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ENH: Add keypoints to episodes #46

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Feb 28, 2024
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ENH: Add keypoints to episodes #46

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5 changes: 4 additions & 1 deletion episodes/anatomy-of-nifti.md
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```

`t1_data` contains 3 dimensions. You can think of the data as a 3D version of a picture (more accurately, a volume).
![](fig/numpy_arrays.png)

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While typical 2D pictures are made out of squares called **pixels**, a 3D MR image is made up of 3D cubes called **voxels**.
![](fig/mri_slices.jpg)

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What about the how big each dimension is (shape)?

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Giving our 3D volume, we pull out a 2D slice of our data.
Here's an example of slicing from left to right (sagittal slicing):

![](fig/T1w.gif)

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This gif is a series of 2D images or **slices** moving from left to right.

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Applying the affine matrix (`t1_affine`) is done through using a *linear map* (matrix multiplication) on voxel coordinates (defined in `t1_data`).

![](fig/coordinate_systems.png)

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The concept of an affine matrix may seem confusing at first but an example might help gain an intuition:

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-
- NIfTI image contain a header, which describes the contents, and the data.
- The position of the NIfTI data in space is determined by the affine matrix.
- NIfTI data is a multi-dimensional array of values.

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3 changes: 2 additions & 1 deletion episodes/bids-derivatives.md
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- **Singularity**
- for running containers on high performance compute clusters

![](fig/bids_app.png)

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Building a singularity container is as easy as:

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-
- BIDS Apps are containerized applications that run on BIDS-compatible datasets.

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4 changes: 3 additions & 1 deletion episodes/data-organization-bids.md
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-
- BIDS is an organizational principle for neuroimaging data.
- Converting a raw MRI dataset to a BIDS-compatible dataset streamlines data processing pipelines.

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4 changes: 2 additions & 2 deletions episodes/open-mri-datasets.md
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- BIDS is an organizational principle for neuroimaging data
- PyBIDS is a Python-based tool that allows for easy exploration of BIDS-formatted neuroimaging data
- Public neuroimaging BIDS-compatible data repositories allow for pulling data easily.
- PyBIDS is a Python-based tool that allows for easy exploration of BIDS-formatted neuroimaging data.

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4 changes: 3 additions & 1 deletion episodes/scanner-to-computer.md
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### Anatomical

![](fig/t1t2flairbrain.jpg)

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*Sourced from [https://case.edu/med/neurology/NR/MRI%20Basics.htm](https://case.edu/med/neurology/NR/MRI%20Basics.htm)*

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### Functional

![](fig/bold.gif)

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![](fig/fmri_timeseries.png)

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*Sourced from Wagner and Lindquist, 2015*

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### Diffusion

![](fig/dwi.gif)

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![](fig/dwi_tracts.png)

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*Sourced from [http://brainsuite.org/processing/diffusion/tractography/](https://brainsuite.org/processing/diffusion/tractography/)*

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-
- MRI can capture anatomical (structural), functional, or diffusion features.
- A number of file formats exist to store neuroimaging data.

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