From 5e9ff4d0bf208f2d46cf4ad47c079afedb79fca3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Wed, 28 Feb 2024 18:50:36 -0500 Subject: [PATCH] ENH: Add keypoints to episodes Add keypoints to episodes, and re-organize the existing keypoints to better match the episodes. --- episodes/anatomy-of-nifti.md | 5 ++++- episodes/bids-derivatives.md | 3 ++- episodes/data-organization-bids.md | 4 +++- episodes/open-mri-datasets.md | 4 ++-- episodes/scanner-to-computer.md | 4 +++- 5 files changed, 14 insertions(+), 6 deletions(-) diff --git a/episodes/anatomy-of-nifti.md b/episodes/anatomy-of-nifti.md index 1e9e4e6..5da69bd 100644 --- a/episodes/anatomy-of-nifti.md +++ b/episodes/anatomy-of-nifti.md @@ -548,7 +548,10 @@ This is a key component to reproducible analysis and so we'll spend a bit of tim :::::::::::::::::::::::::::::::::::::::: keypoints -- +- 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. + :::::::::::::::::::::::::::::::::::::::::::::::::: diff --git a/episodes/bids-derivatives.md b/episodes/bids-derivatives.md index 13d8352..52149b7 100644 --- a/episodes/bids-derivatives.md +++ b/episodes/bids-derivatives.md @@ -57,7 +57,8 @@ singularity run --cleanenv \ :::::::::::::::::::::::::::::::::::::::: keypoints -- +- BIDS Apps are containerized applications that run on BIDS-compatible datasets. + :::::::::::::::::::::::::::::::::::::::::::::::::: diff --git a/episodes/data-organization-bids.md b/episodes/data-organization-bids.md index 98ab3ab..3b3ba43 100644 --- a/episodes/data-organization-bids.md +++ b/episodes/data-organization-bids.md @@ -44,7 +44,9 @@ Using the same structure for all of your studies will allow you to easily reuse :::::::::::::::::::::::::::::::::::::::: keypoints -- +- BIDS is an organizational principle for neuroimaging data. +- Converting a raw MRI dataset to a BIDS-compatible dataset streamlines data processing pipelines. + :::::::::::::::::::::::::::::::::::::::::::::::::: diff --git a/episodes/open-mri-datasets.md b/episodes/open-mri-datasets.md index 6910dbc..fad273e 100644 --- a/episodes/open-mri-datasets.md +++ b/episodes/open-mri-datasets.md @@ -198,8 +198,8 @@ df.head() :::::::::::::::::::::::::::::::::::::::: keypoints -- 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. :::::::::::::::::::::::::::::::::::::::::::::::::: diff --git a/episodes/scanner-to-computer.md b/episodes/scanner-to-computer.md index a0b6e57..7288312 100644 --- a/episodes/scanner-to-computer.md +++ b/episodes/scanner-to-computer.md @@ -110,7 +110,9 @@ dcm2niix -z y -o ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystu :::::::::::::::::::::::::::::::::::::::: keypoints -- +- MRI can capture anatomical (structural), functional, or diffusion features. +- A number of file formats exist to store neuroimaging data. + ::::::::::::::::::::::::::::::::::::::::::::::::::