From 71198e084d7d6a4962a356cb99890db49a131fac Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sun, 23 Jun 2024 20:47:29 +0000 Subject: [PATCH] site deploy Auto-generated via {sandpaper} Source : 33788066ee93e7770207a3ec40770bddecb1453d Branch : md-outputs Author : GitHub Actions Time : 2024-06-23 20:47:15 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 7da304deb9a43d28da32588a9bc82d47611abe49 Branch : main Author : davecash75 Time : 2024-06-23 20:46:21 +0000 Message : Merge pull request #2 from HealthBioscienceIDEAS/fmri_luigi Update questions and objectives functional-mri.Rmd --- aio.html | 26 ++++++++++--------- command-line.html | 2 +- diffusion-weighted-imaging.html | 4 +-- functional-mri.html | 10 ++++--- images.html | 6 ++--- imaging-data-structure-and-formats.html | 2 +- index.html | 19 +++++++------- instructor/aio.html | 26 ++++++++++--------- instructor/command-line.html | 2 +- instructor/diffusion-weighted-imaging.html | 4 +-- instructor/functional-mri.html | 10 ++++--- instructor/images.html | 6 ++--- .../imaging-data-structure-and-formats.html | 2 +- instructor/index.html | 23 ++++++++-------- instructor/structural-mri.html | 8 +++--- md5sum.txt | 8 +++--- pkgdown.yml | 2 +- structural-mri.html | 8 +++--- 18 files changed, 89 insertions(+), 79 deletions(-) diff --git a/aio.html b/aio.html index 9258463..05ac4f4 100644 --- a/aio.html +++ b/aio.html @@ -932,7 +932,7 @@

Unlinking cursors {alt=“eye icon” height=‘24px’} ), or by double +
  • Show/hide each overlay with the eye button ( eye icon ), or by double clicking on the overlay name.
  • Link overlay display properties with the chainlink button ( chain icon ).
  • Save an overlay if it has been edited, with the floppy disk button ( @@ -1583,7 +1583,7 @@

    Quality check

    Select the MNI152_T1_1mm_brain from this list of files. -Choose MNI image

    +

    We can now check if our image is registered by flicking back and forth between the MNI image and our image.

    @@ -1611,7 +1611,7 @@

    BONUS Exercise 1

    Getting started session for more details!

    @@ -2823,7 +2823,7 @@

    Give me a hint

    -
    +

    TODO: Add the number of files and how you can tell

    @@ -3272,7 +3272,7 @@

    Questions

    • What generates the signal that fMRI is measuring?
    • What preprocessing steps are needed before analysing fMRI data?
      • -
    • How can I extract brain network information from the images.
      • +
    • What type of analysis can I perform on pre-processed fMRI data?
    @@ -3282,9 +3282,11 @@

    Questions

    Objectives

      -
    • Explain how the BOLD signal works
      • -
    • Demonstrate the pre-processing steps commonly used in fMRI
      • -
    • Identify common resting state networks
      • +
    • Explain main sources of variability in BOLD signal and how to handle +them
      • +
    • Demonstrate basic pre-processing steps commonly used in fMRI
      • +
    • Get to know what type of information we can obtain from +pre-processed data (e.g. resting state networks)
    @@ -3994,7 +3996,7 @@

    That just flew off the screen1!

    -
    +

    OUTPUT diff --git a/command-line.html b/command-line.html index 19995f1..af548ff 100644 --- a/command-line.html +++ b/command-line.html @@ -591,7 +591,7 @@

    That just flew off the screen1!

    -
    +

    OUTPUT diff --git a/diffusion-weighted-imaging.html b/diffusion-weighted-imaging.html index 3937f84..473ff3f 100644 --- a/diffusion-weighted-imaging.html +++ b/diffusion-weighted-imaging.html @@ -402,7 +402,7 @@

    Challenge

    Getting started session for more details!

    @@ -415,7 +415,7 @@

    Give me a hint

    -
    +

    TODO: Add the number of files and how you can tell

    diff --git a/functional-mri.html b/functional-mri.html index 2aff973..a1ab5b5 100644 --- a/functional-mri.html +++ b/functional-mri.html @@ -299,7 +299,7 @@

    Overview

    Questions

    • What generates the signal that fMRI is measuring?
    • What preprocessing steps are needed before analysing fMRI data?
      • -
    • How can I extract brain network information from the images.
      • +
    • What type of analysis can I perform on pre-processed fMRI data?
    @@ -307,9 +307,11 @@

    Questions

    Objectives

    -
    • Explain how the BOLD signal works
      • -
    • Demonstrate the pre-processing steps commonly used in fMRI
      • -
    • Identify common resting state networks
      • +
      • Explain main sources of variability in BOLD signal and how to handle +them
        • +
      • Demonstrate basic pre-processing steps commonly used in fMRI
        • +
      • Get to know what type of information we can obtain from +pre-processed data (e.g. resting state networks)
    diff --git a/images.html b/images.html index d496379..aa471f6 100644 --- a/images.html +++ b/images.html @@ -472,7 +472,8 @@

    Figure 21

    - the overlay list. Overlay list

    Figure 22

    -
  • Show/hide each overlay with the eye button ( {alt=“eye icon” height=‘24px’} ), or by double + +
  • Show/hide each overlay with the eye button ( eye icon ), or by double clicking on the overlay name.

    • Figure 23

    @@ -646,9 +647,8 @@

    Figure 16

    them. Add standard function

    Figure 17

    -

    Select the MNI152_T1_1mm_brain from this list of files. -Choose MNI image

    +

    Figure 18

    diff --git a/imaging-data-structure-and-formats.html b/imaging-data-structure-and-formats.html index 54384bc..41489e4 100644 --- a/imaging-data-structure-and-formats.html +++ b/imaging-data-structure-and-formats.html @@ -853,7 +853,7 @@

    Unlinking cursors {alt=“eye icon” height=‘24px’} ), or by double +
  • Show/hide each overlay with the eye button ( eye icon ), or by double clicking on the overlay name.
  • Link overlay display properties with the chainlink button ( chain icon ).
  • Save an overlay if it has been edited, with the floppy disk button ( diff --git a/index.html b/index.html index 2df9d17..cbdfa3f 100644 --- a/index.html +++ b/index.html @@ -403,15 +403,16 @@

    Cloud based instructionsStart accessing your apps using Amazon AppStream 2.0. This will have the link to set your password and log in for the first time. 1. A second email should come from the same email with the title -Amazon AppStream 2.0: New apps available. Appstream Email 1. Click on -the login link, and you should see the following page. Appstream Login 1. Click on -the Desktop item. It will then launch a computer and -you will be able to see the Desktop on the screen Appstream Choose Desktop 1. You will see a status message that -it is starting your machine. After that you should see a desktop of the -computer you will be doing the lesson with. Appstream Desktop 1. IF -you get an error message saying “Resources not available, -please wait a few minutes, as there will be more virtual machines -spinning up to match the demand.

    +Amazon AppStream 2.0: New apps available. 1. +Click on the login link, and you should see the following page. 1. +Click on the Desktop item. It will then launch a +computer and you will be able to see the Desktop on the screen +1. You will see a status message that it is starting your machine. After +that you should see a desktop of the computer you will be doing the +lesson with. 1. +IF you get an error message saying “Resources not +available, please wait a few minutes, as there will be more virtual +machines spinning up to match the demand.

    If you did not supply an email yet, please approach an instructor and we will setup your account

    • diff --git a/instructor/aio.html b/instructor/aio.html index 3f6038b..d4b629c 100644 --- a/instructor/aio.html +++ b/instructor/aio.html @@ -949,7 +949,7 @@

    Unlinking cursors {alt=“eye icon” height=‘24px’} ), or by double +
  • Show/hide each overlay with the eye button ( eye icon ), or by double clicking on the overlay name.
  • Link overlay display properties with the chainlink button ( chain icon ).
  • Save an overlay if it has been edited, with the floppy disk button ( @@ -1601,7 +1601,7 @@

    Quality check

    Select the MNI152_T1_1mm_brain from this list of files. -Choose MNI image

    +

    We can now check if our image is registered by flicking back and forth between the MNI image and our image.

    • @@ -1629,7 +1629,7 @@

    BONUS Exercise 1

    Getting started session for more details!

    @@ -2843,7 +2843,7 @@

    Give me a hint

    -
    +

    TODO: Add the number of files and how you can tell

    @@ -3293,7 +3293,7 @@

    Questions

    • What generates the signal that fMRI is measuring?
    • What preprocessing steps are needed before analysing fMRI data?
      • -
    • How can I extract brain network information from the images.
      • +
    • What type of analysis can I perform on pre-processed fMRI data?
    @@ -3303,9 +3303,11 @@

    Questions

    Objectives

      -
    • Explain how the BOLD signal works
      • -
    • Demonstrate the pre-processing steps commonly used in fMRI
      • -
    • Identify common resting state networks
      • +
    • Explain main sources of variability in BOLD signal and how to handle +them
      • +
    • Demonstrate basic pre-processing steps commonly used in fMRI
      • +
    • Get to know what type of information we can obtain from +pre-processed data (e.g. resting state networks)
    @@ -4016,7 +4018,7 @@

    That just flew off the screen1!

    -
    +

    OUTPUT diff --git a/instructor/command-line.html b/instructor/command-line.html index c1f8fe2..08bb1f4 100644 --- a/instructor/command-line.html +++ b/instructor/command-line.html @@ -593,7 +593,7 @@

    That just flew off the screen1!

    -
    +

    OUTPUT diff --git a/instructor/diffusion-weighted-imaging.html b/instructor/diffusion-weighted-imaging.html index 0dd1588..b0e268d 100644 --- a/instructor/diffusion-weighted-imaging.html +++ b/instructor/diffusion-weighted-imaging.html @@ -404,7 +404,7 @@

    Challenge

    Getting started session for more details!

    @@ -417,7 +417,7 @@

    Give me a hint

    -
    +

    TODO: Add the number of files and how you can tell

    diff --git a/instructor/functional-mri.html b/instructor/functional-mri.html index 215b0b2..c03d8b6 100644 --- a/instructor/functional-mri.html +++ b/instructor/functional-mri.html @@ -301,7 +301,7 @@

    Overview

    Questions

    • What generates the signal that fMRI is measuring?
    • What preprocessing steps are needed before analysing fMRI data?
      • -
    • How can I extract brain network information from the images.
      • +
    • What type of analysis can I perform on pre-processed fMRI data?
    @@ -309,9 +309,11 @@

    Questions

    Objectives

    -
    • Explain how the BOLD signal works
      • -
    • Demonstrate the pre-processing steps commonly used in fMRI
      • -
    • Identify common resting state networks
      • +
      • Explain main sources of variability in BOLD signal and how to handle +them
        • +
      • Demonstrate basic pre-processing steps commonly used in fMRI
        • +
      • Get to know what type of information we can obtain from +pre-processed data (e.g. resting state networks)
    diff --git a/instructor/images.html b/instructor/images.html index 9d1a52a..90e30e9 100644 --- a/instructor/images.html +++ b/instructor/images.html @@ -474,7 +474,8 @@

    Figure 21

    - the overlay list. Overlay list

    Figure 22

    -
  • Show/hide each overlay with the eye button ( {alt=“eye icon” height=‘24px’} ), or by double + +
  • Show/hide each overlay with the eye button ( eye icon ), or by double clicking on the overlay name.

    • Figure 23

    @@ -648,9 +649,8 @@

    Figure 16

    them. Add standard function

    Figure 17

    -

    Select the MNI152_T1_1mm_brain from this list of files. -Choose MNI image

    +

    Figure 18

    diff --git a/instructor/imaging-data-structure-and-formats.html b/instructor/imaging-data-structure-and-formats.html index 2d7feb0..43b9b60 100644 --- a/instructor/imaging-data-structure-and-formats.html +++ b/instructor/imaging-data-structure-and-formats.html @@ -869,7 +869,7 @@

    Unlinking cursors {alt=“eye icon” height=‘24px’} ), or by double +
  • Show/hide each overlay with the eye button ( eye icon ), or by double clicking on the overlay name.
  • Link overlay display properties with the chainlink button ( chain icon ).
  • Save an overlay if it has been edited, with the floppy disk button ( diff --git a/instructor/index.html b/instructor/index.html index a635cfd..bc4cbab 100644 --- a/instructor/index.html +++ b/instructor/index.html @@ -439,8 +439,8 @@

    Agenda< What generates the signal that fMRI is measuring?
    What preprocessing -steps are needed before analysing fMRI data?
    How can I extract brain -network information from the images. +steps are needed before analysing fMRI data?
    What type of analysis +can I perform on pre-processed fMRI data? 02h 46m @@ -481,15 +481,16 @@

    Cloud based instructionsStart accessing your apps using Amazon AppStream 2.0. This will have the link to set your password and log in for the first time. 1. A second email should come from the same email with the title -Amazon AppStream 2.0: New apps available. Appstream Email 1. Click on -the login link, and you should see the following page. Appstream Login 1. Click on -the Desktop item. It will then launch a computer and -you will be able to see the Desktop on the screen Appstream Choose Desktop 1. You will see a status message that -it is starting your machine. After that you should see a desktop of the -computer you will be doing the lesson with. Appstream Desktop 1. IF -you get an error message saying “Resources not available, -please wait a few minutes, as there will be more virtual machines -spinning up to match the demand.

    +Amazon AppStream 2.0: New apps available. 1. +Click on the login link, and you should see the following page. 1. +Click on the Desktop item. It will then launch a +computer and you will be able to see the Desktop on the screen +1. You will see a status message that it is starting your machine. After +that you should see a desktop of the computer you will be doing the +lesson with. 1. +IF you get an error message saying “Resources not +available, please wait a few minutes, as there will be more virtual +machines spinning up to match the demand.

    If you did not supply an email yet, please approach an instructor and we will setup your account

    • diff --git a/instructor/structural-mri.html b/instructor/structural-mri.html index c11b2d4..76fb66d 100644 --- a/instructor/structural-mri.html +++ b/instructor/structural-mri.html @@ -643,7 +643,7 @@

    Quality check

    Select the MNI152_T1_1mm_brain from this list of files. -Choose MNI image

    +

    We can now check if our image is registered by flicking back and forth between the MNI image and our image.

    @@ -670,7 +670,7 @@

    BONUS Exercise 1

    Select the MNI152_T1_1mm_brain from this list of files. -Choose MNI image

    +

    We can now check if our image is registered by flicking back and forth between the MNI image and our image.

    @@ -668,7 +668,7 @@

    BONUS Exercise 1