update tutorial 01 to siibra 0.4a69

01-BasicConcepts.ipynb

@@ -17,23 +17,14 @@
     "The above classes are all derived from the basic `AtlasConcept` class, and represent semantic concepts. When first loading a new siibra version, `siibra` automatically builds a registry with predefined objects for each of these classes. The configuration information is retrieved from a versioned online repository that we maintain with siibra. "
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!pip install siibra==0.4a35"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import siibra\n",
-    "assert siibra.__version__ >= \"0.4a35\"\n",
+    "assert siibra.__version__ >= \"0.4a69\"\n",
     "import os\n",
     "import matplotlib\n",
     "%matplotlib notebook"
@@ -307,6 +298,15 @@
     "To fetch only the left hemisphere, we simply specifiy the fragment in the `fetch()` call:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mpm.volumes[0]._providers['nii']._img_loaders"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -449,7 +449,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "bigbrain = siibra.spaces.BIG_BRAIN_HISTOLOGY.get_template()\n",
+    "bigbrain = siibra.spaces.get('bigbrain').get_template()\n",
     "bigbrain_img = bigbrain.fetch()\n",
     "plotting.plot_img(bigbrain_img, cmap='gray')"
    ]
@@ -486,7 +486,7 @@
     "voi = siibra.locations.BoundingBox(\n",
     "    (-3.979, -61.256, 3.906),\n",
     "    (5.863, -55.356, -2.487),\n",
-    "    space=siibra.spaces.BIG_BRAIN_HISTOLOGY\n",
+    "    space='bigbrain'\n",
     ")"
    ]
   },
@@ -537,7 +537,7 @@
    "outputs": [],
    "source": [
     "layermap = siibra.parcellations.get('cortical layers').get_map(space='bigbrain')\n",
-    "mask = layermap.fetch(resolution_mm=0.16,voi=voi)\n",
+    "mask = layermap.fetch(resolution_mm=0.16, voi=voi, fragment='left')\n",
     "plotting.view_img(mask, bg_img=bigbrainchunk, opacity=.1, symmetric_cmap=False)"
    ]
   },
@@ -555,7 +555,7 @@
    "outputs": [],
    "source": [
     "area44l = julichbrain.get_region('44 left')\n",
-    "voi = area44l.get_bounding_box(space=siibra.spaces.BIG_BRAIN_HISTOLOGY)"
+    "voi = area44l.get_bounding_box(space=\"bigbrain\")"
    ]
   },
   {
@@ -598,7 +598,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.13"
   },
   "vscode": {
    "interpreter": {