Refine BIDSDataGrabber example

Author: adelavega

notebooks/basic_data_input_bids.ipynb

@@ -212,9 +212,34 @@
     "from nipype.interfaces.utility import Function\n",
     "\n",
     "bg = Node(BIDSDataGrabber(), name='bids-grabber')\n",
-    "bg.inputs.base_dir = '/data/ds000114'\n",
+    "bg.inputs.base_dir = '/data/ds000114'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can define static filters, that will apply to all queries, by modifying the appropriate input"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "bg.inputs.subject = '01'\n",
-    "bg.inputs.output_query = {'bolds': dict(type='bold')}"
+    "res = bg.run()\n",
+    "res.outputs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note that by default `BIDSDataGrabber` will fetch `nifti` files matching modality `func` and `anat`, and output them as two output fields. \n",
+    "\n",
+    "To define custom fields, simply define the arguments to pass to `BIDSLayout.get` as dictionary, like so:"
    ]
   },
   {
@@ -223,6 +248,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "bg.inputs.output_query = {'bolds': dict(type='bold')}\n",
     "res = bg.run()\n",
     "res.outputs"
    ]
@@ -231,7 +257,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Works like a charm! Lets put it in a workflow. We are not going to analyze any data, but for demonstration purposes, we will add a couple of nodes that pretend to analyze their inputs"
+    "This results in a single output field `bold`, which returns all files with `type:bold` for `subject:\"01\"` \n",
+    "\n",
+    "Now, lets put it in a workflow. We are not going to analyze any data, but for demonstration purposes, we will add a couple of nodes that pretend to analyze their inputs"
    ]
   },
   {
@@ -289,7 +317,7 @@
     "from nipype.pipeline import Node, MapNode, Workflow\n",
     "from nipype.interfaces.io import BIDSDataGrabber\n",
     "\n",
-    "ex2_BIDSDataGrabber = BIDSDataGrabber(outfields = ['T1w'])\n",
+    "ex2_BIDSDataGrabber = BIDSDataGrabber()\n",
     "ex2_BIDSDataGrabber.inputs.base_dir = '/data/ds000114'\n",
     "ex2_BIDSDataGrabber.inputs.subject = '10'\n",
     "ex2_BIDSDataGrabber.inputs.output_query = {'T1w': dict(modality='anat')}\n",
@@ -303,7 +331,7 @@
    "metadata": {},
    "source": [
     "## Iterating over subject labels\n",
-    "In the previous example, we demonstrated how to use `pybids` to \"analyze\" one subject. How can we scale it for all subjects? Easy - using `iterables` (more in [Iteration/Iterables](basic_iteration.ipynb)."
+    "In the previous example, we demonstrated how to use `pybids` to \"analyze\" one subject. How can we scale it for all subjects? Easy - using `iterables` (more in [Iteration/Iterables](basic_iteration.ipynb))."
    ]
   },
   {
@@ -342,7 +370,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Can we incorporate this into our pipeline? Yes, we can!\n",
+    "Can we incorporate this into our pipeline? Yes, we can! To do so, let's use a `Function` node to use `BIDSLayout` in a custom way.\n",
     "(More about MapNode in [MapNode](basic_mapnodes.ipynb))"
    ]
   },