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Update data input bids tutorial to use nipype BIDSDataGrabber
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‎notebooks/basic_data_input_bids.ipynb‎

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Lines changed: 39 additions & 98 deletions
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@@ -171,7 +171,7 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden",
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"solution2": "shown",
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"solution2_first": true
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},
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"outputs": [],
@@ -183,7 +183,7 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
@@ -198,40 +198,7 @@
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"metadata": {},
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"source": [
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"## Including `pybids` in your `nipype` workflow\n",
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"This is great, but what we really want is to include this into our `nipype` workflows. How to do this? We can create our own custom `BIDSDataGrabber` using a `Function` Interface. First, we need a plain Python function that for a given subject label and dataset location will return a list of BOLD files."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"def get_niftis(subject_id, data_dir):\n",
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" # Remember that all the necessary imports need to be INSIDE the function for the Function Interface to work!\n",
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" from bids.layout import BIDSLayout\n",
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" \n",
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" layout = BIDSLayout(data_dir)\n",
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" \n",
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" bolds = layout.get(subject=subject_id, type=\"bold\", return_type='file', extensions=['nii', 'nii.gz'])\n",
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" \n",
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" return bolds"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"get_niftis('01', '/data/ds000114')"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Ok we got our function. Now we need to wrap it inside a Node object."
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"This is great, but what we really want is to include this into our nipype workflows. To do this, we can import the BIDSDataGrabber Interface, which wraps around pybids."
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]
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},
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{
@@ -240,20 +207,14 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype.interfaces.io import BIDSDataGrabber\n",
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"from nipype.pipeline import Node, MapNode, Workflow\n",
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"from nipype.interfaces.utility import IdentityInterface, Function"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"BIDSDataGrabber = Node(Function(function=get_niftis, input_names=[\"subject_id\",\n",
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" \"data_dir\"],\n",
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" output_names=[\"bolds\"]), name=\"BIDSDataGrabber\")\n",
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"BIDSDataGrabber.inputs.data_dir = \"/data/ds000114\""
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"from nipype.interfaces.utility import Function\n",
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"\n",
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"bg = Node(BIDSDataGrabber(), name='bids-grabber')\n",
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"bg.inputs.base_dir = '/data/ds000114'\n",
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"bg.inputs.subject = '01'\n",
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"bg.inputs.output_query = {'bolds': dict(type='bold')}"
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]
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},
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{
@@ -262,16 +223,15 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"BIDSDataGrabber.inputs.subject_id='01'\n",
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"res = BIDSDataGrabber.run()\n",
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"res = bg.run()\n",
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"res.outputs"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Works like a charm! (hopefully :) 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"
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"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"
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]
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},
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{
@@ -294,7 +254,7 @@
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"outputs": [],
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"source": [
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"wf = Workflow(name=\"bids_demo\")\n",
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"wf.connect(BIDSDataGrabber, \"bolds\", analyzeBOLD, \"paths\")\n",
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"wf.connect(bg, \"bolds\", analyzeBOLD, \"paths\")\n",
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"wf.run()"
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]
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},
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden",
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"solution2": "shown",
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"solution2_first": true
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
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"from nipype.pipeline import Node, MapNode, Workflow\n",
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"from nipype.interfaces.utility import IdentityInterface, Function\n",
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"\n",
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"def get_T1w(subject_id, data_dir):\n",
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" from bids.layout import BIDSLayout\n",
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" \n",
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" layout = BIDSLayout(data_dir)\n",
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" \n",
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" T1w = layout.get(subject=subject_id, modality=\"anat\", return_type='file')\n",
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" \n",
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" return T1w\n",
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"from nipype.interfaces.io import BIDSDataGrabber\n",
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"\n",
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"ex2_BIDSDataGrabber = Node(Function(function=get_T1w, \n",
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" input_names=[\"subject_id\", \"data_dir\"],\n",
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" output_names=[\"T1w\"]), \n",
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" name=\"ex2\")\n",
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"ex2_BIDSDataGrabber.inputs.data_dir = \"/data/ds000114\"\n",
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"ex2_BIDSDataGrabber = BIDSDataGrabber(outfields = ['T1w'])\n",
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"ex2_BIDSDataGrabber.inputs.base_dir = '/data/ds000114'\n",
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"ex2_BIDSDataGrabber.inputs.subject = '10'\n",
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"ex2_BIDSDataGrabber.inputs.output_query = {'T1w': dict(modality='anat')}\n",
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"\n",
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"ex2_BIDSDataGrabber.inputs.subject_id='10'\n",
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"ex2_res = ex2_BIDSDataGrabber.run()\n",
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"ex2_res.outputs"
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]
@@ -363,7 +312,12 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"BIDSDataGrabber.iterables = ('subject_id', layout.get_subjects()[:2])\n",
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"bg_all = Node(BIDSDataGrabber(), name='bids-grabber')\n",
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"bg_all.inputs.base_dir = '/data/ds000114'\n",
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"bg_all.inputs.output_query = {'bolds': dict(type='bold')}\n",
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"bg_all.iterables = ('subject', layout.get_subjects()[:2])\n",
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"wf = Workflow(name=\"bids_demo\")\n",
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"wf.connect(bg_all, \"bolds\", analyzeBOLD, \"paths\")\n",
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"wf.run()"
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]
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},
@@ -411,11 +365,13 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"metadata": {
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"scrolled": false
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},
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"outputs": [],
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"source": [
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"wf = Workflow(name=\"bids_demo\")\n",
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"wf.connect(BIDSDataGrabber, \"bolds\", analyzeBOLD2, \"path\")\n",
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"wf.connect(bg, \"bolds\", analyzeBOLD2, \"path\")\n",
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"wf.run()"
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]
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},
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden",
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"solution2": "shown",
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"solution2_first": true
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
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"from nipype.pipeline import Node, MapNode, Workflow\n",
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"from nipype.interfaces.utility import IdentityInterface, Function\n",
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"\n",
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"# let's start from BidsDataGrabber again\n",
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"def get_niftis(subject_id, data_dir):\n",
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" # Remember that all the necesary imports need to be INSIDE the function \n",
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" # for the Function Interface to work!\n",
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" from bids.layout import BIDSLayout\n",
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" \n",
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" layout = BIDSLayout(data_dir)\n",
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" \n",
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" bolds = layout.get(subject=subject_id, type=\"bold\", return_type='file', extensions=['nii', 'nii.gz'])\n",
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" \n",
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" return bolds\n",
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"\n",
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"from nipype.interfaces.io import BIDSDataGrabber\n",
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"\n",
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"ex3_BIDSDataGrabber = Node(Function(function=get_niftis, \n",
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" input_names=[\"subject_id\", \"data_dir\"],\n",
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" output_names=[\"bolds\"]), \n",
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" name=\"ex3_BIDSDataGrabber\")\n",
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"ex3_BIDSDataGrabber.inputs.data_dir = \"/data/ds000114\"\n",
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"ex3_BIDSDataGrabber.inputs.subject_id='01'"
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"ex3_BIDSDataGrabber = Node(BIDSDataGrabber(), name='bids-grabber')\n",
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"ex3_BIDSDataGrabber.inputs.base_dir = '/data/ds000114'\n",
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"ex3_BIDSDataGrabber.inputs.subject = '01'\n",
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"ex3_BIDSDataGrabber.inputs.output_query = {'bolds': dict(type='bold')}"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"solution2": "hidden"
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"solution2": "shown"
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},
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"outputs": [],
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"source": [
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.5"
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"version": "3.6.6"
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}
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},
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"nbformat": 4,

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