final version

Author: oesteban

docs/assets/EPFL2023/index.html

@@ -417,11 +417,148 @@
 
 ---
 
-# *TemplateFlow* | Archive
+.pull-left[
+<p align="center">
+<img src="../card-nipype.svg" width="100%" />
+</p>
+<br />
+
+``` Python
+from nipype.interfaces.fsl import BET
+brain_extract = BET(
+  in_file="/data/coolproject/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii",
+  out_file="/out/sub-01/ses-01/anat/sub-01_ses-01_desc-brain_T1w.nii"
+)
+brain_extract.run()
+```
+]
+
+.pull-right[
+<p align="center">
+<img src="https://nipype.readthedocs.io/en/latest/_images/nipype_architecture_overview2.png" width="65%" />
+</p>
+]
+
+---
+
+# WDL Example - Translation into Nipype
+
+
+```Python
+import nipype.interfaces.fsl as fsl
+import nipype.pipeline.engine as pe
+
+input_image = 'input.nii.gz'
+output_dir = 'results'
+
+preprocess = pe.Node(fsl.BET(), name='preprocess')
+preprocess.inputs.in_file = input_image
+preprocess.inputs.out_file = f'{output_dir}/brain.nii.gz'
+
+stats = pe.Node(fsl.ImageStats(), name='stats')
+stats.inputs.in_file = f'{output_dir}/brain.nii.gz'
+stats.inputs.op_string = '-m -p 50'
+
+workflow = pe.Workflow(name='my_workflow')
+workflow.connect([(preprocess, stats, [('out_file', 'in_file')])])
+workflow.base_dir = 'working_dir'
+workflow.run()
+```
+
+
+---
+
+# Facets to standardize
+
+.boxed-content[
+.distribute.large[
+* **Outer interface** (inputs and outputs). Also, consider an internal data structure format for high throughput.
+* **Implementation** (WDL vs. programmed): code styling, best practices, BIDS-Apps.
+* **Modularize** (see *NiPreps* and *TemplateFlow*).
+* Use **containers** to ensure software delivery and reproducibility.
+* Implement testing and **continuous integration** to catch errors early and streamline development.
+* **Version** the workflow and its components to ensure compatibility and track changes, issue **LTS**.
+* Promote **community** and social standardization through collaboration, documentation, telemetry, and open-source practices.
+* **Visual reporting**
+]]
+
+---
+
+# BIDS-Apps: subject-wise parallelization
+
+<p align="center">
+<a href="https://doi.org/10.1371/journal.pcbi.1005209">
+<img src="../journal.pcbi.1005209.g002.png" width="90%" /><br /><br />
+(Gorgolewski et al., 2017)
+</a>
+</p>
+
+---
+
+## The individual report
+<p align="center">
+<video controls="controls" width="70%"
+       name="Video Name" src="../fmriprep-report.mov"></video>
+</p>
+
+---
+
+# Why standarizing?
+
+.boxed-content[
+.distribute.large[
+* Pushing the *truck factor* above 1.0.
+* Engage users
+]]
+
+---
+
+# "Analysis-grade" data
+
+.larger[
+The *NeuroImaging PREProcessing toolS* (*[NiPreps](https://nipreps.org).org*) augment scanners to produce *analysis-grade* data (= **directly consumable by analyses**)
+]
+
+<br />
+.pull-left[
+
+***Analysis-grade* data** is an analogy to the concept of "*sushi-grade (or [sashimi-grade](https://en.wikipedia.org/wiki/Sashimi)) fish*" in that both are:
+
+.large[**minimally preprocessed**,]
+
+and
+
+.large[**safe to consume** directly.]
+]
+
+.pull-right[
+<img align="right" style='margin-right: 50px' src="https://1.bp.blogspot.com/-Osh4H4WXka0/WlMJmVgkZTI/AAAAAAAAEMY/GynUzSomJ-EBiyqv2m-maiOyKSM7SOmNACLcBGAs/s400/yellowfin%2Btuna%2Bsteaks%2Bnutrition.jpg" />
+]
+
+---
+
+<p align="center">
+<img src="../nipreps-chart.png" width="63%" /><br />
+<em>NiPreps</em> (<a href="https://doi.org/10.31219/osf.io/ujxp6">Esteban et al., 2020</a>)
+</p>
+
+---
+
+template: title
+layout: false
+.middle[
+<p align="center">
+<img src="https://github.com/oesteban/fmriprep/raw/f4c7a9804be26c912b24ef4dccba54bdd72fa1fd/docs/_static/fmriprep-21.0.0.svg" width="95%" />
+</p>
+]
+
+---
+
+# *TemplateFlow*
 
 <p align="center">
-<img src="../torw2020/assets/templateflow-datatypes.png" width="78%" /><br />
-(<a href="https://doi.org/10.1101/2021.02.10.430678">Ciric et al., 2022</a>)
+<img src="https://www.templateflow.org/assets/templateflow_fig-birdsview.png" width="60%" /><br />
+(<a href="https://doi.org/10.1038/s41592-022-01681-2">Ciric et al., 2022</a>)
 </p>
 
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