mwaskom@users.noreply.github.com>
Date: Tue, 30 Jul 2019 15:05:34 -0400
Subject: [PATCH 08/46] Set annotation LUT directly (#271)

---
 surfer/viz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index 14b921c..f76184f 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -3304,7 +3304,7 @@ def add_annotation(self, annot, ids, cmap):
 
         # Set the color table
         l_m = surf.module_manager.scalar_lut_manager
-        l_m.load_lut_from_list(cmap / 255.)
+        l_m.lut.table = np.round(cmap).astype(np.uint8)
 
         # Set the brain attributes
         return dict(surface=surf, name=annot, colormap=cmap, brain=self,

From 80c3ccb8161baca59a875c30da668bb4f8b52a93 Mon Sep 17 00:00:00 2001
From: Michael Waskom <mwaskom@users.noreply.github.com>
Date: Mon, 12 Aug 2019 13:21:08 -0400
Subject: [PATCH 09/46] Allow painting all annotation vertices in a single
 color (#273)

---
 surfer/tests/test_viz.py |  6 ++++++
 surfer/viz.py            | 12 +++++++++++-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 158518d..f62d1ca 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -165,6 +165,12 @@ def test_annot():
     labels, ctab, names = nib.freesurfer.read_annot(annot_path)
     brain.add_annotation((labels, ctab))
 
+    brain.add_annotation('aparc', color="red", remove_existing=True)
+    surf = brain.annot["surface"]
+    ctab = surf.module_manager.scalar_lut_manager.lut.table
+    for color in ctab:
+        assert color[:3] == (255, 0, 0)
+
     brain.close()
 
 
diff --git a/surfer/viz.py b/surfer/viz.py
index f76184f..5ff64dd 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -1196,7 +1196,7 @@ def time_label(x):
         self._toggle_render(True, views)
 
     def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
-                       remove_existing=True):
+                       remove_existing=True, color=None):
         """Add an annotation file.
 
         Parameters
@@ -1220,6 +1220,10 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
             for both hemispheres.
         remove_existing : bool
             If True (default), remove old annotations.
+        color : matplotlib-style color code
+            If used, show all annotations in the same (specified) color.
+            Probably useful only when showing annotation borders.
+
         """
         hemis = self._check_hemis(hemi)
 
@@ -1292,6 +1296,12 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
             alpha_vec = cmap[:, 3]
             alpha_vec[alpha_vec > 0] = alpha * 255
 
+            # Override the cmap when a single color is used
+            if color is not None:
+                from matplotlib.colors import colorConverter
+                rgb = np.round(np.multiply(colorConverter.to_rgb(color), 255))
+                cmap[:, :3] = rgb.astype(cmap.dtype)
+
             for brain in self._brain_list:
                 if brain['hemi'] == hemi:
                     self.annot_list.append(

From 9cd751178d1bad6f03199d651a3c359aa540f59a Mon Sep 17 00:00:00 2001
From: Christian Brodbeck <christianmbrodbeck@gmail.com>
Date: Mon, 9 Sep 2019 12:19:47 -0400
Subject: [PATCH 10/46] FIX:  don't change view when adding foci (#274)

---
 surfer/viz.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index 5ff64dd..102482d 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -3365,7 +3365,8 @@ def add_foci(self, foci_coords, scale_factor, color, alpha, name):
             points = mlab.points3d(
                 foci_coords[:, 0], foci_coords[:, 1], foci_coords[:, 2],
                 np.ones(foci_coords.shape[0]), name=name, figure=self._f,
-                scale_factor=(10. * scale_factor), color=color, opacity=alpha)
+                scale_factor=(10. * scale_factor), color=color, opacity=alpha,
+                reset_zoom=False)
         return points
 
     def add_contour_overlay(self, scalar_data, min=None, max=None,

From 1fb7dafbde8a0b2e40ac31701daa222b72ea2910 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Tue, 15 Oct 2019 10:52:42 -0400
Subject: [PATCH 11/46] ENH: Add option to smooth to nearest (#275)

* ENH: Add option to smooth to nearest

* DOC: Update docstring

* FIX: Flake

* FIX: Undordered vertices are the worst

* FIX: Orders are hard

* DOC: Changes
---
 .gitignore                            |  1 +
 CHANGES                               | 23 ++++++++++++++++++--
 doc/changes.rst                       |  1 +
 doc/index.rst                         |  1 +
 examples/plot_meg_inverse_solution.py |  5 +++--
 surfer/tests/test_utils.py            | 25 +++++++++++++++++++---
 surfer/utils.py                       | 30 +++++++++++++++++++++++++--
 surfer/viz.py                         | 19 +++++++++++------
 8 files changed, 90 insertions(+), 15 deletions(-)
 create mode 100644 doc/changes.rst

diff --git a/.gitignore b/.gitignore
index 35adb4a..884e2b8 100755
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
 .#*
 *.swp
 *.orig
+*.mov
 build
 
 dist/
diff --git a/CHANGES b/CHANGES
index dc0902e..fae96a9 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,5 +1,24 @@
-PySurfer Changes
-================
+Changelog
+=========
+
+.. currentmodule:: surfer
+
+Development version (0.10.dev0)
+-------------------------------
+
+- Added an option to smooth to nearest vertex in :meth:`Brain.add_data` using
+  ``smoothing_steps='nearest'``
+- Added options for using offscreen mode
+- Improved integration with Jupyter notebook
+- Avoided view changes when using :meth:`Brain.add_foci`
+
+Version 0.9
+-----------
+
+- Fixed transparency issues with colormaps with
+  :meth:`Brain.scale_data_colormap`
+- Added an example of using custom colors
+- Added options for choosing units for :class:`Brain` (``m`` or ``mm``)
 
 Version 0.8
 -----------
diff --git a/doc/changes.rst b/doc/changes.rst
new file mode 100644
index 0000000..8a05a51
--- /dev/null
+++ b/doc/changes.rst
@@ -0,0 +1 @@
+.. include:: ../CHANGES
\ No newline at end of file
diff --git a/doc/index.rst b/doc/index.rst
index 4a95f39..940ffad 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -19,6 +19,7 @@ More Information
     auto_examples/index.rst
     documentation/index.rst
     python_reference.rst
+    changes.rst
 
 Authors
 -------
diff --git a/examples/plot_meg_inverse_solution.py b/examples/plot_meg_inverse_solution.py
index b3cb23e..9dd20a5 100644
--- a/examples/plot_meg_inverse_solution.py
+++ b/examples/plot_meg_inverse_solution.py
@@ -50,9 +50,10 @@ def time_label(t):
     # colormap to use
     colormap = 'hot'
 
-    # add data and set the initial time displayed to 100 ms
+    # add data and set the initial time displayed to 100 ms,
+    # plotted using the nearest relevant colors
     brain.add_data(data, colormap=colormap, vertices=vertices,
-                   smoothing_steps=5, time=time, time_label=time_label,
+                   smoothing_steps='nearest', time=time, time_label=time_label,
                    hemi=hemi, initial_time=0.1, verbose=False)
 
 # scale colormap
diff --git a/surfer/tests/test_utils.py b/surfer/tests/test_utils.py
index d9a6d72..f04cd82 100644
--- a/surfer/tests/test_utils.py
+++ b/surfer/tests/test_utils.py
@@ -1,6 +1,10 @@
+from distutils.version import LooseVersion
 import numpy as np
+import scipy
+from scipy import sparse
+import pytest
 import matplotlib as mpl
-from numpy.testing import assert_array_almost_equal, assert_array_equal
+from numpy.testing import assert_allclose, assert_array_equal
 
 from surfer import utils
 
@@ -44,12 +48,12 @@ def test_surface():
         x = surface.x
         surface.apply_xfm(xfm)
         x_ = surface.x
-        assert_array_almost_equal(x + 2, x_)
+        assert_allclose(x + 2, x_)
 
         # normals
         nn = _slow_compute_normals(surface.coords, surface.faces[:10000])
         nn_fast = utils._compute_normals(surface.coords, surface.faces[:10000])
-        assert_array_almost_equal(nn, nn_fast)
+        assert_allclose(nn, nn_fast)
         assert 50 < np.linalg.norm(surface.coords, axis=-1).mean() < 100  # mm
     surface = utils.Surface('fsaverage', 'lh', 'inflated',
                             subjects_dir=subj_dir, units='m')
@@ -99,3 +103,18 @@ def test_create_color_lut():
     # Test that we can ask for a specific number of colors
     cmap_out = utils.create_color_lut("Reds", 12)
     assert cmap_out.shape == (12, 4)
+
+
+def test_smooth():
+    """Test smoothing support."""
+    adj_mat = sparse.csc_matrix(np.repeat(np.repeat(np.eye(2), 2, 0), 2, 1))
+    vertices = np.array([0, 2])
+    want = np.repeat(np.eye(2), 2, axis=0)
+    smooth = utils.smoothing_matrix(vertices, adj_mat).toarray()
+    assert_allclose(smooth, want)
+    if LooseVersion(scipy.__version__) < LooseVersion('1.3'):
+        with pytest.raises(RuntimeError, match='nearest.*requires'):
+            utils.smoothing_matrix(vertices, adj_mat, 'nearest')
+    else:
+        smooth = utils.smoothing_matrix(vertices, adj_mat, 'nearest').toarray()
+        assert_allclose(smooth, want)
diff --git a/surfer/utils.py b/surfer/utils.py
index 8e3e22c..4a6e4cf 100644
--- a/surfer/utils.py
+++ b/surfer/utils.py
@@ -579,10 +579,36 @@ def smoothing_matrix(vertices, adj_mat, smoothing_steps=20, verbose=None):
     smooth_mat : sparse matrix
         smoothing matrix with size N x len(vertices)
     """
+    if smoothing_steps == 'nearest':
+        mat = _nearest(vertices, adj_mat)
+    else:
+        mat = _smooth(vertices, adj_mat, smoothing_steps)
+    return mat
+
+
+def _nearest(vertices, adj_mat):
+    import scipy
+    from scipy.sparse.csgraph import dijkstra
+    if LooseVersion(scipy.__version__) < LooseVersion('1.3'):
+        raise RuntimeError('smoothing_steps="nearest" requires SciPy >= 1.3')
+    # Vertices can be out of order, so sort them to start ...
+    order = np.argsort(vertices)
+    vertices = vertices[order]
+    _, _, sources = dijkstra(adj_mat, False, indices=vertices, min_only=True,
+                             return_predecessors=True)
+    col = np.searchsorted(vertices, sources)
+    # ... then get things back to the correct configuration.
+    col = order[col]
+    row = np.arange(len(col))
+    data = np.ones(len(col))
+    mat = sparse.coo_matrix((data, (row, col)))
+    assert mat.shape == (adj_mat.shape[0], len(vertices)), mat.shape
+    return mat
+
+
+def _smooth(vertices, adj_mat, smoothing_steps):
     from scipy import sparse
-
     logger.info("Updating smoothing matrix, be patient..")
-
     e = adj_mat.copy()
     e.data[e.data == 2] = 1
     n_vertices = e.shape[0]
diff --git a/surfer/viz.py b/surfer/viz.py
index 102482d..c4ed3a8 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -1005,9 +1005,12 @@ def add_data(self, array, min=None, max=None, thresh=None,
             alpha level to control opacity of the overlay.
         vertices : numpy array
             vertices for which the data is defined (needed if len(data) < nvtx)
-        smoothing_steps : int or None
-            number of smoothing steps (smoothing is used if len(data) < nvtx)
-            Default : 20
+        smoothing_steps : int | str | None
+            Number of smoothing steps (if data come from surface subsampling).
+            Can be None to use the fewest steps that result in all vertices
+            taking on data values, or "nearest" such that each high resolution
+            vertex takes the value of the its nearest (on the sphere)
+            low-resolution vertex. Default is 20.
         time : numpy array
             time points in the data array (if data is 2D or 3D)
         time_label : str | callable | None
@@ -2114,13 +2117,17 @@ def data_time_index(self):
         raise RuntimeError("Brain instance has no data overlay")
 
     @verbose
-    def set_data_smoothing_steps(self, smoothing_steps, verbose=None):
+    def set_data_smoothing_steps(self, smoothing_steps=20, verbose=None):
         """Set the number of smoothing steps
 
         Parameters
         ----------
-        smoothing_steps : int
-            Number of smoothing steps
+        smoothing_steps : int | str | None
+            Number of smoothing steps (if data come from surface subsampling).
+            Can be None to use the fewest steps that result in all vertices
+            taking on data values, or "nearest" such that each high resolution
+            vertex takes the value of the its nearest (on the sphere)
+            low-resolution vertex. Default is 20.
         verbose : bool, str, int, or None
             If not None, override default verbose level (see surfer.verbose).
         """

From 64a10695f5c3173f7805e9accd75e28713588be2 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Tue, 15 Oct 2019 12:08:43 -0400
Subject: [PATCH 12/46] MAINT: CircleCI for latest pip (#277)

---
 .circleci/config.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index dd7ca25..0071f48 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -47,9 +47,9 @@ jobs:
         - run:
             name: Get Python running
             command: |
-              pip install --user -q --upgrade pip numpy
-              pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg sphinx-gallery
-              pip install --user -q --upgrade mayavi "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
+              python -m pip install --user -q --upgrade pip numpy
+              python -m pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg sphinx-gallery
+              python -m pip install --user -q --upgrade mayavi "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
         - save_cache:
             key: pip-cache
             paths:

From e85753e35a2afa63cc7b232b4890ca9f9c8e0084 Mon Sep 17 00:00:00 2001
From: "Dingkun.Liu" <liudkun15@gmail.com>
Date: Fri, 1 Nov 2019 22:23:57 +0800
Subject: [PATCH 13/46] ENH: Add kwargs in Brain.add_* and pass it to mayavi
 modules (#276)

* Feat: add kwargs in Brain.add_* and pass it to mayavi modules, so that we could directly manipulate mayavi display settings, like point resolution and overlay opacity.

* Fix: Fix code styles which failed in the flake test.

* Modify test_viz to pass the kwargs to the mayavi module.

* fix flake test.

* Specifying `kwargs` as `mlab_kws` and make the documentation more clear.

* Revert "Specifying `kwargs` as `mlab_kws` and make the documentation more clear."

This reverts commit c7a5912e593fa075fb658dda75f05d6a5009eb02.

* Link mayavi documents.

* Give detailed explanations about the kwargs passed to the functions.

* Revert "Link mayavi documents."

This reverts commit 2c86a04e18b7fbb5502e1d9255a831526286f5b7.

* Change the position of line breaking.

* Fix the typo and unavailable links.

* Fix render errors.

* Revert "Fix render errors."

This reverts commit ac0b7b8466e62b01c83ace43b8e56be99e2f1410.

* Fix render error.

* Improve code rendering.

* Revert "Fix render error."

This reverts commit bbf76311b6d626cb33a973784dd21cb5f4580e8e.

* Fix line breaking error.

* Revert "Fix line breaking error."

This reverts commit 6efccace7ea95defb397ba6d099c3d50c61c2acc.

* Fix line breaking error.

* Revert "Fix line breaking error."

This reverts commit a7abf6174ef184a367f8277711ed34299f914ac4.

* Force line breaking to fix the rendering error on long code.

* Revert "Force line breaking to fix the rendering error on long code."

This reverts commit 6a9cdf1b6455c7980ae98c22d0df0f0afd51a02e.

* Force line breaking to fix the rendering error on long code.

* Revert "Force line breaking to fix the rendering error on long code."

This reverts commit c7f6a9fc33322ae01e9ed8ea7346e1e45212c282.

* Force line breaking to fix the rendering error on long code.

* Revert "Force line breaking to fix the rendering error on long code."

This reverts commit de31e5fd7232d12bd360a4e8c0c0d22d0bd94296.

* Fix render error

Force line breaking to avoid render error.

* Render undocumented function as plain code.

* Fix sectioning.

* FIX: Formatting
---
 .gitignore               |   1 +
 doc/_static/navy.css     |   6 ++-
 surfer/tests/test_viz.py |  10 ++--
 surfer/viz.py            | 102 +++++++++++++++++++++++++--------------
 4 files changed, 79 insertions(+), 40 deletions(-)

diff --git a/.gitignore b/.gitignore
index 884e2b8..5ded8ed 100755
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,7 @@
 *.orig
 *.mov
 build
+.idea/
 
 dist/
 doc/_build/
diff --git a/doc/_static/navy.css b/doc/_static/navy.css
index 4b1c4e7..79b3038 100755
--- a/doc/_static/navy.css
+++ b/doc/_static/navy.css
@@ -546,4 +546,8 @@ ul.keywordmatches li.goodmatch a {
     div.sphx-glr-footer-example a code span:last-child {
 	font-size: unset;
     }
-}
\ No newline at end of file
+}
+
+table.longtable.align-default {
+    width: 100%;
+}
diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index f62d1ca..46dfce6 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -153,7 +153,7 @@ def test_annot():
     view = get_view(brain)
 
     for a, b, p in zip(annots, borders, alphas):
-        brain.add_annotation(a, b, p)
+        brain.add_annotation(a, b, p, opacity=0.8)
     check_view(brain, view)
 
     brain.set_surf('white')
@@ -226,7 +226,11 @@ def test_foci():
     coords = [[-36, 18, -3],
               [-43, 25, 24],
               [-48, 26, -2]]
-    brain.add_foci(coords, map_surface="white", color="gold", name='test1')
+    brain.add_foci(coords,
+                   map_surface="white",
+                   color="gold",
+                   name='test1',
+                   resolution=25)
 
     subj_dir = utils._get_subjects_dir()
     annot_path = pjoin(subj_dir, subject_id, 'label', 'lh.aparc.a2009s.annot')
@@ -398,7 +402,7 @@ def test_overlay():
     brain = Brain(*std_args)
     brain.add_overlay(overlay_file)
     brain.overlays["sig"].remove()
-    brain.add_overlay(overlay_file, min=5, max=20, sign="pos")
+    brain.add_overlay(overlay_file, min=5, max=20, sign="pos", opacity=0.7)
     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"))
 
diff --git a/surfer/viz.py b/surfer/viz.py
index c4ed3a8..2405c50 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -913,7 +913,7 @@ def _iter_time(self, time_idx, interpolation):
     ###########################################################################
     # ADDING DATA PLOTS
     def add_overlay(self, source, min=2, max="robust_max", sign="abs",
-                    name=None, hemi=None):
+                    name=None, hemi=None, **kwargs):
         """Add an overlay to the overlay dict from a file or array.
 
         Parameters
@@ -932,6 +932,10 @@ def add_overlay(self, source, min=2, max="robust_max", sign="abs",
             If None, it is assumed to belong to the hemipshere being
             shown. If two hemispheres are being shown, an error will
             be thrown.
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+            ``mayavi.mlab.pipeline.surface`` call.
+
         """
         hemi = self._check_hemi(hemi)
         # load data here
@@ -944,7 +948,7 @@ def add_overlay(self, source, min=2, max="robust_max", sign="abs",
         views = self._toggle_render(False)
         for brain in self._brain_list:
             if brain['hemi'] == hemi:
-                ol.append(brain['brain'].add_overlay(old))
+                ol.append(brain['brain'].add_overlay(old, **kwargs))
         if name in self.overlays_dict:
             name = "%s%d" % (name, len(self.overlays_dict) + 1)
         self.overlays_dict[name] = ol
@@ -957,7 +961,8 @@ def add_data(self, array, min=None, max=None, thresh=None,
                  time_label="time index=%d", colorbar=True,
                  hemi=None, remove_existing=False, time_label_size=14,
                  initial_time=None, scale_factor=None, vector_alpha=None,
-                 mid=None, center=None, transparent=False, verbose=None):
+                 mid=None, center=None, transparent=False, verbose=None,
+                 **kwargs):
         """Display data from a numpy array on the surface.
 
         This provides a similar interface to
@@ -1038,6 +1043,9 @@ def add_data(self, array, min=None, max=None, thresh=None,
             vector-valued data. If None (default), ``alpha`` is used.
         verbose : bool, str, int, or None
             If not None, override default verbose level (see surfer.verbose).
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+            ``mayavi.mlab.pipeline.surface`` call.
 
         Notes
         -----
@@ -1175,7 +1183,7 @@ def time_label(x):
                 s, ct, bar, gl = brain['brain'].add_data(
                     array, min, mid, max, thresh, lut, colormap, alpha,
                     colorbar, layer_id, smooth_mat, magnitude, magnitude_max,
-                    scale_factor, vertices, vector_alpha)
+                    scale_factor, vertices, vector_alpha, **kwargs)
                 surfs.append(s)
                 bars.append(bar)
                 glyphs.append(gl)
@@ -1199,7 +1207,7 @@ def time_label(x):
         self._toggle_render(True, views)
 
     def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
-                       remove_existing=True, color=None):
+                       remove_existing=True, color=None, **kwargs):
         """Add an annotation file.
 
         Parameters
@@ -1226,7 +1234,9 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
         color : matplotlib-style color code
             If used, show all annotations in the same (specified) color.
             Probably useful only when showing annotation borders.
-
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+            ``mayavi.mlab.pipeline.surface`` call.
         """
         hemis = self._check_hemis(hemi)
 
@@ -1308,11 +1318,12 @@ def add_annotation(self, annot, borders=True, alpha=1, hemi=None,
             for brain in self._brain_list:
                 if brain['hemi'] == hemi:
                     self.annot_list.append(
-                        brain['brain'].add_annotation(annot, ids, cmap))
+                        brain['brain'].add_annotation(annot, ids, cmap,
+                                                      **kwargs))
         self._toggle_render(True, views)
 
     def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
-                  borders=False, hemi=None, subdir=None):
+                  borders=False, hemi=None, subdir=None, **kwargs):
         """Add an ROI label to the image.
 
         Parameters
@@ -1344,6 +1355,9 @@ def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
             label directory rather than in the label directory itself (e.g.
             for ``$SUBJECTS_DIR/$SUBJECT/label/aparc/lh.cuneus.label``
             ``brain.add_label('cuneus', subdir='aparc')``).
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+            ``mayavi.mlab.pipeline.surface`` call.
 
         Notes
         -----
@@ -1425,7 +1439,7 @@ def add_label(self, label, color=None, alpha=1, scalar_thresh=None,
         for brain in self.brains:
             if brain.hemi == hemi:
                 array_id, surf = brain.add_label(label, label_name, color,
-                                                 alpha)
+                                                 alpha, **kwargs)
                 surfaces.append(surf)
                 array_ids.append((brain, array_id))
         self._label_dicts[label_name] = {'surfaces': surfaces,
@@ -1535,7 +1549,7 @@ def remove_labels(self, labels=None, hemi=None):
 
     def add_morphometry(self, measure, grayscale=False, hemi=None,
                         remove_existing=True, colormap=None,
-                        min=None, max=None, colorbar=True):
+                        min=None, max=None, colorbar=True, **kwargs):
         """Add a morphometry overlay to the image.
 
         Parameters
@@ -1557,7 +1571,9 @@ def add_morphometry(self, measure, grayscale=False, hemi=None,
             of the data is used.
         colorbar : bool
             If True, show a colorbar corresponding to the overlay data.
-
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+            ``mayavi.mlab.pipeline.surface`` call.
         """
         hemis = self._check_hemis(hemi)
         morph_files = []
@@ -1618,12 +1634,13 @@ def add_morphometry(self, measure, grayscale=False, hemi=None,
             for brain in self.brains:
                 if brain.hemi == hemi:
                     self.morphometry_list.append(brain.add_morphometry(
-                        morph_data, colormap, measure, min, max, colorbar))
+                        morph_data, colormap, measure, min, max, colorbar,
+                        **kwargs))
         self._toggle_render(True, views)
 
     def add_foci(self, coords, coords_as_verts=False, map_surface=None,
                  scale_factor=1, color="white", alpha=1, name=None,
-                 hemi=None):
+                 hemi=None, **kwargs):
         """Add spherical foci, possibly mapping to displayed surf.
 
         The foci spheres can be displayed at the coordinates given, or
@@ -1653,6 +1670,9 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             If None, it is assumed to belong to the hemipshere being
             shown. If two hemispheres are being shown, an error will
             be thrown.
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+             :func:`mayavi.mlab.points3d` call.
         """
         from matplotlib.colors import colorConverter
         hemi = self._check_hemi(hemi)
@@ -1688,13 +1708,15 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
         for brain in self._brain_list:
             if brain['hemi'] == hemi:
                 fl.append(brain['brain'].add_foci(foci_coords, scale_factor,
-                                                  color, alpha, name))
+                                                  color, alpha, name,
+                                                  **kwargs))
         self.foci_dict[name] = fl
         self._toggle_render(True, views)
 
     def add_contour_overlay(self, source, min=None, max=None,
                             n_contours=7, line_width=1.5, colormap="YlOrRd_r",
-                            hemi=None, remove_existing=True, colorbar=True):
+                            hemi=None, remove_existing=True, colorbar=True,
+                            **kwargs):
         """Add a topographic contour overlay of the positive data.
 
         Note: This visualization will look best when using the "low_contrast"
@@ -1724,7 +1746,9 @@ def add_contour_overlay(self, source, min=None, max=None,
             If there is an existing contour overlay, remove it before plotting.
         colorbar : bool
             If True, show the colorbar for the scalar value.
-
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+            ``mayavi.mlab.pipeline.contour_surface`` call.
         """
         hemi = self._check_hemi(hemi)
 
@@ -1751,11 +1775,11 @@ def add_contour_overlay(self, source, min=None, max=None,
             if brain.hemi == hemi:
                 self.contour_list.append(brain.add_contour_overlay(
                     scalar_data, min, max, n_contours, line_width, lut,
-                    colorbar))
+                    colorbar, **kwargs))
         self._toggle_render(True, views)
 
     def add_text(self, x, y, text, name, color=None, opacity=1.0,
-                 row=-1, col=-1, font_size=None, justification=None):
+                 row=-1, col=-1, font_size=None, justification=None, **kwargs):
         """ Add a text to the visualization
 
         Parameters
@@ -1778,11 +1802,15 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0,
             Row index of which brain to use
         col : int
             Column index of which brain to use
+        **kwargs : additional keyword arguments
+            These are passed to the underlying
+            :func:`mayavi.mlab.text3d` call.
         """
         if name in self.texts_dict:
             self.texts_dict[name]['text'].remove()
         text = self.brain_matrix[row, col].add_text(x, y, text,
-                                                    name, color, opacity)
+                                                    name, color, opacity,
+                                                    **kwargs)
         self.texts_dict[name] = dict(row=row, col=col, text=text)
         if font_size is not None:
             text.property.font_size = font_size
@@ -3203,7 +3231,7 @@ def _remove_vector_data(self, glyphs):
         if glyphs is not None:
             glyphs.parent.parent.remove()
 
-    def add_overlay(self, old):
+    def add_overlay(self, old, **kwargs):
         """Add an overlay to the overlay dict from a file or array"""
         array_id, mesh = self._add_scalar_data(old.mlab_data)
 
@@ -3213,7 +3241,7 @@ def add_overlay(self, old):
                 pos = mlab.pipeline.surface(
                     pos_thresh, colormap="YlOrRd", figure=self._f,
                     vmin=old.pos_lims[1], vmax=old.pos_lims[2],
-                    reset_zoom=False)
+                    reset_zoom=False, **kwargs)
                 pos.actor.property.backface_culling = False
                 pos_bar = mlab.scalarbar(pos, nb_labels=5)
             pos_bar.reverse_lut = True
@@ -3229,7 +3257,7 @@ def add_overlay(self, old):
                 neg = mlab.pipeline.surface(
                     neg_thresh, colormap="PuBu", figure=self._f,
                     vmin=old.neg_lims[1], vmax=old.neg_lims[2],
-                    reset_zoom=False)
+                    reset_zoom=False, **kwargs)
                 neg.actor.property.backface_culling = False
                 neg_bar = mlab.scalarbar(neg, nb_labels=5)
             neg_bar.scalar_bar_representation.position = (0.05, 0.01)
@@ -3243,7 +3271,7 @@ def add_overlay(self, old):
     @verbose
     def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
                  colorbar, layer_id, smooth_mat, magnitude, magnitude_max,
-                 scale_factor, vertices, vector_alpha):
+                 scale_factor, vertices, vector_alpha, **kwargs):
         """Add data to the brain"""
         # Calculate initial data to plot
         if array.ndim == 1:
@@ -3285,7 +3313,8 @@ def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
         with warnings.catch_warnings(record=True):
             surf = mlab.pipeline.surface(
                 pipe, colormap=colormap, vmin=fmin, vmax=fmax,
-                opacity=float(alpha), figure=self._f, reset_zoom=False)
+                opacity=float(alpha), figure=self._f, reset_zoom=False,
+                **kwargs)
             surf.actor.property.backface_culling = False
 
         # apply look up table if given
@@ -3310,13 +3339,13 @@ def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
             scale_factor_norm=scale_factor_norm)
         return surf, orig_ctable, bar, glyphs
 
-    def add_annotation(self, annot, ids, cmap):
+    def add_annotation(self, annot, ids, cmap, **kwargs):
         """Add an annotation file"""
         # Add scalar values to dataset
         array_id, pipe = self._add_scalar_data(ids)
         with warnings.catch_warnings(record=True):
             surf = mlab.pipeline.surface(pipe, name=annot, figure=self._f,
-                                         reset_zoom=False)
+                                         reset_zoom=False, **kwargs)
             surf.actor.property.backface_culling = False
 
         # Set the color table
@@ -3327,13 +3356,13 @@ def add_annotation(self, annot, ids, cmap):
         return dict(surface=surf, name=annot, colormap=cmap, brain=self,
                     array_id=array_id)
 
-    def add_label(self, label, label_name, color, alpha):
+    def add_label(self, label, label_name, color, alpha, **kwargs):
         """Add an ROI label to the image"""
         from matplotlib.colors import colorConverter
         array_id, pipe = self._add_scalar_data(label)
         with warnings.catch_warnings(record=True):
             surf = mlab.pipeline.surface(pipe, name=label_name, figure=self._f,
-                                         reset_zoom=False)
+                                         reset_zoom=False, **kwargs)
             surf.actor.property.backface_culling = False
         color = colorConverter.to_rgba(color, alpha)
         cmap = np.array([(0, 0, 0, 0,), color])
@@ -3345,13 +3374,13 @@ def add_label(self, label, label_name, color, alpha):
         return array_id, surf
 
     def add_morphometry(self, morph_data, colormap, measure,
-                        min, max, colorbar):
+                        min, max, colorbar, **kwargs):
         """Add a morphometry overlay to the image"""
         array_id, pipe = self._add_scalar_data(morph_data)
         with warnings.catch_warnings(record=True):
             surf = mlab.pipeline.surface(
                 pipe, colormap=colormap, vmin=min, vmax=max, name=measure,
-                figure=self._f, reset_zoom=False)
+                figure=self._f, reset_zoom=False, **kwargs)
 
         # Get the colorbar
         if colorbar:
@@ -3365,7 +3394,8 @@ def add_morphometry(self, morph_data, colormap, measure,
         return dict(surface=surf, colorbar=bar, measure=measure, brain=self,
                     array_id=array_id)
 
-    def add_foci(self, foci_coords, scale_factor, color, alpha, name):
+    def add_foci(self, foci_coords, scale_factor, color, alpha, name,
+                 **kwargs):
         """Add spherical foci, possibly mapping to displayed surf"""
         # Create the visualization
         with warnings.catch_warnings(record=True):  # traits
@@ -3373,19 +3403,19 @@ def add_foci(self, foci_coords, scale_factor, color, alpha, name):
                 foci_coords[:, 0], foci_coords[:, 1], foci_coords[:, 2],
                 np.ones(foci_coords.shape[0]), name=name, figure=self._f,
                 scale_factor=(10. * scale_factor), color=color, opacity=alpha,
-                reset_zoom=False)
+                reset_zoom=False, **kwargs)
         return points
 
     def add_contour_overlay(self, scalar_data, min=None, max=None,
                             n_contours=7, line_width=1.5, lut=None,
-                            colorbar=True):
+                            colorbar=True, **kwargs):
         """Add a topographic contour overlay of the positive data"""
         array_id, pipe = self._add_scalar_data(scalar_data)
         with warnings.catch_warnings(record=True):
             thresh = threshold_filter(pipe, low=min)
             surf = mlab.pipeline.contour_surface(
                 thresh, contours=n_contours, line_width=line_width,
-                reset_zoom=False)
+                reset_zoom=False, **kwargs)
         if lut is not None:
             l_m = surf.module_manager.scalar_lut_manager
             l_m.load_lut_from_list(lut / 255.)
@@ -3403,12 +3433,12 @@ def add_contour_overlay(self, scalar_data, min=None, max=None,
         # Set up a dict attribute with pointers at important things
         return dict(surface=surf, colorbar=bar, brain=self, array_id=array_id)
 
-    def add_text(self, x, y, text, name, color=None, opacity=1.0):
+    def add_text(self, x, y, text, name, color=None, opacity=1.0, **kwargs):
         """ Add a text to the visualization"""
         color = self._fg_color if color is None else color
         with warnings.catch_warnings(record=True):
             text = mlab.text(x, y, text, name=name, color=color,
-                             opacity=opacity, figure=self._f)
+                             opacity=opacity, figure=self._f, **kwargs)
             return text
 
     def remove_data(self, layer_id):

From 0e1da27ac77de470e2cff3ebcb178ca9ab177029 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Tue, 10 Dec 2019 10:05:12 -0500
Subject: [PATCH 14/46] BUG: Properly clean up on del

---
 surfer/viz.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index 2405c50..094fc37 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2298,14 +2298,12 @@ def close(self):
         _force_render([])
 
         # should we tear down other variables?
-        if self._v is not None:
+        if getattr(self, '_v', None) is not None:
             self._v.dispose()
             self._v = None
 
     def __del__(self):
-        if hasattr(self, '_v') and self._v is not None:
-            self._v.dispose()
-            self._v = None
+        self.close()
 
     ###########################################################################
     # SAVING OUTPUT

From e79624d5bc53fd6763cbcf73df6fd9c8fc5b7bcc Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 6 Feb 2020 14:38:51 -0500
Subject: [PATCH 15/46] FIX: Safer exit

---
 surfer/viz.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index 094fc37..b13b21a 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2290,20 +2290,30 @@ def hide_colorbar(self, row=-1, col=-1):
 
     def close(self):
         """Close all figures and cleanup data structure."""
+
+    def _close(self, force_render=True):
         for ri, ff in enumerate(self._figures):
             for ci, f in enumerate(ff):
                 if f is not None:
-                    mlab.close(f)
+                    try:
+                        mlab.close(f)
+                    except Exception:
+                        pass
                     self._figures[ri][ci] = None
-        _force_render([])
+
+        if force_render:
+            _force_render([])
 
         # should we tear down other variables?
         if getattr(self, '_v', None) is not None:
-            self._v.dispose()
+            try:
+                self._v.dispose()
+            except Exception:
+                pass
             self._v = None
 
     def __del__(self):
-        self.close()
+        self._close(force_render=False)
 
     ###########################################################################
     # SAVING OUTPUT

From 78950ed3690be87915ca9ccc92c4fcdb30e292b8 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 7 Feb 2020 09:35:06 -0500
Subject: [PATCH 16/46] FIX: Actually close

---
 surfer/io.py             | 2 +-
 surfer/tests/test_viz.py | 2 ++
 surfer/viz.py            | 1 +
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/surfer/io.py b/surfer/io.py
index 8ddcf69..efda923 100644
--- a/surfer/io.py
+++ b/surfer/io.py
@@ -29,7 +29,7 @@ def read_scalar_data(filepath):
         flat numpy array of scalar data
     """
     try:
-        scalar_data = nib.load(filepath).get_data()
+        scalar_data = np.asanyarray(nib.load(filepath).dataobj)
         scalar_data = np.ravel(scalar_data, order="F")
         return scalar_data
 
diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 46dfce6..6a17762 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -87,6 +87,8 @@ def test_image(tmpdir):
     brain.close()
 
     brain = Brain(*std_args, size=100)
+    for b in brain.brain_matrix.ravel():
+        assert b._f.scene is not None
     brain.save_image(tmp_name)
     brain.save_image(tmp_name, 'rgba', True)
     brain.screenshot()
diff --git a/surfer/viz.py b/surfer/viz.py
index b13b21a..6c4ddd8 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2290,6 +2290,7 @@ def hide_colorbar(self, row=-1, col=-1):
 
     def close(self):
         """Close all figures and cleanup data structure."""
+        self._close()
 
     def _close(self, force_render=True):
         for ri, ff in enumerate(self._figures):

From e79e15d128fe113f566db34c3b7c1d2a6209d923 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 7 Feb 2020 09:45:22 -0500
Subject: [PATCH 17/46] FIX: Try again

---
 surfer/viz.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/surfer/viz.py b/surfer/viz.py
index 6c4ddd8..0067974 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -1,4 +1,5 @@
 from copy import deepcopy
+import gc
 import logging
 from math import floor
 import os
@@ -2312,6 +2313,7 @@ def _close(self, force_render=True):
             except Exception:
                 pass
             self._v = None
+        gc.collect()
 
     def __del__(self):
         self._close(force_render=False)

From 0b20e8b84a5935c5167ac1c03c5a96ecc4d0aa92 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 7 Feb 2020 09:54:37 -0500
Subject: [PATCH 18/46] FIX: Again again

---
 surfer/tests/test_viz.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 6a17762..70dd9c2 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -1,3 +1,4 @@
+import gc
 import os
 import os.path as op
 from os.path import join as pjoin
@@ -85,6 +86,7 @@ def test_image(tmpdir):
     brain.add_overlay(overlay_fname, hemi='lh', min=5, max=20, sign="pos")
     brain.save_imageset(tmp_name, ['med', 'lat'], 'jpg')
     brain.close()
+    del brain
 
     brain = Brain(*std_args, size=100)
     for b in brain.brain_matrix.ravel():
@@ -151,6 +153,7 @@ def test_annot():
     annots = ['aparc', 'aparc.a2005s']
     borders = [True, False, 2]
     alphas = [1, 0.5]
+    gc.collect()
     brain = Brain(*std_args)
     view = get_view(brain)
 

From 1435b57b3a40e67257a983e785c39b71d28da45e Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 7 Feb 2020 10:05:11 -0500
Subject: [PATCH 19/46] FIX: Different

---
 surfer/tests/test_viz.py | 30 +++++++-----------------------
 surfer/viz.py            | 10 ++--------
 2 files changed, 9 insertions(+), 31 deletions(-)

diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 70dd9c2..8d355be 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -3,7 +3,6 @@
 import os.path as op
 from os.path import join as pjoin
 import sys
-import warnings
 
 import pytest
 from mayavi import mlab
@@ -17,8 +16,6 @@
 from surfer.utils import (requires_fsaverage, requires_imageio, requires_fs,
                           _get_extra)
 
-warnings.simplefilter('always')
-
 subject_id = 'fsaverage'
 std_args = [subject_id, 'lh', 'inflated']
 data_dir = pjoin(op.dirname(__file__), '..', '..', 'examples', 'example_data')
@@ -85,21 +82,12 @@ def test_image(tmpdir):
     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()
-    del brain
-
-    brain = Brain(*std_args, size=100)
-    for b in brain.brain_matrix.ravel():
-        assert b._f.scene is not None
     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()
+    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']])
 
 
 @requires_fsaverage()
@@ -108,8 +96,7 @@ def test_brains():
     # testing backend breaks when passing in a figure, so we use 'auto' here
     # (shouldn't affect usability, but it makes testing more annoying)
     _set_backend('auto')
-    with warnings.catch_warnings(record=True):  # traits for mlab.figure()
-        mlab.figure(101)
+    mlab.figure(101)
     surfs = ['inflated', 'white', 'white', 'white', 'white', 'white', 'white']
     hemis = ['lh', 'rh', 'both', 'both', 'rh', 'both', 'both']
     titles = [None, 'Hello', 'Good bye!', 'lut test',
@@ -122,8 +109,7 @@ def test_brains():
                    (0.2, 0.2, 0.2), "black", "0.75"]
     foregrounds = ["black", "white", "0.75", "red",
                    (0.2, 0.2, 0.2), "blue", "black"]
-    with warnings.catch_warnings(record=True):  # traits for mlab.figure()
-        figs = [101, mlab.figure(), None, None, mlab.figure(), None, None]
+    figs = [101, mlab.figure(), None, None, mlab.figure(), None, None]
     subj_dir = utils._get_subjects_dir()
     subj_dirs = [None, subj_dir, subj_dir, subj_dir,
                  subj_dir, subj_dir, subj_dir]
@@ -153,7 +139,6 @@ def test_annot():
     annots = ['aparc', 'aparc.a2005s']
     borders = [True, False, 2]
     alphas = [1, 0.5]
-    gc.collect()
     brain = Brain(*std_args)
     view = get_view(brain)
 
@@ -463,9 +448,8 @@ def test_probabilistic_labels():
     prob_field[ids] = probs
     brain.add_data(prob_field, thresh=1e-5)
 
-    with warnings.catch_warnings(record=True):
-        brain.data["colorbar"].number_of_colors = 10
-        brain.data["colorbar"].number_of_labels = 11
+    brain.data["colorbar"].number_of_colors = 10
+    brain.data["colorbar"].number_of_labels = 11
     brain.close()
 
 
diff --git a/surfer/viz.py b/surfer/viz.py
index 0067974..45e2ea3 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -1,5 +1,4 @@
 from copy import deepcopy
-import gc
 import logging
 from math import floor
 import os
@@ -2291,9 +2290,6 @@ def hide_colorbar(self, row=-1, col=-1):
 
     def close(self):
         """Close all figures and cleanup data structure."""
-        self._close()
-
-    def _close(self, force_render=True):
         for ri, ff in enumerate(self._figures):
             for ci, f in enumerate(ff):
                 if f is not None:
@@ -2303,8 +2299,7 @@ def _close(self, force_render=True):
                         pass
                     self._figures[ri][ci] = None
 
-        if force_render:
-            _force_render([])
+        _force_render([])
 
         # should we tear down other variables?
         if getattr(self, '_v', None) is not None:
@@ -2313,10 +2308,9 @@ def _close(self, force_render=True):
             except Exception:
                 pass
             self._v = None
-        gc.collect()
 
     def __del__(self):
-        self._close(force_render=False)
+        self.close()
 
     ###########################################################################
     # SAVING OUTPUT

From 2cf1d7381ee16f76e2e4d59293fbd0f0a2d06a0d Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 7 Feb 2020 10:29:41 -0500
Subject: [PATCH 20/46] FIX: One more

---
 surfer/tests/test_viz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 8d355be..3f7ced5 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -1,4 +1,3 @@
-import gc
 import os
 import os.path as op
 from os.path import join as pjoin
@@ -88,6 +87,7 @@ def test_image(tmpdir):
     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()
 
 
 @requires_fsaverage()

From 5aaf0430e43c700dc358ad946e193f78d1137ad4 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Mon, 10 Feb 2020 10:41:50 -0500
Subject: [PATCH 21/46] FIX: Dont reuse by default

---
 surfer/tests/test_viz.py | 13 +++++++++++++
 surfer/viz.py            |  4 ++--
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 3f7ced5..5bb6b18 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -90,6 +90,19 @@ def test_image(tmpdir):
     brain.close()
 
 
+@requires_fsaverage()
+def test_brain_separate():
+    """Test that Brain does not reuse existing figures by default."""
+    _set_backend('auto')
+    brain = Brain(*std_args)
+    assert brain.brain_matrix.size == 1
+    brain_2 = Brain(*std_args)
+    assert brain_2.brain_matrix.size == 1
+    assert brain._figures[0][0] is not brain_2._figures[0][0]
+    brain_3 = Brain(*std_args, figure=brain._figures[0][0])
+    assert brain._figures[0][0] is brain_3._figures[0][0]
+
+
 @requires_fsaverage()
 def test_brains():
     """Test plotting of Brain with different arguments."""
diff --git a/surfer/viz.py b/surfer/viz.py
index 45e2ea3..f600d69 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -217,8 +217,8 @@ def _make_viewer(figure, n_row, n_col, title, scene_size, offscreen,
             # Triage: don't make TraitsUI if we don't have to
             if n_row == 1 and n_col == 1:
                 with warnings.catch_warnings(record=True):  # traits
-                    figure = mlab.figure(title, size=(w, h))
-                mlab.clf(figure)
+                    figure = mlab.figure(size=(w, h))
+                figure.name = title  # should set the figure title
                 figures = [[figure]]
                 _v = None
             else:

From dd9f3b5d2225dc78b339d61c7e7bc4d5316fc6ea Mon Sep 17 00:00:00 2001
From: Marijn van Vliet <w.m.vanvliet@gmail.com>
Date: Tue, 11 Feb 2020 18:06:59 +0000
Subject: [PATCH 22/46] Fix (#286)

---
 surfer/viz.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/surfer/viz.py b/surfer/viz.py
index f600d69..2b46ff1 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -3322,6 +3322,11 @@ def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
                 **kwargs)
             surf.actor.property.backface_culling = False
 
+            # There is a bug on some graphics cards concerning transparant
+            # overlays that is fixed by setting force_opaque.
+            if float(alpha) == 1:
+                surf.actor.actor.force_opaque = True
+
         # apply look up table if given
         if lut is not None:
             l_m = surf.module_manager.scalar_lut_manager

From cd2f074fe3c458c02fa9fd2d57e332ef64b8d179 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Feb 2020 07:31:29 -0500
Subject: [PATCH 23/46] MRG, FIX: Fix bug with scale_data_colormap (#287)

* FIX: Fix bug with scale_data_colormap

* FIX: Fix for deprecation

* FIX: One more
---
 setup.cfg                |  2 ++
 surfer/tests/test_viz.py | 10 +++++++---
 surfer/viz.py            | 20 +++++++++++++-------
 3 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 9bc24df..b869886 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -12,4 +12,6 @@ filterwarnings =
     ignore:.*ufunc size changed.*:RuntimeWarning
     ignore:Using or importing the ABCs:DeprecationWarning
     ignore:the imp module is deprecated in favour of importlib:DeprecationWarning
+    ignore:.*trait handler has been deprecated.*:DeprecationWarning
+    ignore:.*rich_compare.*metadata.*deprecated.*:DeprecationWarning
     ignore:Matplotlib is building the font cache using fc-list. This may take a moment.:UserWarning
diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 5bb6b18..206d1f2 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -214,10 +214,14 @@ def test_data():
 def test_data_limits():
     """Test handling of data limits."""
     _set_backend()
-    brain = Brain(*std_args)
-    surf_data = np.zeros(163842)
+    brain = Brain('fsaverage', 'both', 'inflated')
+    surf_data = np.linspace(0, 1, 163842)
     pytest.raises(ValueError, brain.add_data, surf_data, 0, 0)
-    brain.add_data(surf_data, 0, 1)
+    brain.add_data(surf_data, 0, 1, hemi='lh')
+    assert brain.data_dict['lh']['fmax'] == 1.
+    brain.add_data(surf_data, 0, 0.5, hemi='rh')
+    assert brain.data_dict['lh']['fmax'] == 1.  # unmodified
+    assert brain.data_dict['rh']['fmax'] == 0.5
     brain.close()
 
 
diff --git a/surfer/viz.py b/surfer/viz.py
index 2b46ff1..846d3e5 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -1200,7 +1200,7 @@ def time_label(x):
         self._data_dicts[hemi].append(data)
 
         self.scale_data_colormap(min, mid, max, transparent, center, alpha,
-                                 data)
+                                 data, hemi=hemi)
 
         if initial_time_index is not None:
             self.set_data_time_index(initial_time_index)
@@ -1951,7 +1951,8 @@ def _brain_color(self):
 
     @verbose
     def scale_data_colormap(self, fmin, fmid, fmax, transparent,
-                            center=None, alpha=1.0, data=None, verbose=None):
+                            center=None, alpha=1.0, data=None,
+                            hemi=None, verbose=None):
         """Scale the data colormap.
 
         The colormap may be sequential or divergent. When the colormap is
@@ -1994,15 +1995,19 @@ def scale_data_colormap(self, fmin, fmid, fmax, transparent,
             The data entry for which to scale the colormap.
             If None, will use the data dict from either the left or right
             hemisphere (in that order).
+        hemi : str | None
+            If None, all hemispheres will be scaled.
         verbose : bool, str, int, or None
             If not None, override default verbose level (see surfer.verbose).
         """
         divergent = center is not None
+        hemis = self._check_hemis(hemi)
+        del hemi
 
         # Get the original colormap
         if data is None:
-            for h in ['lh', 'rh']:
-                data = self.data_dict[h]
+            for hemi in hemis:
+                data = self.data_dict[hemi]
                 if data is not None:
                     break
         table = data["orig_ctable"].copy()
@@ -2015,14 +2020,15 @@ def scale_data_colormap(self, fmin, fmid, fmax, transparent,
 
         views = self._toggle_render(False)
         # Use the new colormap
-        for hemi in ['lh', 'rh']:
+        for hemi in hemis:
             data = self.data_dict[hemi]
             if data is not None:
                 for surf in data['surfaces']:
                     cmap = surf.module_manager.scalar_lut_manager
                     cmap.load_lut_from_list(lut / 255.)
                     if divergent:
-                        cmap.data_range = np.array([center-fmax, center+fmax])
+                        cmap.data_range = np.array(
+                            [center - fmax, center + fmax])
                     else:
                         cmap.data_range = np.array([fmin, fmax])
 
@@ -2050,7 +2056,7 @@ def scale_data_colormap(self, fmin, fmid, fmax, transparent,
                         l_m.load_lut_from_list(lut / 255.)
                         if divergent:
                             l_m.data_range = np.array(
-                                    [center-fmax, center+fmax])
+                                [center - fmax, center + fmax])
                         else:
                             l_m.data_range = np.array([fmin, fmax])
 

From 6962fe93522a34cdc806f4517407db5a1a6ac936 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jean-R=C3=A9mi=20KING?= <jeanremi.king@gmail.com>
Date: Fri, 21 Feb 2020 13:38:51 +0100
Subject: [PATCH 24/46] fix int (#288)

---
 surfer/viz.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index 846d3e5..df6763b 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2909,8 +2909,8 @@ def _get_fill_colors(cols, n_fill):
     if ind.size > 0:
         # choose the two colors between which there is the large step
         ind = ind[0] + 1
-        fillcols = np.r_[np.tile(cols[ind, :], (n_fill / 2, 1)),
-                         np.tile(cols[ind + 1, :], (n_fill - n_fill / 2, 1))]
+        fillcols = np.r_[np.tile(cols[ind, :], (n_fill // 2, 1)),
+                         np.tile(cols[ind + 1, :], (n_fill - n_fill // 2, 1))]
     else:
         # choose a color from the middle of the colormap
         fillcols = np.tile(cols[int(cols.shape[0] / 2), :], (n_fill, 1))

From f5761451fb9d98b33a06dbdaea4e72c6ffe6c149 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Feb 2020 07:39:39 -0500
Subject: [PATCH 25/46] Update __init__.py

---
 surfer/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/surfer/__init__.py b/surfer/__init__.py
index 5af068d..d5dee54 100644
--- a/surfer/__init__.py
+++ b/surfer/__init__.py
@@ -2,7 +2,7 @@
 from .utils import Surface, verbose, set_log_level, set_log_file  # noqa
 from .io import project_volume_data  # noqa
 
-__version__ = "0.10.dev0"
+__version__ = "0.10.0"
 
 set_log_file()  # initialize handlers
 set_log_level()  # initialize logging level

From bd2bbfe397ca9a261e42ce26186d91bda3fefc73 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Feb 2020 07:40:26 -0500
Subject: [PATCH 26/46] Update __init__.py

---
 surfer/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/surfer/__init__.py b/surfer/__init__.py
index d5dee54..54f3e64 100644
--- a/surfer/__init__.py
+++ b/surfer/__init__.py
@@ -2,7 +2,7 @@
 from .utils import Surface, verbose, set_log_level, set_log_file  # noqa
 from .io import project_volume_data  # noqa
 
-__version__ = "0.10.0"
+__version__ = "0.11.dev0"
 
 set_log_file()  # initialize handlers
 set_log_level()  # initialize logging level

From f67f4443c96025387b9e3adedf01a23e3d8d4714 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Feb 2020 08:01:14 -0500
Subject: [PATCH 27/46] FIX: CSS

---
 doc/_static/navy.css | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/_static/navy.css b/doc/_static/navy.css
index 79b3038..b8d38e7 100755
--- a/doc/_static/navy.css
+++ b/doc/_static/navy.css
@@ -514,9 +514,11 @@ ul.keywordmatches li.goodmatch a {
 }
 .sphx-glr-thumbcontainer .figure {
     width: 250px !important;
+    max-width: 250px !important;
 }
 .sphx-glr-thumbcontainer img {
     max-height: 250px !important;
+    max-width: 250px !important;
     width: 250px !important;
 }
 .sphx-glr-thumbcontainer a.internal {

From 696730654fc882c6a8b5a4bd48193904639c8849 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Fri, 21 Feb 2020 10:12:14 -0500
Subject: [PATCH 28/46] FIX: Update changes

---
 CHANGES | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGES b/CHANGES
index fae96a9..2da1611 100644
--- a/CHANGES
+++ b/CHANGES
@@ -6,6 +6,10 @@ Changelog
 Development version (0.10.dev0)
 -------------------------------
 
+
+Version 0.10.0
+--------------
+
 - Added an option to smooth to nearest vertex in :meth:`Brain.add_data` using
   ``smoothing_steps='nearest'``
 - Added options for using offscreen mode

From 7952423aab1fb59e048a4606d6f8411a513f3f3c Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 11:01:41 -0500
Subject: [PATCH 29/46] Set up CI with Azure Pipelines

[skip ci]
---
 azure-pipelines.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 azure-pipelines.yml

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
new file mode 100644
index 0000000..aa91291
--- /dev/null
+++ b/azure-pipelines.yml
@@ -0,0 +1,19 @@
+# Starter pipeline
+# Start with a minimal pipeline that you can customize to build and deploy your code.
+# Add steps that build, run tests, deploy, and more:
+# https://aka.ms/yaml
+
+trigger:
+- master
+
+pool:
+  vmImage: 'ubuntu-latest'
+
+steps:
+- script: echo Hello, world!
+  displayName: 'Run a one-line script'
+
+- script: |
+    echo Add other tasks to build, test, and deploy your project.
+    echo See https://aka.ms/yaml
+  displayName: 'Run a multi-line script'

From 9c43880da987e1c7bc03348928603f4aecec572a Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 10:34:42 -0500
Subject: [PATCH 30/46] FIX: Remove force render

---
 surfer/viz.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index df6763b..935b0f8 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2296,6 +2296,9 @@ def hide_colorbar(self, row=-1, col=-1):
 
     def close(self):
         """Close all figures and cleanup data structure."""
+        self._close()
+
+    def _close(self, force_render=True):
         for ri, ff in enumerate(self._figures):
             for ci, f in enumerate(ff):
                 if f is not None:
@@ -2305,7 +2308,8 @@ def close(self):
                         pass
                     self._figures[ri][ci] = None
 
-        _force_render([])
+        if force_render:
+            _force_render([])
 
         # should we tear down other variables?
         if getattr(self, '_v', None) is not None:
@@ -2316,7 +2320,8 @@ def close(self):
             self._v = None
 
     def __del__(self):
-        self.close()
+        # Forcing the GUI updates during GC seems to be problematic
+        self.close(force_render=False)
 
     ###########################################################################
     # SAVING OUTPUT

From 38db2038b8de9c0fdc33cc511b81f8885391e28d Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 11:10:55 -0500
Subject: [PATCH 31/46] ENH: Azure

---
 azure-pipelines.yml | 65 +++++++++++++++++++++++++++++++++------------
 1 file changed, 48 insertions(+), 17 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index aa91291..cc162c3 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -1,19 +1,50 @@
-# Starter pipeline
-# Start with a minimal pipeline that you can customize to build and deploy your code.
-# Add steps that build, run tests, deploy, and more:
-# https://aka.ms/yaml
-
 trigger:
-- master
-
-pool:
-  vmImage: 'ubuntu-latest'
-
-steps:
-- script: echo Hello, world!
-  displayName: 'Run a one-line script'
+  # start a new build for every push
+  batch: False
+  branches:
+    include:
+      - master
 
-- script: |
-    echo Add other tasks to build, test, and deploy your project.
-    echo See https://aka.ms/yaml
-  displayName: 'Run a multi-line script'
+jobs:
+- job: Windows
+  pool:
+    vmIMage: 'VS2017-Win2016'
+  strategy:
+    maxParallel: 4
+    matrix:
+      Python37-64bit:
+        PYTHON_VERSION: '3.7'
+        PYTHON_ARCH: 'x64'
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: $(PYTHON_VERSION)
+      architecture: $(PYTHON_ARCH)
+      addToPath: true
+  - powershell: |
+     pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9
+     pip install traits traitsui pyface vtk mayavi nibabel
+    displayName: 'Install pip dependencies'
+  - powershell: |
+     powershell make/get_fsaverage.ps1
+     $env:SUBJECTS_DIR = '$(System.DefaultWorkingDirectory)' + '\subjects'
+     Write-Host ("##vso[task.setvariable variable=PATH]" + $env:PATH)     SET SUBJECTS_DIR=%CD%\\subjects"
+    displayName: 'Get fsaverage'
+  - powershell: |
+     git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git
+     powershell gl-ci-helpers/appveyor/install_opengl.ps1
+    displayName: 'Get OpenGL'
+  - script: python setup.py develop
+    displayName: 'Install'
+  - script: pytest surfer --cov=surfer -v
+    displayName: 'Run tests'
+  - script: codecov --root %BUILD_REPOSITORY_LOCALPATH% -t %CODECOV_TOKEN%
+    displayName: 'Codecov'
+    env:
+      CODECOV_TOKEN: $(CODECOV_TOKEN)
+    condition: always()
+  - task: PublishTestResults@2
+    inputs:
+      testResultsFiles: 'junit-*.xml'
+      testRunTitle: 'Publish test results for Python $(python.version)'
+    condition: always()

From b7f25dba1fe53a1417a4722c4f87d0fc76ffd38c Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 11:15:37 -0500
Subject: [PATCH 32/46] FIX: Missed

---
 azure-pipelines.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index cc162c3..a4b0840 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -28,7 +28,7 @@ jobs:
   - powershell: |
      powershell make/get_fsaverage.ps1
      $env:SUBJECTS_DIR = '$(System.DefaultWorkingDirectory)' + '\subjects'
-     Write-Host ("##vso[task.setvariable variable=PATH]" + $env:PATH)     SET SUBJECTS_DIR=%CD%\\subjects"
+     Write-Host ("##vso[task.setvariable variable=PATH]" + $env:PATH)
     displayName: 'Get fsaverage'
   - powershell: |
      git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git

From 963c9b655704bb0257f95836d90e034a441068d2 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 11:22:12 -0500
Subject: [PATCH 33/46] FIX: Missed again

---
 azure-pipelines.yml | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index a4b0840..1b25558 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -7,6 +7,8 @@ trigger:
 
 jobs:
 - job: Windows
+  variables:
+    PIP_CACHE_FOLDER: $(Pipeline.Workspace)/.cache/pip
   pool:
     vmIMage: 'VS2017-Win2016'
   strategy:
@@ -21,14 +23,19 @@ jobs:
       versionSpec: $(PYTHON_VERSION)
       architecture: $(PYTHON_ARCH)
       addToPath: true
+- task: Cache@2
+  inputs:
+    key: 'python -VV'
+    path: $(PIP_CACHE_FOLDER)
+  displayName: Cache pip packages
   - powershell: |
-     pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9
-     pip install traits traitsui pyface vtk mayavi nibabel
+     pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9 --cache-dir $(PIP_CACHE_FOLDER)
+     pip install traits traitsui pyface vtk mayavi nibabel --cache-dir $(PIP_CACHE_FOLDER)
     displayName: 'Install pip dependencies'
   - powershell: |
      powershell make/get_fsaverage.ps1
      $env:SUBJECTS_DIR = '$(System.DefaultWorkingDirectory)' + '\subjects'
-     Write-Host ("##vso[task.setvariable variable=PATH]" + $env:PATH)
+     Write-Host ("##vso[task.setvariable variable=SUBJECTS_DIR]" + $env:SUBJECTS_DIR)
     displayName: 'Get fsaverage'
   - powershell: |
      git clone --depth 1 git://github.com/pyvista/gl-ci-helpers.git

From b3522d472f87a3dfa86396c25d1b022a81d3d2d8 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 11:29:01 -0500
Subject: [PATCH 34/46] FIX: Try again

---
 azure-pipelines.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 1b25558..7d98a8e 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -23,11 +23,11 @@ jobs:
       versionSpec: $(PYTHON_VERSION)
       architecture: $(PYTHON_ARCH)
       addToPath: true
-- task: Cache@2
-  inputs:
-    key: 'python -VV'
-    path: $(PIP_CACHE_FOLDER)
-  displayName: Cache pip packages
+  - task: Cache@2
+    inputs:
+      key: 'pip'
+      path: $(PIP_CACHE_FOLDER)
+    displayName: Cache pip packages
   - powershell: |
      pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9 --cache-dir $(PIP_CACHE_FOLDER)
      pip install traits traitsui pyface vtk mayavi nibabel --cache-dir $(PIP_CACHE_FOLDER)

From 11afc4ae48623d9ff04872ba573f892dd4d7a831 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 11:49:21 -0500
Subject: [PATCH 35/46] FIX: Wrong call

---
 surfer/viz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index 935b0f8..8df843c 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2321,7 +2321,7 @@ def _close(self, force_render=True):
 
     def __del__(self):
         # Forcing the GUI updates during GC seems to be problematic
-        self.close(force_render=False)
+        self._close(force_render=False)
 
     ###########################################################################
     # SAVING OUTPUT

From 283a5800228176c80bec1a83f1b7d80229e8a9b0 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Wed, 26 Feb 2020 11:56:55 -0500
Subject: [PATCH 36/46] FIX: Explicit close/del

---
 surfer/tests/test_viz.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/surfer/tests/test_viz.py b/surfer/tests/test_viz.py
index 206d1f2..ac96fe2 100644
--- a/surfer/tests/test_viz.py
+++ b/surfer/tests/test_viz.py
@@ -1,3 +1,4 @@
+import gc
 import os
 import os.path as op
 from os.path import join as pjoin
@@ -210,6 +211,17 @@ def test_data():
     brain.close()
 
 
+@requires_fsaverage()
+def test_close():
+    """Test that close and del actually work."""
+    _set_backend()
+    brain = Brain('fsaverage', 'both', 'inflated')
+    brain.close()
+    brain.__del__()
+    del brain
+    gc.collect()
+
+
 @requires_fsaverage()
 def test_data_limits():
     """Test handling of data limits."""

From ce7ac2dbcd290765fbb1ca80981faded3a48f20c Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 27 Feb 2020 11:26:34 -0500
Subject: [PATCH 37/46] FIX: Safer del

---
 surfer/viz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index 8df843c..b6579c9 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2299,7 +2299,7 @@ def close(self):
         self._close()
 
     def _close(self, force_render=True):
-        for ri, ff in enumerate(self._figures):
+        for ri, ff in enumerate(getattr(self, '_figures', [])):
             for ci, f in enumerate(ff):
                 if f is not None:
                     try:

From 1afce4bf3e4e122909dc59a6926adfea50cca076 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Mon, 18 May 2020 13:30:31 -0400
Subject: [PATCH 38/46] STY: Dont log info messages by default (#293)

* FIX: Verbose

* FIX: MNE vers
---
 .travis.yml     | 6 +++++-
 surfer/io.py    | 2 +-
 surfer/utils.py | 6 +++---
 surfer/viz.py   | 7 ++++---
 4 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 523612e..9896ed0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -40,7 +40,11 @@ before_install:
     - pip install vtk
     - pip install mayavi
     - mkdir -p $SUBJECTS_DIR
-    - pip install "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
+    - if [ "${PYTHON_VERSION}" == "3.5" ]; then
+        pip install "mne<0.21";
+      else
+        pip install "https://api.github.com/repos/mne-tools/mne-python/zipball/master";
+      fi;
     - python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)"
 
 install:
diff --git a/surfer/io.py b/surfer/io.py
index efda923..69e7ba4 100644
--- a/surfer/io.py
+++ b/surfer/io.py
@@ -229,7 +229,7 @@ def project_volume_data(filepath, hemi, reg_file=None, subject_id=None,
     # Execute the command
     out_file = mktemp(prefix="pysurfer-v2s", suffix='.mgz')
     cmd_list.extend(["--o", out_file])
-    logger.info(" ".join(cmd_list))
+    logger.debug(" ".join(cmd_list))
     p = Popen(cmd_list, stdout=PIPE, stderr=PIPE, env=env)
     stdout, stderr = p.communicate()
     out = p.returncode
diff --git a/surfer/utils.py b/surfer/utils.py
index 4a6e4cf..0b1f9ed 100644
--- a/surfer/utils.py
+++ b/surfer/utils.py
@@ -608,7 +608,7 @@ def _nearest(vertices, adj_mat):
 
 def _smooth(vertices, adj_mat, smoothing_steps):
     from scipy import sparse
-    logger.info("Updating smoothing matrix, be patient..")
+    logger.debug("Updating smoothing matrix, be patient..")
     e = adj_mat.copy()
     e.data[e.data == 2] = 1
     n_vertices = e.shape[0]
@@ -626,7 +626,7 @@ def _smooth(vertices, adj_mat, smoothing_steps):
 
         smooth_mat = scale_mat * e_use[idx_use, :] * smooth_mat
 
-        logger.info("Smoothing matrix creation, step %d" % (k + 1))
+        logger.debug("Smoothing matrix creation, step %d" % (k + 1))
         if smoothing_steps is None and len(idx_use) >= n_vertices:
             break
 
@@ -690,7 +690,7 @@ def coord_to_label(subject_id, coord, label, hemi='lh', n_steps=30,
     idx = np.where(data.ravel() > 0)[0]
     # Write label
     label_fname = label + '-' + hemi + '.label'
-    logger.info("Saving label : %s" % label_fname)
+    logger.debug("Saving label : %s" % label_fname)
     f = open(label_fname, 'w')
     f.write('#label at %s from subject %s\n' % (coord, subject_id))
     f.write('%d\n' % len(idx))
diff --git a/surfer/viz.py b/surfer/viz.py
index b6579c9..f0af97d 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -2977,12 +2977,13 @@ def _scale_mayavi_lut(lut_table, fmin, fmid, fmax, transparent,
 
     trstr = ['(opaque)', '(transparent)']
     if divergent:
-        logger.info(
+        logger.debug(
             "colormap divergent: center=%0.2e, [%0.2e, %0.2e, %0.2e] %s"
             % (center, fmin, fmid, fmax, trstr[transparent]))
     else:
-        logger.info("colormap sequential: [%0.2e, %0.2e, %0.2e] %s"
-                    % (fmin, fmid, fmax, trstr[transparent]))
+        logger.debug(
+            "colormap sequential: [%0.2e, %0.2e, %0.2e] %s"
+            % (fmin, fmid, fmax, trstr[transparent]))
 
     n_colors = lut_table.shape[0]
 

From 09513f9dd1a18af70b319a15872b66302288ccfd Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Mon, 18 May 2020 14:24:55 -0400
Subject: [PATCH 39/46] ENH: Move up to 3.8 (#294)

* ENH: Move up to 3.8

* FIX: Newer

* FIX: Newer
---
 .travis.yml     | 26 ++++++++++++++++----------
 doc/install.rst |  6 +-----
 setup.py        |  4 +++-
 3 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 9896ed0..ca83d67 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,11 +1,11 @@
 language: c
 sudo: false
-dist: xenial
+dist: bionic
 services:
     - xvfb
 env:
-    global: PYTHON_VERSION=3.7
-            CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt>=5.9 coverage pytest pytest-cov flake8 pygments traits traitsui pyface"
+    global: PYTHON_VERSION=3.8
+            CONDA_DEPENDENCIES="numpy scipy matplotlib pyqt coverage pytest pytest-cov flake8 pygments traits traitsui pyface"
             PIP_DEPENDENCIES="codecov pytest-sugar pytest-faulthandler nibabel imageio imageio-ffmpeg"
             DISPLAY=:99.0
             SUBJECTS_DIR=~/subjects
@@ -18,10 +18,15 @@ matrix:
             apt:
               packages:
                 - mencoder
+                - libosmesa6
+                - libglx-mesa0
+                - libopengl0
+                - libglx0
+                - libdbus-1-3
 
         # 3.5, no mencoder
         - os: linux
-          env: PYTHON_VERSION=3.5
+          env: PYTHON_VERSION=3.6
                CONDA_DEPENDENCIES="numpy scipy matplotlib coverage pytest pytest-cov flake8"
                PIP_DEPENDENCIES="codecov pytest-sugar nibabel imageio imageio-ffmpeg"
 
@@ -37,14 +42,15 @@ before_install:
       fi;
     - git clone https://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda.sh
-    - pip install vtk
-    - pip install mayavi
-    - mkdir -p $SUBJECTS_DIR
-    - if [ "${PYTHON_VERSION}" == "3.5" ]; then
-        pip install "mne<0.21";
+    - if [ "${PYTHON_VERSION}" == "3.6" ]; then
+        pip install --only-binary ":all:" "vtk<9";
+        pip install mayavi;
       else
-        pip install "https://api.github.com/repos/mne-tools/mne-python/zipball/master";
+        pip install --only-binary ":all:" -f "https://vtk.org/download" "vtk>=9";
+        pip install https://github.com/enthought/mayavi/zipball/master;
       fi;
+    - mkdir -p $SUBJECTS_DIR
+    - pip install "https://api.github.com/repos/mne-tools/mne-python/zipball/master";
     - python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)"
 
 install:
diff --git a/doc/install.rst b/doc/install.rst
index 91b5691..5fc7d13 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -30,10 +30,7 @@ install from your local source directory::
 Dependencies
 ~~~~~~~~~~~~
 
-PySurfer works on Python 2.7 and 3.6+.
-(Older Python 3 versions will probably work, but are not tested.)
-
-To use PySurfer, you will need to have the following Python packages:
+PySurfer works on Python 3.6+ and requires the following Python packages:
 
 * numpy_
 * scipy_
@@ -91,4 +88,3 @@ as a static PNG image, or ``'x3d'`` to render it using
 If you are having trouble getting started using PySurfer, please describe the problem on the `nipy mailing list`_.
 
 .. include:: links_names.txt
-
diff --git a/setup.py b/setup.py
index 7df6fbd..3d53a9a 100644
--- a/setup.py
+++ b/setup.py
@@ -66,6 +66,8 @@
           platforms='any',
           packages=['surfer', 'surfer.tests'],
           scripts=['bin/pysurfer'],
-          install_requires=['numpy', 'scipy', 'matplotlib', 'nibabel >= 1.2', 'mayavi'],
+          python_requires='>=3.6',
+          install_requires=[
+              'numpy', 'scipy', 'matplotlib', 'nibabel >= 1.2', 'mayavi'],
           extras_require={'save_movie': ['imageio >= 1.5']},
           )

From b0ca3a15b4c3b816de5b78f02de5c2cf8907ee9d Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Thu, 11 Jun 2020 12:02:39 -0400
Subject: [PATCH 40/46] ENH: Add FXAA option (#295)

* ENH: Add FXAA option

* FIX: Mayavi for VTK9
---
 appveyor.yml        |  2 +-
 azure-pipelines.yml |  2 +-
 surfer/viz.py       | 22 ++++++++++++++--------
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 39520c5..edf1435 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -7,7 +7,7 @@ install:
   - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
   - "python --version"
   - "pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9"
-  - "pip install traits traitsui pyface vtk mayavi nibabel"
+  - "pip install traits traitsui pyface vtk https://github.com/enthought/mayavi/archive/master.zip nibabel"
   - "powershell make/get_fsaverage.ps1"
   - "python setup.py develop"
   - "SET SUBJECTS_DIR=%CD%\\subjects"
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 7d98a8e..bb560b7 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -30,7 +30,7 @@ jobs:
     displayName: Cache pip packages
   - powershell: |
      pip install numpy scipy matplotlib nose pillow pytest pytest-cov pytest-faulthandler coverage imageio imageio-ffmpeg codecov pyqt5==5.9 --cache-dir $(PIP_CACHE_FOLDER)
-     pip install traits traitsui pyface vtk mayavi nibabel --cache-dir $(PIP_CACHE_FOLDER)
+     pip install traits traitsui pyface vtk https://github.com/enthought/mayavi/archive/master.zip nibabel --cache-dir $(PIP_CACHE_FOLDER)
     displayName: 'Install pip dependencies'
   - powershell: |
      powershell make/get_fsaverage.ps1
diff --git a/surfer/viz.py b/surfer/viz.py
index f0af97d..014b19a 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -190,7 +190,7 @@ def _force_render(figures):
 
 
 def _make_viewer(figure, n_row, n_col, title, scene_size, offscreen,
-                 interaction='trackball'):
+                 interaction='trackball', antialias=True):
     """Triage viewer creation
 
     If n_row == n_col == 1, then we can use a Mayavi figure, which
@@ -229,11 +229,13 @@ def _make_viewer(figure, n_row, n_col, title, scene_size, offscreen,
                     for f in figure:
                         f.scene.interactor.interactor_style = \
                             tvtk.InteractorStyleTerrain()
-            for figure in figures:
-                for f in figure:
-                    # on a non-testing backend, and using modern VTK/Mayavi
-                    if hasattr(getattr(f.scene, 'renderer', None), 'use_fxaa'):
-                        f.scene.renderer.use_fxaa = True
+            if antialias:
+                for figure in figures:
+                    for f in figure:
+                        # on a non-testing backend, and using modern VTK/Mayavi
+                        if hasattr(getattr(f.scene, 'renderer', None),
+                                   'use_fxaa'):
+                            f.scene.renderer.use_fxaa = True
     else:
         if isinstance(figure, int):  # use figure with specified id
             figure = [mlab.figure(figure, size=scene_size)]
@@ -374,6 +376,9 @@ class Brain(object):
         camera.
     units : str
         Can be 'm' or 'mm' (default).
+    antialias : bool
+        If True (default), turn on antialiasing. Can be problematic for
+        some renderers (e.g., software rendering with MESA).
 
     Attributes
     ----------
@@ -397,7 +402,8 @@ def __init__(self, subject_id, hemi, surf, title=None,
                  cortex="classic", alpha=1.0, size=800, background="black",
                  foreground=None, figure=None, subjects_dir=None,
                  views=['lat'], offset=True, show_toolbar=False,
-                 offscreen='auto', interaction='trackball', units='mm'):
+                 offscreen='auto', interaction='trackball', units='mm',
+                 antialias=True):
 
         if not isinstance(interaction, string_types) or \
                 interaction not in ('trackball', 'terrain'):
@@ -448,7 +454,7 @@ def __init__(self, subject_id, hemi, surf, title=None,
         del background, foreground
         figures, _v = _make_viewer(figure, n_row, n_col, title,
                                    self._scene_size, offscreen,
-                                   interaction)
+                                   interaction, antialias)
         self._figures = figures
         self._v = _v
         self._window_backend = 'Mayavi' if self._v is None else 'TraitsUI'

From 9e5fe1f0301c9af77d1e9b86b4c74a38c094e459 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Tue, 23 Jun 2020 10:32:34 -0400
Subject: [PATCH 41/46] MRG, MAINT: Simpler vector params (#291)

* MAINT: Simpler vector params

* FIX: Undo auto scaling

* FIX: Dup

* FIX: URL

* FIX: Better

* FIX: More tolerant of type
---
 .circleci/config.yml |  2 +-
 .travis.yml          |  2 +-
 surfer/viz.py        | 46 ++++++++++++++++++--------------------------
 3 files changed, 21 insertions(+), 29 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 0071f48..18f52af 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -49,7 +49,7 @@ jobs:
             command: |
               python -m pip install --user -q --upgrade pip numpy
               python -m pip install --user -q --upgrade --progress-bar off scipy matplotlib vtk pyqt5 pyqt5-sip nibabel sphinx numpydoc pillow imageio imageio-ffmpeg sphinx-gallery
-              python -m pip install --user -q --upgrade mayavi "https://api.github.com/repos/mne-tools/mne-python/zipball/master"
+              python -m pip install --user -q --upgrade mayavi "https://github.com/mne-tools/mne-python/archive/master.zip"
         - save_cache:
             key: pip-cache
             paths:
diff --git a/.travis.yml b/.travis.yml
index ca83d67..569e241 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -50,7 +50,7 @@ before_install:
         pip install https://github.com/enthought/mayavi/zipball/master;
       fi;
     - mkdir -p $SUBJECTS_DIR
-    - pip install "https://api.github.com/repos/mne-tools/mne-python/zipball/master";
+    - pip install "https://github.com/mne-tools/mne-python/archive/master.zip"
     - python -c "import mne; mne.datasets.fetch_fsaverage(verbose=True)"
 
 install:
diff --git a/surfer/viz.py b/surfer/viz.py
index 014b19a..e42c491 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -423,7 +423,7 @@ def __init__(self, subject_id, hemi, surf, title=None,
             title = subject_id
         self.subject_id = subject_id
 
-        if not isinstance(views, list):
+        if not isinstance(views, (list, tuple)):
             views = [views]
         n_row = len(views)
 
@@ -1095,15 +1095,13 @@ def add_data(self, array, min=None, max=None, thresh=None,
             smooth_mat = None
 
         magnitude = None
-        magnitude_max = None
         if array.ndim == 3:
             if array.shape[1] != 3:
                 raise ValueError('If array has 3 dimensions, array.shape[1] '
                                  'must equal 3, got %s' % (array.shape[1],))
             magnitude = np.linalg.norm(array, axis=1)
             if scale_factor is None:
-                distance = np.sum([array[:, dim, :].ptp(axis=0).max() ** 2
-                                   for dim in range(3)])
+                distance = 4 * np.linalg.norm(array, axis=1).max()
                 if distance == 0:
                     scale_factor = 1
                 else:
@@ -1111,7 +1109,6 @@ def add_data(self, array, min=None, max=None, thresh=None,
                                     (4 * array.shape[0] ** (0.33)))
             if self._units == 'm':
                 scale_factor = scale_factor / 1000.
-            magnitude_max = magnitude.max()
         elif array.ndim not in (1, 2):
             raise ValueError('array has must have 1, 2, or 3 dimensions, '
                              'got (%s)' % (array.ndim,))
@@ -1188,7 +1185,7 @@ def time_label(x):
             if brain['hemi'] == hemi:
                 s, ct, bar, gl = brain['brain'].add_data(
                     array, min, mid, max, thresh, lut, colormap, alpha,
-                    colorbar, layer_id, smooth_mat, magnitude, magnitude_max,
+                    colorbar, layer_id, smooth_mat, magnitude,
                     scale_factor, vertices, vector_alpha, **kwargs)
                 surfs.append(s)
                 bars.append(bar)
@@ -2115,13 +2112,11 @@ def set_data_time_index(self, time_idx, interpolation='quadratic'):
                     if vectors is not None:
                         vectors = vectors[:, :, time_idx]
 
-                vector_values = scalar_data.copy()
                 if data['smooth_mat'] is not None:
                     scalar_data = data['smooth_mat'] * scalar_data
                 for brain in self.brains:
                     if brain.hemi == hemi:
-                        brain.set_data(data['layer_id'], scalar_data,
-                                       vectors, vector_values)
+                        brain.set_data(data['layer_id'], scalar_data, vectors)
                 del brain
                 data["time_idx"] = time_idx
 
@@ -3225,24 +3220,25 @@ def _remove_scalar_data(self, array_id):
         self._mesh_clones.pop(array_id).remove()
         self._mesh_dataset.point_data.remove_array(array_id)
 
-    def _add_vector_data(self, vectors, vector_values, fmin, fmid, fmax,
-                         scale_factor_norm, vertices, vector_alpha, lut):
+    def _add_vector_data(self, vectors, fmin, fmid, fmax,
+                         scale_factor, vertices, vector_alpha, lut):
         vertices = slice(None) if vertices is None else vertices
         x, y, z = np.array(self._geo_mesh.data.points.data)[vertices].T
         vector_alpha = min(vector_alpha, 0.9999999)
         with warnings.catch_warnings(record=True):  # HasTraits
             quiver = mlab.quiver3d(
                 x, y, z, vectors[:, 0], vectors[:, 1], vectors[:, 2],
-                scalars=vector_values, colormap='hot', vmin=fmin,
+                colormap='hot', vmin=fmin, scale_mode='vector',
                 vmax=fmax, figure=self._f, opacity=vector_alpha)
 
         # Enable backface culling
         quiver.actor.property.backface_culling = True
         quiver.mlab_source.update()
 
-        # Compute scaling for the glyphs
-        quiver.glyph.glyph.scale_factor = (scale_factor_norm *
-                                           vector_values.max())
+        # Set scaling for the glyphs
+        quiver.glyph.glyph.scale_factor = scale_factor
+        quiver.glyph.glyph.clamping = False
+        quiver.glyph.glyph.range = (0., 1.)
 
         # Scale colormap used for the glyphs
         l_m = quiver.parent.vector_lut_manager
@@ -3293,7 +3289,7 @@ def add_overlay(self, old, **kwargs):
 
     @verbose
     def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
-                 colorbar, layer_id, smooth_mat, magnitude, magnitude_max,
+                 colorbar, layer_id, smooth_mat, magnitude,
                  scale_factor, vertices, vector_alpha, **kwargs):
         """Add data to the brain"""
         # Calculate initial data to plot
@@ -3308,7 +3304,6 @@ def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
             array_plot = magnitude[:, 0]
         else:
             raise ValueError("data has to be 1D, 2D, or 3D")
-        vector_values = array_plot
         if smooth_mat is not None:
             array_plot = smooth_mat * array_plot
 
@@ -3316,16 +3311,13 @@ def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
         array_plot = _prepare_data(array_plot)
 
         array_id, pipe = self._add_scalar_data(array_plot)
-        scale_factor_norm = None
         if array.ndim == 3:
-            scale_factor_norm = scale_factor / magnitude_max
             vectors = array[:, :, 0].copy()
             glyphs = self._add_vector_data(
-                vectors, vector_values, fmin, fmid, fmax,
-                scale_factor_norm, vertices, vector_alpha, lut)
+                vectors, fmin, fmid, fmax,
+                scale_factor, vertices, vector_alpha, lut)
         else:
             glyphs = None
-        del scale_factor
         mesh = pipe.parent
         if thresh is not None:
             if array_plot.min() >= thresh:
@@ -3364,7 +3356,7 @@ def add_data(self, array, fmin, fmid, fmax, thresh, lut, colormap, alpha,
 
         self.data[layer_id] = dict(
             array_id=array_id, mesh=mesh, glyphs=glyphs,
-            scale_factor_norm=scale_factor_norm)
+            scale_factor=scale_factor)
         return surf, orig_ctable, bar, glyphs
 
     def add_annotation(self, annot, ids, cmap, **kwargs):
@@ -3475,7 +3467,7 @@ def remove_data(self, layer_id):
         self._remove_scalar_data(data['array_id'])
         self._remove_vector_data(data['glyphs'])
 
-    def set_data(self, layer_id, values, vectors=None, vector_values=None):
+    def set_data(self, layer_id, values, vectors=None):
         """Set displayed data values and vectors."""
         data = self.data[layer_id]
         self._mesh_dataset.point_data.get_array(
@@ -3492,12 +3484,12 @@ def set_data(self, layer_id, values, vectors=None, vector_values=None):
 
             # Update glyphs
             q.mlab_source.vectors = vectors
-            q.mlab_source.scalars = vector_values
             q.mlab_source.update()
 
             # Update changed parameters, and glyph scaling
-            q.glyph.glyph.scale_factor = (data['scale_factor_norm'] *
-                                          values.max())
+            q.glyph.glyph.scale_factor = data['scale_factor']
+            q.glyph.glyph.range = (0., 1.)
+            q.glyph.glyph.clamping = False
             l_m.load_lut_from_list(lut / 255.)
             l_m.data_range = data_range
 

From 85e9e6ca20586957dbbbf53b188be91380211ff1 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Tue, 23 Jun 2020 10:44:12 -0400
Subject: [PATCH 42/46] MAINT: Bump version

---
 CHANGES            | 12 ++++++++++--
 surfer/__init__.py |  2 +-
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/CHANGES b/CHANGES
index 2da1611..a8150e1 100644
--- a/CHANGES
+++ b/CHANGES
@@ -3,8 +3,16 @@ Changelog
 
 .. currentmodule:: surfer
 
-Development version (0.10.dev0)
--------------------------------
+Version 0.11.0
+--------------
+
+- Minimum Python version increased to 3.6
+- Add support to turn off full-screen antialiasing, which can be problematic on
+  some drivers (e.g., MESA software rendering on Linux)
+- Simplification and refactoring of vector-valued data plotting
+- Removal of unnecessary ``info`` log messages about smoothing matrix and
+  colormap generation (changed to ``debug`` level)
+- Clean up of exit functions like ``__del__`` to avoid segfaults
 
 
 Version 0.10.0
diff --git a/surfer/__init__.py b/surfer/__init__.py
index 54f3e64..d1297a4 100644
--- a/surfer/__init__.py
+++ b/surfer/__init__.py
@@ -2,7 +2,7 @@
 from .utils import Surface, verbose, set_log_level, set_log_file  # noqa
 from .io import project_volume_data  # noqa
 
-__version__ = "0.11.dev0"
+__version__ = "0.11.0"
 
 set_log_file()  # initialize handlers
 set_log_level()  # initialize logging level

From f02cca8f1e10f21996ab85d292c8a423faa11af4 Mon Sep 17 00:00:00 2001
From: Eric Larson <larson.eric.d@gmail.com>
Date: Tue, 23 Jun 2020 13:07:18 -0400
Subject: [PATCH 43/46] MAINT: Bump version

---
 surfer/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/surfer/__init__.py b/surfer/__init__.py
index d1297a4..65a815b 100644
--- a/surfer/__init__.py
+++ b/surfer/__init__.py
@@ -2,7 +2,7 @@
 from .utils import Surface, verbose, set_log_level, set_log_file  # noqa
 from .io import project_volume_data  # noqa
 
-__version__ = "0.11.0"
+__version__ = "0.12.dev0"
 
 set_log_file()  # initialize handlers
 set_log_level()  # initialize logging level

From 2512fc600dcc7428c73e159e375060af5f198195 Mon Sep 17 00:00:00 2001
From: Cristi Donos <cristidonos@yahoo.com>
Date: Wed, 11 Nov 2020 14:41:01 +0200
Subject: [PATCH 44/46] option to apply xfrom from surface files

---
 surfer/utils.py | 16 ++++++++++++++--
 surfer/viz.py   | 13 ++++++++++---
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/surfer/utils.py b/surfer/utils.py
index 19d6cf3..7fcb048 100644
--- a/surfer/utils.py
+++ b/surfer/utils.py
@@ -79,10 +79,14 @@ class Surface(object):
         If None, do not change coordinates (default).
     units : str
         Can be 'm' or 'mm' (default).
+    apply_surf_xfm: bool | False
+        If True, the transform defined by xras, yras,zras and cras
+        in Freesurfer's surface file will be applied to the surface
+        node coordinates.
     """
 
     def __init__(self, subject_id, hemi, surf, subjects_dir=None,
-                 offset=None, units='mm'):
+                 offset=None, units='mm', apply_surf_xfm=False):
         """Surface
 
         Parameters
@@ -97,6 +101,10 @@ def __init__(self, subject_id, hemi, surf, subjects_dir=None,
             If 0.0, the surface will be offset such that the medial
             wall is aligned with the origin. If None, no offset will
             be applied. If != 0.0, an additional offset will be used.
+        apply_surf_xfm: bool | False
+            If True, the transform defined by xras, yras,zras and cras
+            in Freesurfer's surface file will be applied to the surface
+            node coordinates.
         """
         if hemi not in ['lh', 'rh']:
             raise ValueError('hemi must be "lh" or "rh')
@@ -108,6 +116,7 @@ def __init__(self, subject_id, hemi, surf, subjects_dir=None,
         self.faces = None
         self.nn = None
         self.units = _check_units(units)
+        self.apply_surf_xfm = apply_surf_xfm
 
         subjects_dir = _get_subjects_dir(subjects_dir)
         self.data_path = op.join(subjects_dir, subject_id)
@@ -115,7 +124,7 @@ def __init__(self, subject_id, hemi, surf, subjects_dir=None,
     def load_geometry(self):
         surf_path = op.join(self.data_path, "surf",
                             "%s.%s" % (self.hemi, self.surf))
-        coords, faces = nib.freesurfer.read_geometry(surf_path)
+        coords, faces, metadata = nib.freesurfer.read_geometry(surf_path, read_metadata=True)
         if self.units == 'm':
             coords /= 1000.
         if self.offset is not None:
@@ -123,6 +132,9 @@ def load_geometry(self):
                 coords[:, 0] -= (np.max(coords[:, 0]) + self.offset)
             else:
                 coords[:, 0] -= (np.min(coords[:, 0]) + self.offset)
+        if self.apply_surf_xfm:
+            sxfm = np.vstack([np.stack([metadata[k] for k in metadata.keys() if 'ras' in k]).T, np.array([0, 0, 0, 1])])
+            coords = np.hstack([coords, np.ones((coords.shape[0], 1))]).dot(np.linalg.inv(sxfm))[:,0:3]
         nn = _compute_normals(coords, faces)
 
         if self.coords is None:
diff --git a/surfer/viz.py b/surfer/viz.py
index 6c2204b..2ad30d0 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -365,6 +365,10 @@ class Brain(object):
         camera.
     units : str
         Can be 'm' or 'mm' (default).
+    apply_surf_xfm: bool | False
+        If True, the transform defined by xras, yras,zras and cras
+        in Freesurfer's surface file will be applied to the surface
+        node coordinates.
 
     Attributes
     ----------
@@ -387,7 +391,8 @@ def __init__(self, subject_id, hemi, surf, title=None,
                  cortex="classic", alpha=1.0, size=800, background="black",
                  foreground=None, figure=None, subjects_dir=None,
                  views=['lat'], offset=True, show_toolbar=False,
-                 offscreen=False, interaction='trackball', units='mm'):
+                 offscreen=False, interaction='trackball', units='mm',
+                 apply_surf_xfm=False):
 
         if not isinstance(interaction, string_types) or \
                 interaction not in ('trackball', 'terrain'):
@@ -406,6 +411,7 @@ def __init__(self, subject_id, hemi, surf, title=None,
         if title is None:
             title = subject_id
         self.subject_id = subject_id
+        self.apply_surf_xfm = apply_surf_xfm
 
         if not isinstance(views, list):
             views = [views]
@@ -426,7 +432,7 @@ def __init__(self, subject_id, hemi, surf, title=None,
         for h in geo_hemis:
             # Initialize a Surface object as the geometry
             geo = Surface(subject_id, h, surf, subjects_dir, offset,
-                          units=self._units)
+                          units=self._units, apply_surf_xfm=self.apply_surf_xfm)
             # Load in the geometry and (maybe) curvature
             geo.load_geometry()
             if geo_curv:
@@ -1623,7 +1629,8 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             foci_coords = np.atleast_2d(coords)
         else:
             foci_surf = Surface(self.subject_id, hemi, map_surface,
-                                subjects_dir=self.subjects_dir)
+                                subjects_dir=self.subjects_dir,
+                                apply_surf_xfm=self.apply_surf_xfm)
             foci_surf.load_geometry()
             foci_vtxs = utils.find_closest_vertices(foci_surf.coords, coords)
             foci_coords = self.geo[hemi].coords[foci_vtxs]

From d3749dc5605f7200731ef5c716f6aebe4fd65b31 Mon Sep 17 00:00:00 2001
From: Cristi Donos <cristidonos@yahoo.com>
Date: Wed, 11 Nov 2020 19:21:33 +0200
Subject: [PATCH 45/46] merged changes by CD on top of nipy's f02cca8 version
 from Jun 23

---
 surfer/viz.py | 105 +++++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 91 insertions(+), 14 deletions(-)

diff --git a/surfer/viz.py b/surfer/viz.py
index e42c491..ed934bf 100644
--- a/surfer/viz.py
+++ b/surfer/viz.py
@@ -379,6 +379,10 @@ class Brain(object):
     antialias : bool
         If True (default), turn on antialiasing. Can be problematic for
         some renderers (e.g., software rendering with MESA).
+    apply_surf_xfm: bool | False
+        If True, the transform defined by xras, yras,zras and cras
+        in Freesurfer's surface file will be applied to the surface
+        node coordinates.
 
     Attributes
     ----------
@@ -403,7 +407,7 @@ def __init__(self, subject_id, hemi, surf, title=None,
                  foreground=None, figure=None, subjects_dir=None,
                  views=['lat'], offset=True, show_toolbar=False,
                  offscreen='auto', interaction='trackball', units='mm',
-                 antialias=True):
+                 antialias=True, apply_surf_xfm=False):
 
         if not isinstance(interaction, string_types) or \
                 interaction not in ('trackball', 'terrain'):
@@ -422,6 +426,7 @@ def __init__(self, subject_id, hemi, surf, title=None,
         if title is None:
             title = subject_id
         self.subject_id = subject_id
+        self.apply_surf_xfm = apply_surf_xfm
 
         if not isinstance(views, (list, tuple)):
             views = [views]
@@ -442,7 +447,7 @@ def __init__(self, subject_id, hemi, surf, title=None,
         for h in geo_hemis:
             # Initialize a Surface object as the geometry
             geo = Surface(subject_id, h, surf, subjects_dir, offset,
-                          units=self._units)
+                          units=self._units, apply_surf_xfm=self.apply_surf_xfm)
             # Load in the geometry and (maybe) curvature
             geo.load_geometry()
             if geo_curv:
@@ -1643,7 +1648,7 @@ def add_morphometry(self, measure, grayscale=False, hemi=None,
 
     def add_foci(self, coords, coords_as_verts=False, map_surface=None,
                  scale_factor=1, color="white", alpha=1, name=None,
-                 hemi=None, **kwargs):
+                 hemi=None, data=None, colormap=None, **kwargs):
         """Add spherical foci, possibly mapping to displayed surf.
 
         The foci spheres can be displayed at the coordinates given, or
@@ -1673,6 +1678,14 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             If None, it is assumed to belong to the hemipshere being
             shown. If two hemispheres are being shown, an error will
             be thrown.
+        data : numpy array
+            None or 1D array the same size as the number of foci (n,).
+            Spheres sizes will be coded using the absolute values of data.
+            If data is None, all spheres will have the same size.
+        colormap : str
+            Mayavi colormap name. Default is None, which means all foci will
+            have the same color given by the 'color' argument. If colormap is
+            not None, foci will be colorcoded acording to data values.
         **kwargs : additional keyword arguments
             These are passed to the underlying
              :func:`mayavi.mlab.points3d` call.
@@ -1691,7 +1704,8 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
         else:
             foci_surf = Surface(self.subject_id, hemi, map_surface,
                                 subjects_dir=self.subjects_dir,
-                                units=self._units)
+                                units=self._units,
+                                apply_surf_xfm=self.apply_surf_xfm)
             foci_surf.load_geometry()
             foci_vtxs = utils.find_closest_vertices(foci_surf.coords, coords)
             foci_coords = self.geo[hemi].coords[foci_vtxs]
@@ -1710,9 +1724,12 @@ def add_foci(self, coords, coords_as_verts=False, map_surface=None,
             scale_factor = scale_factor / 1000.
         for brain in self._brain_list:
             if brain['hemi'] == hemi:
+                vtxs = utils.find_closest_vertices(self.geo[hemi].coords,
+                                                   foci_coords)
                 fl.append(brain['brain'].add_foci(foci_coords, scale_factor,
-                                                  color, alpha, name,
-                                                  **kwargs))
+                                                  color, alpha, name, data,
+                                                  self.geo[hemi].nn[vtxs, :],
+                                                  colormap, **kwargs))
         self.foci_dict[name] = fl
         self._toggle_render(True, views)
 
@@ -1821,6 +1838,44 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0,
         if justification is not None:
             text.property.justification = justification
 
+    def add_text3d(self, x, y, z, text, name, color=None, opacity=1.0,
+                 row=-1, col=-1, font_size=None, justification=None):
+        """ Add a text to the visualization
+
+        Parameters
+        ----------
+        x : Float
+            x coordinate
+        y : Float
+            y coordinate
+        z : Float
+            z coordinate
+        text : str
+            Text to add
+        name : str
+            Name of the text (text label can be updated using update_text())
+        color : Tuple
+            Color of the text. Default is the foreground color set during
+            initialization (default is black or white depending on the
+            background color).
+        opacity : Float
+            Opacity of the text. Default: 1.0
+        row : int
+            Row index of which brain to use
+        col : int
+            Column index of which brain to use
+        """
+        if name in self.texts_dict:
+            self.texts_dict[name]['text'].remove()
+        text = self.brain_matrix[row, col].add_text3d(x, y, z, text,
+                                                    name, color, opacity, **kwargs)
+        self.texts_dict[name] = dict(row=row, col=col, text=text)
+        if font_size is not None:
+            text.property.font_size = font_size
+            text.actor.text_scale_mode = 'viewport'
+        if justification is not None:
+            text.property.justification = justification
+
     def update_text(self, text, name, row=-1, col=-1):
         """Update text label
 
@@ -3414,16 +3469,30 @@ def add_morphometry(self, morph_data, colormap, measure,
         return dict(surface=surf, colorbar=bar, measure=measure, brain=self,
                     array_id=array_id)
 
-    def add_foci(self, foci_coords, scale_factor, color, alpha, name,
-                 **kwargs):
-        """Add spherical foci, possibly mapping to displayed surf"""
+    def add_foci(self, foci_coords, scale_factor, color, alpha, name, data, normals, colormap):
+        """Add spherical foci with attached data, possibly mapping to displayed surf"""
         # Create the visualization
+        if data is None:
+            u = np.array(normals[:,0])
+            v = np.array(normals[:,1])
+            w = np.array(normals[:,2])
+        else:
+            u = normals[:,0] * np.abs(data)
+            v = normals[:,1] * np.abs(data)
+            w = normals[:,2] * np.abs(data)
         with warnings.catch_warnings(record=True):  # traits
-            points = mlab.points3d(
-                foci_coords[:, 0], foci_coords[:, 1], foci_coords[:, 2],
-                np.ones(foci_coords.shape[0]), name=name, figure=self._f,
-                scale_factor=(10. * scale_factor), color=color, opacity=alpha,
-                reset_zoom=False, **kwargs)
+            if colormap is None:
+                points = mlab.quiver3d(foci_coords[:, 0],foci_coords[:, 1],foci_coords[:, 2],
+                    u,v,w, scalars = data, mode='sphere',
+                    name=name, figure=self._f, scale_factor=(10. * scale_factor),
+                    color=color, opacity=alpha)
+            else:
+                points = mlab.quiver3d(foci_coords[:, 0],foci_coords[:, 1],foci_coords[:, 2],
+                    u,v,w, scalars = data, colormap=colormap, mode='sphere',
+                    name=name, figure=self._f, scale_factor=(10. * scale_factor),
+                    color=color, opacity=alpha)
+                points.glyph.color_mode = 'color_by_scalar'
+            points.glyph.glyph_source.glyph_source.center = [0, 0, 0]
         return points
 
     def add_contour_overlay(self, scalar_data, min=None, max=None,
@@ -3461,6 +3530,14 @@ def add_text(self, x, y, text, name, color=None, opacity=1.0, **kwargs):
                              opacity=opacity, figure=self._f, **kwargs)
             return text
 
+    def add_text3d(self, x, y, z, text, name, color=None, opacity=1.0):
+        """ Add a text in 3D to the visualization"""
+        color = self._fg_color if color is None else color
+        with warnings.catch_warnings(record=True):
+            text = mlab.text3d(x, y, z, text, name=name, color=color,
+                             opacity=opacity, figure=self._f)
+            return text
+
     def remove_data(self, layer_id):
         """Remove data shown with .add_data()"""
         data = self.data.pop(layer_id)

From 6c9cb10ac77e4a9523250da80482187da0ed011d Mon Sep 17 00:00:00 2001
From: Cristi Donos <cristidonos@yahoo.com>
Date: Wed, 11 Nov 2020 19:22:24 +0200
Subject: [PATCH 46/46] merged changes by CD on top of nipy's f02cca8 version
 from Jun 23

---
 surfer/utils.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/surfer/utils.py b/surfer/utils.py
index 0b1f9ed..2bbd1c1 100644
--- a/surfer/utils.py
+++ b/surfer/utils.py
@@ -79,10 +79,14 @@ class Surface(object):
         If None, do not change coordinates (default).
     units : str
         Can be 'm' or 'mm' (default).
+    apply_surf_xfm: bool | False
+        If True, the transform defined by xras, yras,zras and cras
+        in Freesurfer's surface file will be applied to the surface
+        node coordinates.
     """
 
     def __init__(self, subject_id, hemi, surf, subjects_dir=None,
-                 offset=None, units='mm'):
+                 offset=None, units='mm', apply_surf_xfm=False):
         """Surface
 
         Parameters
@@ -97,6 +101,10 @@ def __init__(self, subject_id, hemi, surf, subjects_dir=None,
             If 0.0, the surface will be offset such that the medial
             wall is aligned with the origin. If None, no offset will
             be applied. If != 0.0, an additional offset will be used.
+        apply_surf_xfm: bool | False
+            If True, the transform defined by xras, yras,zras and cras
+            in Freesurfer's surface file will be applied to the surface
+            node coordinates.
         """
         if hemi not in ['lh', 'rh']:
             raise ValueError('hemi must be "lh" or "rh')
@@ -108,6 +116,7 @@ def __init__(self, subject_id, hemi, surf, subjects_dir=None,
         self.faces = None
         self.nn = None
         self.units = _check_units(units)
+        self.apply_surf_xfm = apply_surf_xfm
 
         subjects_dir = _get_subjects_dir(subjects_dir)
         self.data_path = op.join(subjects_dir, subject_id)
@@ -115,7 +124,7 @@ def __init__(self, subject_id, hemi, surf, subjects_dir=None,
     def load_geometry(self):
         surf_path = op.join(self.data_path, "surf",
                             "%s.%s" % (self.hemi, self.surf))
-        coords, faces = nib.freesurfer.read_geometry(surf_path)
+        coords, faces, metadata = nib.freesurfer.read_geometry(surf_path, read_metadata=True)
         if self.units == 'm':
             coords /= 1000.
         if self.offset is not None:
@@ -123,6 +132,9 @@ def load_geometry(self):
                 coords[:, 0] -= (np.max(coords[:, 0]) + self.offset)
             else:
                 coords[:, 0] -= (np.min(coords[:, 0]) + self.offset)
+        if self.apply_surf_xfm:
+            sxfm = np.vstack([np.stack([metadata[k] for k in metadata.keys() if 'ras' in k]).T, np.array([0, 0, 0, 1])])
+            coords = np.hstack([coords, np.ones((coords.shape[0], 1))]).dot(np.linalg.inv(sxfm))[:,0:3]
         nn = _compute_normals(coords, faces)
 
         if self.coords is None: