fMRIPrep Bootcamp

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|<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[ Get started] https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/ |
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<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>
 Day 1 :: Welcome

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# About us | Instructors

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

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| ![frederic-grouiller](https://cibm.ch/wp-content/uploads/MRI-UNIGE-GrouillerFred-BWcropped-982x1024.jpg)| **Frédéric Grouiller** 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** Postdoctoral Researcher, CIBM MRI EPFL. |
| ![elda-fischi](https://cibm.ch/wp-content/uploads/Fischi-GomezE_PhotoBW.jpg)| **Elda Fischi-Gómez** Research Staff Scientist, CIBM CHUV-EPFL. |
| ![sebastien-courvoisier](https://cibm.ch/wp-content/uploads/S%C3%A9bastien-Courvoisier.jpg)| **Sébastien Courvoisier** MRI Operational Manager, Research Staff Scientist, CIBM HUG-UNIGE. |
| ![pina-marziliano](https://cibm.ch/wp-content/uploads/i01_Pina-705x1024.jpg)| **Pina Marziliano** Executive Director, CIBM |
| ![oscar-esteban](https://cibm.ch/wp-content/uploads/OscarEsteban-300x300-1.jpg)| **Oscar Esteban** Research and Teaching FNS Fellow, Lausanne University Hospital (CHUV) and the University of Lausanne. |
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# Rules

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* .large[ **Code of Conduct**]
 * [https://www.nipreps.org/community/CODE_OF_CONDUCT/](https://www.nipreps.org/community/CODE_OF_CONDUCT/)
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# Rules

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<a href="https://www.nipreps.org/community/CODE_OF_CONDUCT/"><img src="images/qr-coc-url.svg" style="width: 100%" />NiPreps CoC</a>
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* .large[   **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]
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* .large[   **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!]
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* .large[   **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]
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# Room D02.1549.A

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.large[This is located at the CMU Building D, 2nd floor.]

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

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* .large[ Bring **your laptop**]
 * You'll need it to follow the units and exercise on your own

* .large[ Bring your **data** for days 2 & 3]
 * The hackathon is for you to work on a different environment

* .large[ Join the **welcome dinner**]
 * Please let us know if you can join and you haven't already

* .large[ Check you can **access** UNIGE's HPC]
 * Contact **Sébastien Courvoisier** *ASAP* if you can't.
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# Program | Day 1

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<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/">
 <img src="images/qr-talk-url.svg" alt="workflow" style="width: 100%" />
 
 https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/
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| 9h00 | Welcome & opening |
| 9h30 | [Overview of the fMRI neuroimaging pipeline & fMRIPrep](/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 |
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# Program | Day 2

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| 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 |
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# Program | Day 3 (Hackathon)

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<a href="https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/#3">
 <img src="images/qr-talk-url.svg" alt="workflow" style="width: 100%" />
 
 https://www.nipreps.org/assets/fmriprep-bootcamp-geneva2024/home/
</a>
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| 9h00 | Project pitches |
| | Coffee break |
| | **Hacking!** |
| 12h30 | Lunch break |
| 14h00 | **Hacking!** |
| 15h00 | Coffee break |
| 15h15 | Round table and showcasing results |
| 16h30 | End |
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# Hackathon (Day 3)

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* .large[ 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]

* .large[ BYOD (bring your own dataset)]

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

* .large[ **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]
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# Pitch roulette

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* 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
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