From 17a7b40ca1ee1e0dd643ff50c9142434f68fc383 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Tue, 27 Aug 2024 00:45:33 +0000 Subject: [PATCH] site deploy MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Auto-generated via {sandpaper} Source : 72e20e6de86e76a534bc5c4593ec682431dafb7c Branch : md-outputs Author : GitHub Actions Time : 2024-02-19 14:50:37 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : e5521f88de169018c12707c21abc1e31fb4d18f5 Branch : main Author : Jon Haitz Legarreta Gorroño Time : 2024-02-19 14:33:58 +0000 Message : [automation] final workbench updates --- 01-Image_Modalities.html | 46 ++---- 02-Image_Cleanup.html | 25 ++- 03-Image_Spatial_Normalization.html | 41 ++--- 04-Image_Quantification.html | 61 +++---- 05-Image_QC.html | 22 ++- 06-Statistical_Analysis.html | 51 +++--- 07-Reproducibility.html | 28 ++-- 404.html | 15 +- CODE_OF_CONDUCT.html | 10 +- LICENSE.html | 19 +-- aio.html | 152 ++++++------------ assets/styles.css | 2 +- assets/styles.css.map | 2 +- discuss.html | 10 +- images.html | 12 +- index.html | 27 ++-- instructor-notes.html | 12 +- instructor/01-Image_Modalities.html | 46 ++---- instructor/02-Image_Cleanup.html | 25 ++- .../03-Image_Spatial_Normalization.html | 41 ++--- instructor/04-Image_Quantification.html | 61 +++---- instructor/05-Image_QC.html | 22 ++- instructor/06-Statistical_Analysis.html | 51 +++--- instructor/07-Reproducibility.html | 28 ++-- instructor/404.html | 15 +- instructor/CODE_OF_CONDUCT.html | 10 +- instructor/LICENSE.html | 19 +-- instructor/aio.html | 152 ++++++------------ instructor/discuss.html | 10 +- instructor/images.html | 12 +- instructor/index.html | 27 ++-- instructor/instructor-notes.html | 12 +- instructor/key-points.html | 12 +- instructor/profiles.html | 12 +- instructor/reference.html | 13 +- key-points.html | 12 +- pkgdown.yml | 2 +- profiles.html | 12 +- reference.html | 13 +- 39 files changed, 441 insertions(+), 701 deletions(-) diff --git a/01-Image_Modalities.html b/01-Image_Modalities.html index 97a89d9..8d84904 100644 --- a/01-Image_Modalities.html +++ b/01-Image_Modalities.html @@ -290,10 +290,10 @@

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See all in one page +
See all in one page
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Objectives

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You Are Here! -

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course_flow

Image acquisition -

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You Are Here!

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course_flow

Image acquisition


  1. The acquisition starts with application of strong magnetic field B0 (e.g. 1.5 or 3.0 Tesla > 10000x earth’s magnetic field) which forces the hydrogen nuclei of the abundant water molecules in soft @@ -410,8 +408,7 @@

    Objectives

    parameter: echo time (TE)) and how fast you repeat the tilt-relax process i.e. RF pulse frequency (design parameter: repetition time (TR)).

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T1 and T2 relaxation -

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T1 and T2 relaxation


Here we see signal from two different tissues as the nuclei are tilted and realigned. The figure on the left shows a single nucleus (i.e. tiny magnet) being tilted away and then precessing back to the the @@ -419,13 +416,11 @@

Objectives

corresponding registered T1 and T2 signal profiles for two different “tissues”. The difference in their signal intensities results in the image contrast.

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MR_relax

Brain tissue comparison -

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MR_relax

Brain tissue comparison


The dotted-black line represents the epoch when you “listen” to the signal (i.e. echo time or TE).

relax_tissue_contrast)

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T1w, T2w, and PD acquisition -

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T1w, T2w, and PD acquisition


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Objectives

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pulse sequence parameters and image contrast -

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pulse sequence parameters and image contrast

What are the two basic pulse sequence parameters that impact T1w and T2w image contrasts? Which one is larger?

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T1 and T2 relaxation tim

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Tissue type and image contrast -

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Tissue type and image contrast

In the T1w image, which one is brighter: White matter, Grey Matter, or CSF?

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Applications per modalitySimilar to T2 with the CSF signal suppressed

TE short TE long (~ T2 of tissue of interest) Identify demyelination
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Image acquisition process and parameters -

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Drawing

What do we want? -

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Image acquisition process and parameters

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Drawing

What do we want?


  • High image contrast
  • High spatial resolution
  • Low scan time!
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What can we control? -

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What can we control?


Magnetic strengths 1.5T vs 3T vs 7T


PYTHON

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PYTHON