markdown source builds

Auto-generated via {sandpaper} Source : 7da304d Branch : main Author : davecash75 <[email protected]> Time : 2024-06-23 20:46:21 +0000 Message : Merge pull request #2 from HealthBioscienceIDEAS/fmri_luigi Update questions and objectives functional-mri.Rmd
HealthBioscienceIDEAS · Jun 23, 2024 · 3378806 · 3378806
1 parent e6975e2
commit 3378806
Show file tree

Hide file tree

Showing 5 changed files with 14 additions and 15 deletions.
diff --git a/functional-mri.md b/functional-mri.md
@@ -8,15 +8,15 @@ exercises: 2
 
 - 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?
 
 ::::::::::::::::::::::::::::::::::::::::::::::::
 
 ::::::::::::::::::::::::::::::::::::: 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/imaging-data-structure-and-formats.md b/imaging-data-structure-and-formats.md
@@ -471,8 +471,7 @@ The overlay list allows you to do the following:
 * Identify the currently selected overlay (highlighted in blue).
 * Add/remove overlays with the + and - buttons.
 * Change the overlay display order with the &#x25B2; and &#x25BC; buttons.
-* Show/hide each overlay with the eye button ( ![](fig/eye_icon.png)
-{alt="eye icon" height='24px'} ), or by double clicking on the overlay name.
+* Show/hide each overlay with the eye button ( ![](fig/eye_icon.png){alt="eye icon" height='24px'} ), or by double clicking on the overlay name.
 * Link overlay display properties with the chainlink button
   ( ![](fig/chainlink_icon.png){alt="chain icon" height='24px'} ).
 * Save an overlay if it has been edited, with the floppy disk button

diff --git a/md5sum.txt b/md5sum.txt
@@ -4,14 +4,14 @@
 "config.yaml" "1ffcb908aaa07803663daa40efd14b41" "site/built/config.yaml" "2024-06-23"
 "index.md" "da6599e527279b75af5d416cf293c514" "site/built/index.md" "2024-06-23"
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-06-23"
-"episodes/imaging-data-structure-and-formats.Rmd" "71b9a479a59db29c6369a0bbbb9c5ab7" "site/built/imaging-data-structure-and-formats.md" "2024-06-23"
-"episodes/structural-mri.Rmd" "3be352bd8438890b21ae5b208959c535" "site/built/structural-mri.md" "2024-06-23"
+"episodes/imaging-data-structure-and-formats.Rmd" "2ac7be9f41ec0c3592d96d7ec01f03a2" "site/built/imaging-data-structure-and-formats.md" "2024-06-23"
+"episodes/structural-mri.Rmd" "d2d4c1671dd21b1cf5677ee4fe93a0fc" "site/built/structural-mri.md" "2024-06-23"
 "episodes/pet-imaging.Rmd" "63836785bdc4085fb03ff16b8a04d151" "site/built/pet-imaging.md" "2024-06-23"
 "episodes/diffusion-weighted-imaging.Rmd" "ff86108444c48fb7147adc00d5e9698c" "site/built/diffusion-weighted-imaging.md" "2024-06-23"
-"episodes/functional-mri.Rmd" "c1b69ca6e193a922af0a5f9b5fb7e2c3" "site/built/functional-mri.md" "2024-06-23"
+"episodes/functional-mri.Rmd" "dd4e504186071abf6ccf12f3286c51a3" "site/built/functional-mri.md" "2024-06-23"
 "episodes/command-line.Rmd" "8733a1e565f18e6fee58edf75762ba6e" "site/built/command-line.md" "2024-06-23"
 "instructors/instructor-notes.md" "5cf113fd22defb29d17b64597f3c9bc0" "site/built/instructor-notes.md" "2024-06-23"
 "learners/reference.md" "527a12e217602daae51c5fd9ef8958df" "site/built/reference.md" "2024-06-23"
-"learners/setup.md" "0b2a8aac2aa65eb169e3ea584884eb95" "site/built/setup.md" "2024-06-23"
+"learners/setup.md" "6f3568491fe49e569dc8b5913d7ea78b" "site/built/setup.md" "2024-06-23"
 "profiles/learner-profiles.md" "5fe5bf7537072422b91ed393ada03f9a" "site/built/learner-profiles.md" "2024-06-23"
 "renv/profiles/lesson-requirements/renv.lock" "a09e8b910f6d5de500bec6e099357d63" "site/built/renv.lock" "2024-06-23"
diff --git a/setup.md b/setup.md
@@ -10,13 +10,13 @@ This page will tell you how to access your personal virtual (VM) to run these le
 If you have completed the pre-survey questionnaire, then you should have received two emails. These may be located in your spam email:
 1. One should be from the email address [email protected] with the title _Start 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](fig/aic_appstream_email.png)
+ ![](fig/aic_appstream_email.png{alt="Appstream Email"})
 1. Click on the login link, and you should see the following page.
- ![Appstream Login](fig/aic_appstream_login.png)
+ ![](fig/aic_appstream_login.png{alt="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](fig/aic_appstream_choose_desktop.png)
+ ![](fig/aic_appstream_choose_desktop.png{alt="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](fig/aic_smri_desktop.png)
+ ![](fig/aic_smri_desktop.png{alt="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.
 
 **If you did not supply an email yet, please approach an instructor and we will setup your account**

diff --git a/structural-mri.md b/structural-mri.md
@@ -302,7 +302,7 @@ standard atlases and templates so that you can quickly access them.
 ![Add Standard image](fig/aic_smri_fsleyes_addstd.png){alt="Add standard function"}
 
 Select the `MNI152_T1_1mm_brain` from this list of files.
-![Choose MNI image](fig/aic_smri_fsleyes_choosemni.png)
+![](fig/aic_smri_fsleyes_choosemni.png {alt="Choose MNI image"})
 
 We can now check if our image is registered by flicking back and forth between 
 the MNI image and our image.