Loading [MathJax]/extensions/mml2jax.js

name: title
layout: true
class: center
---
layout: false
count: false

.center.pad-top[
<img class="pad-top" src="https://cibm.ch/wp-content/uploads/bannerfMRIPrep.jpg" width="100%" />
]

.boxed-content[
| | |
|---:|---|
|<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/"> <img src="images/qr-talk-url.svg" alt="workflow" style="width: 100%" /></a> | .large[<i class="fa-solid fa-play"></i> Get started] <br /> https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/ |
]

???

---
name: newsection
layout: true

.perma-sidebar[
<p class="rotate">
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0; height: 20px; padding-top: 6px;" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a>
  <span style="padding-left: 10px; font-weight: 600;">Day 1 :: Welcome</span>
</p>
]

---

# About us | Instructors

<br />

.boxed-content[
.people-table.larger[
| | |
|---:|---|
| ![oscar-esteban](https://cibm.ch/wp-content/uploads/OscarEsteban-300x300-1.jpg)| **Oscar Esteban** <br /> Research and Teaching FNS Fellow, Lausanne University Hospital (CHUV) and the University of Lausanne. <br /> <<code>phd@oscaresteban.es</code>> |
| ![chris-markiewicz](https://cibm.ch/wp-content/uploads/chris.jpg)| **Chris Markiewicz** <br /> Senior Research Engineer, Stanford University. <br /> <<code>markiewicz@stanford.edu</code>> |
| ![adrien-albert](https://www.unige.ch/stic/application/files/cache/thumbnails/d6d8cfe20f70dece2f181ff09055f6bd.png) | **Adrien Albert** <br /> Ingénieur infrastructures et systèmes, STIC UNIGE <br /> <<code>adrien.albert@unige.ch</code>> |
]
]

---

# About us | Organizers

.boxed-content.pad-top[
.many-people-table[
| | |
|---:|---|
| ![frederic-grouiller](https://cibm.ch/wp-content/uploads/MRI-UNIGE-GrouillerFred-BWcropped-982x1024.jpg)| **Frédéric Grouiller** <br /> Head, CIBM MRI HUG-UNIGE Clinical MR Imaging Section |
| ![emilie-sleigh](https://people.epfl.ch/private/common/photos/links/233788.jpg?ts=1725608851)| **Emilie Sleight** <br /> Postdoctoral Researcher, CIBM MRI EPFL. |
| ![elda-fischi](https://cibm.ch/wp-content/uploads/Fischi-GomezE_PhotoBW.jpg)| **Elda Fischi-Gómez** <br /> Research Staff Scientist, CIBM CHUV-EPFL. |
| ![sebastien-courvoisier](https://cibm.ch/wp-content/uploads/S%C3%A9bastien-Courvoisier.jpg)| **Sébastien Courvoisier** <br /> MRI Operational Manager, Research Staff Scientist, CIBM HUG-UNIGE. |
| ![pina-marziliano](https://cibm.ch/wp-content/uploads/i01_Pina-705x1024.jpg)| **Pina Marziliano** <br /> Executive Director, CIBM |
| ![oscar-esteban](https://cibm.ch/wp-content/uploads/OscarEsteban-300x300-1.jpg)| **Oscar Esteban** <br /> Research and Teaching FNS Fellow, Lausanne University Hospital (CHUV) and the University of Lausanne. |
]
]

---

# Rules

.boxed-content[
.no-bullet[
* .large[<i class="fa-solid fa-handshake"></i> **Code of Conduct**]
  * [https://www.nipreps.org/community/CODE_OF_CONDUCT/](https://www.nipreps.org/community/CODE_OF_CONDUCT/)
]
]

---
count: false

# Rules

.boxed-content[
.top-right[
<a href="https://www.nipreps.org/community/CODE_OF_CONDUCT/"><img src="images/qr-coc-url.svg" style="width: 100%" />NiPreps CoC</a>
]
]
--
.boxed-content[
.no-bullet.pad-top[
* .large[<i class="fa-solid fa-message"></i>   **Participate at any moment**]
  * .larger[Dynamics more fluid than a lecture mode - raise your hand as soon as you feel something needs further discussion]
  * .larger[**Hive mind**: share your knowledge]
]
]
--
.boxed-content[
.no-bullet[
* .large[<i class="fa-solid fa-mug-hot"></i>   **Feel welcome and ensure your well-being**]
  * .larger[Take breaks, stand up, etc. as you need them]
  * .larger[Override your name in your badge and write down your pronouns]
  * .larger[Mingle and enjoy the bootcamp!]
]
]
--
.boxed-content[
.no-bullet[
* .large[<i class="fa-solid fa-people-pulling"></i>   **Lead during hack times**]
  * .larger[Take this opportunity to pull others into your work]
  * .larger[Unlock some issue that has slowed down your project]
  * .larger[Address some issue that is slowing down others]
]
]

---

# <i class="fa-solid fa-map-location-dot"></i> Room D02.1549.A

.boxed-content[
.large[This is located at the CMU Building D, 2<sup>nd</sup> floor.]

<iframe src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d2069.0208636535194!2d6.1517161492085055!3d46.19430985911478!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x478c7acd97a35cc1%3A0x1017e45635097c72!2sUniversit%C3%A9%20de%20Gen%C3%A8ve%20%2F%20Centre%20M%C3%A9dical%20Universitaire!5e0!3m2!1sen!2sch!4v1725613579689!5m2!1sen!2sch" width="50%" height="450" style="border:0;" allowfullscreen="" loading="lazy" referrerpolicy="no-referrer-when-downgrade"></iframe>

.pull-right[
<img src="https://www.unige.ch/medecine/audio/download_file/view_inline/123" style="width: 100%" /> <br />
Access the building either from Av. Champe (3rd floor) or Rue Lombard (1st floor).
]]

---

# Expected from you

.boxed-content.pad-top[
.no-bullet[
* .large[<i class="fa-solid fa-laptop"></i> Bring **your laptop**]
  * You'll need it to follow the units and exercise on your own

<br />
* .large[<i class="fa-solid fa-hard-drive"></i> Bring your **data** for days 2 & 3]
  * The hackathon is for you to work on a different environment

<br />
* .large[<i class="fa-solid fa-ice-cream"></i> Join the **welcome dinner**]
  * Please let us know if you can join and you haven't already

<br />
* .large[<i class="fa-solid fa-server"></i> Check you can **access** UNIGE's HPC]
  * Contact **Sébastien Courvoisier** *ASAP* if you can't.
]]

---

# Program | Day 1

.right-column3.center[
<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/">
  <img src="images/qr-talk-url.svg" alt="workflow" style="width: 100%" />
  <br />
  https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/
</a>
]

<br />
.left-column3[
.program-table[
| | |
|---:|---|
|  9h00 | Welcome & opening |
|  9h30 | [Overview of the fMRI neuroimaging pipeline & <i>fMRIPrep</i>](/assets/fmriprep-bootcamp-geneva2024/day1-01-fmriprep-primer) |
| 10h30 | Coffee break |
| 10h45 | [The Brain Imaging Data Structure (BIDS)](/assets/fmriprep-bootcamp-geneva2024/day1-02-bids) |
| 11h30 | [BIDS hands-on](/assets/fmriprep-bootcamp-geneva2024/day1-03-bids-hands-on) |
| 12h00 | [Containers](/assets/fmriprep-bootcamp-geneva2024/day1-04-containers) |
| 12h30 | Lunch break |
| 14h00 | Introduction to UNIGE's HPC and running jobs |
| 14h45 | [Making data available on HPC (hands-on)](/assets/fmriprep-bootcamp-geneva2024/day1-05-data-and-hpc) |
| 15h15 | Coffee break |
| 15h30 | [Hands-on: Apptainer in UNIGE's HPC](/assets/fmriprep-bootcamp-geneva2024/day1-06-apptainer) |
| 16h00 | Hands-on: run fMRIPrep on the dataset |
| 17h00 | End |
| 19h00 | Welcome dinner |
]]

???

---

# Program | Day 2

.right-column3.center[
<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/">
  <img src="images/qr-talk-url.svg" alt="workflow" style="width: 100%" />
  <br />
  https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/
</a>
]

<br />
.left-column3[
.program-table[
| | |
|---:|---|
|  9h00 | Execution forensics: did it work? |
|  9h30 | Resource planning, parallelization |
| 10h30 | Coffee break |
| 10h45 | Analysis of the *mixed* task |
| 12h30 | Lunch break |
| 14h00 | MRIQC and QA/QC |
| 15h00 | Coffee break |
| 15h15 | Hands-on: Running *fMRIPrep* on your data on cluster |
| 16h00 | Preparation of the hackathon (groups, projects) |
| 17h00 | End |
]]

???

---

# Program | Day 3 (Hackathon)

.right-column3.center[
<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/#3">
  <img src="images/qr-talk-url.svg" alt="workflow" style="width: 100%" />
  <br />
  https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/
</a>
]

<br />
.left-column3[
.program-table[
| | |
|---:|---|
|  9h00 | Project pitches |
| | Coffee break |
| | **Hacking!** |
| 12h30 | Lunch break |
| 14h00 | **Hacking!** |
| 15h00 | Coffee break |
| 15h15 | Round table and showcasing results |
| 16h30 | End |
]]

???

---

# Hackathon (Day 3)

.boxed-content.no-bullet[
<br />

* .large[<i class="fa-solid fa-circle-chevron-right"></i> Perhaps, address a **current roadblock** in your research pipeline]
  
  * .larger[having neuroimagers around to **ask for responsive help**]
  * .larger[having UNIGE's HPC at your fingertips]

<br />
* .large[<i class="fa-solid fa-circle-chevron-right"></i> BYOD (bring your own dataset)]

* .larger[but you can use the example dataset we provide]

<br />
* .large[<i class="fa-solid fa-circle-chevron-right"></i> **Team up** with other attendees]

* .larger[if you don't have a clear objective for yourself,]
  * .larger[or the objective can be shared with others]
]

---

# Pitch roulette

.boxed-content.large[
* Everyone will be up for 45 secs (max).

* Names will come randomly from a roulette, organizers first.

* Suggested items to mention:

* Preferred name and pronouns
   * Appropriate pronunciation of name
   * Current position
   * General interests
   * Goals for the bootcamp
   * Previous experience with fMRI and fMRIPrep
]

Notes for current slide

Notes for next slide


	Get started https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/

1 / 10

About us | Instructors


	Oscar Esteban Research and Teaching FNS Fellow, Lausanne University Hospital (CHUV) and the University of Lausanne. <`phd@oscaresteban.es`>
	Chris Markiewicz Senior Research Engineer, Stanford University. <`markiewicz@stanford.edu`>
	Adrien Albert Ingénieur infrastructures et systèmes, STIC UNIGE <`adrien.albert@unige.ch`>

1 / 10

About us | Organizers


	Frédéric Grouiller Head, CIBM MRI HUG-UNIGE Clinical MR Imaging Section
	Emilie Sleight Postdoctoral Researcher, CIBM MRI EPFL.
	Elda Fischi-Gómez Research Staff Scientist, CIBM CHUV-EPFL.
	Sébastien Courvoisier MRI Operational Manager, Research Staff Scientist, CIBM HUG-UNIGE.
	Pina Marziliano Executive Director, CIBM
	Oscar Esteban Research and Teaching FNS Fellow, Lausanne University Hospital (CHUV) and the University of Lausanne.

2 / 10

Rules

Code of Conduct
- https://www.nipreps.org/community/CODE_OF_CONDUCT/

3 / 10

Rules

3 / 10

Rules

Participate at any moment
- Dynamics more fluid than a lecture mode - raise your hand as soon as you feel something needs further discussion
- Hive mind: share your knowledge

3 / 10

Rules

Participate at any moment
- Dynamics more fluid than a lecture mode - raise your hand as soon as you feel something needs further discussion
- Hive mind: share your knowledge

Feel welcome and ensure your well-being
- Take breaks, stand up, etc. as you need them
- Override your name in your badge and write down your pronouns
- Mingle and enjoy the bootcamp!

3 / 10

Rules

Participate at any moment
- Dynamics more fluid than a lecture mode - raise your hand as soon as you feel something needs further discussion
- Hive mind: share your knowledge

Feel welcome and ensure your well-being
- Take breaks, stand up, etc. as you need them
- Override your name in your badge and write down your pronouns
- Mingle and enjoy the bootcamp!

Lead during hack times
- Take this opportunity to pull others into your work
- Unlock some issue that has slowed down your project
- Address some issue that is slowing down others

3 / 10

Room D02.1549.A

This is located at the CMU Building D, 2^nd floor.

Access the building either from Av. Champe (3rd floor) or Rue Lombard (1st floor).

4 / 10

Expected from you

Bring your laptop
- You'll need it to follow the units and exercise on your own

Bring your data for days 2 & 3
- The hackathon is for you to work on a different environment

Join the welcome dinner
- Please let us know if you can join and you haven't already

Check you can access UNIGE's HPC
- Contact Sébastien Courvoisier ASAP if you can't.

5 / 10

Program | Day 1

https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/


9h00	Welcome & opening
9h30	Overview of the fMRI neuroimaging pipeline & fMRIPrep
10h30	Coffee break
10h45	The Brain Imaging Data Structure (BIDS)
11h30	BIDS hands-on
12h00	Containers
12h30	Lunch break
14h00	Introduction to UNIGE's HPC and running jobs
14h45	Making data available on HPC (hands-on)
15h15	Coffee break
15h30	Hands-on: Apptainer in UNIGE's HPC
16h00	Hands-on: run fMRIPrep on the dataset
17h00	End
19h00	Welcome dinner

6 / 10

Program | Day 2

https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/


9h00	Execution forensics: did it work?
9h30	Resource planning, parallelization
10h30	Coffee break
10h45	Analysis of the mixed task
12h30	Lunch break
14h00	MRIQC and QA/QC
15h00	Coffee break
15h15	Hands-on: Running fMRIPrep on your data on cluster
16h00	Preparation of the hackathon (groups, projects)
17h00	End

7 / 10

Program | Day 3 (Hackathon)

https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/


9h00	Project pitches
	Coffee break
	Hacking!
12h30	Lunch break
14h00	Hacking!
15h00	Coffee break
15h15	Round table and showcasing results
16h30	End

8 / 10

Hackathon (Day 3)

Perhaps, address a current roadblock in your research pipeline
- having neuroimagers around to ask for responsive help
- having UNIGE's HPC at your fingertips

BYOD (bring your own dataset)
- but you can use the example dataset we provide

Team up with other attendees
- if you don't have a clear objective for yourself,
- or the objective can be shared with others

9 / 10

Pitch roulette

Everyone will be up for 45 secs (max).
Names will come randomly from a roulette, organizers first.
Suggested items to mention:
- Preferred name and pronouns
- Appropriate pronunciation of name
- Current position
- General interests
- Goals for the bootcamp
- Previous experience with fMRI and fMRIPrep

10 / 10

About us | Instructors


	Oscar Esteban Research and Teaching FNS Fellow, Lausanne University Hospital (CHUV) and the University of Lausanne. <`phd@oscaresteban.es`>
	Chris Markiewicz Senior Research Engineer, Stanford University. <`markiewicz@stanford.edu`>
	Adrien Albert Ingénieur infrastructures et systèmes, STIC UNIGE <`adrien.albert@unige.ch`>

1 / 10

Paused

Help

Keyboard shortcuts

↑, ←, Pg Up, k	Go to previous slide
↓, →, Pg Dn, Space, j	Go to next slide
Home	Go to first slide
End	Go to last slide
Number + Return	Go to specific slide
b / m / f	Toggle blackout / mirrored / fullscreen mode
c	Clone slideshow
p	Toggle presenter mode
t	Restart the presentation timer
?, h	Toggle this help

Esc	Back to slideshow