Workshop 1: Ultra-high field image processing using Nighres
Date and time: May 7, 9am - 12 noon (MEZ)
Speaker: Dr. Pierre-Louis Bazin
In this 3 hour workshop, I will provide an overview over Nighres to perform brain parcellation, denoising, cortical reconstruction (including the cerebellum), and qMRI estimation on ultra-high field imaging data.
- I will start by giving a formal introduction presentation of the toolbox, from its general architecture to its many components (45 min, ZOOM).
- 15 min break on Gather.
- I will give an overview of the software installation and discuss some of the common issues, including problems encountered by the audience (15 min, ZOOM).
- We will then proceed to a step-by-step walk through the main Nighres tools and pipelines (45 min, ZOOM).
- Finally we will move to Gather to discuss challenges and opportunities of high-resolution neuroimaging, including but not limited to layer (f)MRI (60 min, Gather).
Please prepare the following:
- If you want to benefit most from the software installation session 3), please install the Nighres toolbox, see https://nighres.readthedocs.io/en/latest/installation.html and install from Github, not PyPI. The installation comes with a series of examples that you can try and run on your own prior to the workshop. If you encounter problems or get stuck, keep a record of what you did and information about your OS, python installation so we can try and solve them during the session, if time permits.
- For the step-by-step walk through session 4), you can benefit from running the toolbox on example data or even your own. I will prepare a pre-computed data set to download prior to the workshop so you can inspect inputs and outputs yourself during the session.
Workshop 2: Hands-on discussion of acquisition and analysis challenges in layer-fMRI
Date and time: May 7, 2pm - 5pm (MEZ)
Speaker: Dr. Laurentius Huber
In this 3 hour workshop, I will try to give a hands-on experience of every step along the entire acquisition and analysis pipeline of layer-fMRI.
- I will start by giving a very brief formal introduction presentation of the pipeline and explain what is important to consider for functional layer imaging (15 min, ZOOM).
- We will briefly visit a SIEMENS 7T scanner (virtually) and note the important steps to be considered for layer-fMRI (15 min, ZOOM).
- I will give a quick click-along overview of how to install and apply the software analysis suite LayNii. Including noise mapping, layer definition, and profile extraction etc. (60 min, ZOOM).
- 30 min break on Gather.
- We will discuss a large variety of common acquisition and analysis artifacts in layer-fMRI. Attendees are invited to submit their favourite artifact to be discussed too. (60 min, Zoom)
- Open end discussion on Gather to discuss common challenges of layer-fMRI, to go into specific example applications
- If you want to follow the click-along LayNii analysis in section 3), please install the LayNii software suite, and any nii viewer of your choice (e.g., ITK-SNAP or Fsleyes). Installation instructions (or ready built Virtual-boxes) of LayNii are here: https://layerfmri.com/laynii-setup/. The installation comes along with a test-dataset that will be used in the workshop.
- If you have any specific layer-fMRI related artifacts that you wish to be discussed in section 5.) please send the data and descriptions to email@example.com until May 1st.
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If you have questions on the workshops, please write to firstname.lastname@example.org.