diff --git a/ohbm-2023-example.ipynb b/ohbm-2023-example.ipynb index b89cb2c..42bb7b3 100644 --- a/ohbm-2023-example.ipynb +++ b/ohbm-2023-example.ipynb @@ -23,7 +23,7 @@ "source": [ "import siibra as sb\n", "from packaging.version import Version\n", - "assert Version(sb.__version__) >= Version('1.0a08')\n", + "assert Version(sb.__version__) >= Version('1.0a14')\n", "from nilearn import plotting\n", "import matplotlib.pyplot as plt\n", "%matplotlib notebook" @@ -185,7 +185,7 @@ "# row 1 - receptor densities for different receptor types\n", "for i, m in enumerate(matches.itertuples()):\n", " features = sb.features.get(\n", - " m.Region, \n", + " m.region, \n", " sb.features.molecular.ReceptorDensityFingerprint\n", " )\n", " features[0].plot(ax=axs[0, i])\n", @@ -193,7 +193,7 @@ "# row 2 - cell densities per cortical layer\n", "for i, m in enumerate(matches.itertuples()):\n", " features = sb.features.get(\n", - " m.Region, \n", + " m.region, \n", " sb.features.cellular.LayerwiseCellDensity\n", " )\n", " features[0].plot(ax=axs[1, i])\n", @@ -201,9 +201,9 @@ "# row 3 - structural connectivity profiles\n", "for i, m in enumerate(matches.itertuples()):\n", " features = sb.features.get(\n", - " m.Region.parcellation, sb.features.connectivity.StreamlineLengths\n", + " m.region.parcellation, sb.features.connectivity.StreamlineLengths\n", " )\n", - " f = features[0].get_profile(m.Region, max_rows=12)\n", + " f = features[0][0].get_profile(m.region, max_rows=12)\n", " f.plot(ax=axs[2, i])\n", "\n", "# optimize plot layout\n", @@ -258,7 +258,7 @@ "# from the full resolution Big Brain (20 micron) at this position.\n", "for i, match in enumerate(matches.itertuples()):\n", "\n", - " point = julich_pmaps.sample_locations(match.Region, 1)[0].warp('bigbrain')\n", + " point = julich_pmaps.sample_locations(match.region, 1)[0].warp('bigbrain')\n", " view = plotting.plot_img(bigbrain_volume, axes=axs[0, i], cut_coords=tuple(point), **plot_kwargs)\n", " view.add_markers([tuple(point)])\n", "\n", @@ -294,7 +294,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.13" + "version": "3.9.15" }, "vscode": { "interpreter": {