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ENH: rerun notebooks with new output for newest docker image
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‎notebooks/basic_configuration.ipynb

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@@ -45,10 +45,8 @@
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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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"collapsed": true
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},
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype import config, logging\n",
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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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"collapsed": true
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},
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype import Workflow\n",
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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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"collapsed": true
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},
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype import Node\n",
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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": "3.5.2"
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"version": "3.6.2"
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}
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},
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"nbformat": 4,

‎notebooks/basic_data_input.ipynb

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@@ -93,10 +93,8 @@
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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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"collapsed": true
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},
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype import DataGrabber, Node\n",
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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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"collapsed": true
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},
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
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"dg.inputs.template_args = {'anat': [['subject_id', 'ses_name']],\n",
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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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"collapsed": true
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},
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"dg.inputs.field_template = {'anat': 'sub-%02d/ses-%s/anat/*_T1w.nii.gz',\n",
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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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"collapsed": true
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},
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"execution_count": 4,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Using the IdentityInterface\n",
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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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"collapsed": true
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},
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Specifying the input fields of DataGrabber directly\n",
@@ -237,9 +227,30 @@
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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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"execution_count": 6,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:02:02,387 workflow INFO:\n",
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"\t Executing node datagrabber in dir: /tmp/tmpiwew6ysu/datagrabber\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"\n",
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"anat = /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\n",
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"func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"dg.run().outputs"
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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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"collapsed": true
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},
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"execution_count": 7,
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype import SelectFiles, Node\n",
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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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"execution_count": 8,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:02:02,435 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmpd3odxyze/selectfiles\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"\n",
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"anat = /data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz\n",
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"func = /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz"
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]
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},
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"execution_count": 8,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"sf.run().outputs"
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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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"execution_count": 9,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:02:02,458 workflow INFO:\n",
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"\t Executing node selectfiles in dir: /tmp/tmp53bxb6rj/selectfiles\n"
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]
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},
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{
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"data": {
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"text/plain": [
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"\n",
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"anat = ['/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz', '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz']"
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]
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},
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"execution_count": 9,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"from nipype import SelectFiles, Node\n",
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"from os.path import abspath as opap\n",
@@ -364,24 +414,43 @@
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"source": [
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"## FreeSurferSource\n",
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"\n",
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"`FreeSurferSource` is a specific case of a file grabber that felicitates the data import of outputs from the FreeSurfer recon-all algorithm. This of course requires that you've already run `recon-all` on your subject.\n",
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"\n",
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"Before you can run `FreeSurferSource`, you first have to specify the path to the FreeSurfer output folder, i.e. you have to specify the SUBJECTS_DIR variable. This can be done as follows:"
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"`FreeSurferSource` is a specific case of a file grabber that felicitates the data import of outputs from the FreeSurfer recon-all algorithm. This of course requires that you've already run `recon-all` on your subject."
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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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"For the tutorial dataset ``ds000114``, `recon-all` was already run. So, let's make sure that you have the anatomy output of one subject on your system:"
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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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"collapsed": true
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"!datalad get -r -J4 /data/ds000114/derivatives/freesurfer/sub-01/"
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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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"Now, before you can run `FreeSurferSource`, you first have to specify the path to the FreeSurfer output folder, i.e. you have to specify the SUBJECTS_DIR variable. This can be done as follows:"
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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": 21,
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype.interfaces.freesurfer import FSCommand\n",
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"from os.path import abspath as opap\n",
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"\n",
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"# Path to your freesurfer output folder\n",
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"fs_dir = opap('/data/ds000114/derivatives/freesurfer')\n",
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"fs_dir = opap('/data/ds000114/derivatives/freesurfer/')\n",
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"\n",
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"# Set SUBJECTS_DIR\n",
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"FSCommand.set_default_subjects_dir(fs_dir)"
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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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"collapsed": true
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},
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"execution_count": 22,
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"metadata": {},
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"outputs": [],
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"source": [
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"from nipype import Node\n",
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},
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{
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"cell_type": "code",
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"execution_count": 23,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:04:52,28 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmpisu77m7r/fssource\n"
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]
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}
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],
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"source": [
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"fssource.inputs.subject_id = 'sub-01'\n",
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"result = fssource.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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"execution_count": 24,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"aparc_aseg: ['/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.a2009s+aseg.mgz', '/data/ds000114/derivatives/freesurfer/sub-01/mri/aparc.dktatlas+aseg.mgz']\n",
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"\n",
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"brainmask: /data/ds000114/derivatives/freesurfer/sub-01/mri/brainmask.mgz\n",
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"\n",
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"inflated: ['/data/ds000114/derivatives/freesurfer/sub-01/surf/rh.inflated', '/data/ds000114/derivatives/freesurfer/sub-01/surf/lh.inflated']\n",
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"\n"
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]
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}
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],
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"source": [
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"print('aparc_aseg: %s\\n' % result.outputs.aparc_aseg)\n",
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"print('brainmask: %s\\n' % result.outputs.brainmask)\n",
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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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"execution_count": 25,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"170904-06:04:54,346 workflow INFO:\n",
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"\t Executing node fssource in dir: /tmp/tmpisu77m7r/fssource\n"
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]
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}
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],
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"source": [
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"fssource.inputs.hemi = 'lh'\n",
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"result = fssource.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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"execution_count": 26,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"'/data/ds000114/derivatives/freesurfer/sub-01/surf/lh.inflated'"
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]
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},
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"execution_count": 26,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"result.outputs.inflated"
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]
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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": "3.5.2"
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"version": "3.6.2"
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}
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},
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"nbformat": 4,

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