), or by double
clicking on the overlay name.
).Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -1697,7 +1697,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1774,7 +1774,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2810,7 +2810,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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. 
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -646,9 +647,8 @@ Figure 16
them. 
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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. 
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.
+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 ( 
), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( 
).
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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -1715,7 +1715,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1792,7 +1792,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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. 
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them. 
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 
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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
MNI152_T1_1mm_brain from this list of files.
-Show me the solution
-
+
@@ -1697,7 +1697,7 @@ BONUS Exercise 3
TODO: add the solution of the three tissue volumes
BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1774,7 +1774,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2810,7 +2810,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -646,9 +647,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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. 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.
+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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -1715,7 +1715,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1792,7 +1792,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: Provide solution
BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2810,7 +2810,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -646,9 +647,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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. 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.
+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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -1715,7 +1715,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1792,7 +1792,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: add key points to solution
Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -646,9 +647,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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. 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.
+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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -1715,7 +1715,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1792,7 +1792,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
Refer to the Getting started session for more details!
@@ -2823,7 +2823,7 @@Give me a hint
-
+
@@ -3272,7 +3272,7 @@
@@ -3282,9 +3282,11 @@ TODO: Add the number of files and how you can tell
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?
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)
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 @@
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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -646,9 +647,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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. 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.
+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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -1715,7 +1715,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1792,7 +1792,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -646,9 +647,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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. 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.
+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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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.
-
+
We can now check if our image is registered by flicking back and
forth between the MNI image and our image.
Give me a hint
-
+
@@ -307,9 +307,11 @@
diff --git a/images.html b/images.html
index d496379..aa471f6 100644
--- a/images.html
+++ b/images.html
@@ -472,7 +472,8 @@
Show/hide each overlay with the eye button ( {alt=“eye icon” height=‘24px’} ), or by double
+
+ Show/hide each overlay with the eye button ( ), or by double
clicking on the overlay name.
Unlinking cursors {alt=“eye icon” height=‘24px’} ), or by double
+
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 @@ Refer to the Getting started session for more details!
@@ -415,7 +415,7 @@Give me a hint
-
+
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 @@
TODO: Add the number of files and how you can tell
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?
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)
Figure 21
- the overlay list.
Figure 22
- {alt=“eye icon” height=‘24px’} ), or by double
+
+ ), or by double
clicking on the overlay name.Figure 23
@@ -646,9 +647,8 @@Figure 16
them.
Figure 17
-Select the MNI152_T1_1mm_brain from this list of files.
-
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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. 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.
+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
), or by double
clicking on the overlay name. ).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. 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.
+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
Unlinking cursors {alt=“eye icon” height=‘24px’} ), or by double
+Show/hide each overlay with the eye button ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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.
-
+
We can now check if our image is registered by flicking back and
forth between the MNI image and our image.
), or by double
clicking on the overlay name. ).Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
We can now check if our image is registered by flicking back and
forth between the MNI image and our image.
MNI152_T1_1mm_brain from this list of files.
-BONUS Exercise 1
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -1715,7 +1715,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1792,7 +1792,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: add the solution of the three tissue volumes
BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -1792,7 +1792,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: Provide solution
BASH
Show me the solution
-
+
TODO: add key points to solution
@@ -2830,7 +2830,7 @@ Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: add key points to solution
Challenge
Give me a hint
-
+
Refer to the 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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
Refer to the Getting started session for more details!
@@ -2843,7 +2843,7 @@Give me a hint
-
+
@@ -3293,7 +3293,7 @@
@@ -3303,9 +3303,11 @@ TODO: Add the number of files and how you can tell
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?
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)
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 @@
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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
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
Give me a hint
-
+
Refer to the 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.
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 ( ), or by double
clicking on the overlay name.
Figure 23
@@ -648,9 +649,8 @@ Figure 16
them.
Figure 17
-
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
Give me a hint
-
+
@@ -309,9 +309,11 @@
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 @@
Show/hide each overlay with the eye button ( {alt=“eye icon” height=‘24px’} ), or by double
+
+ Show/hide each overlay with the eye button ( ), or by double
clicking on the overlay name.
Unlinking cursors {alt=“eye icon” height=‘24px’} ), or by double
+
Refer to the Getting started session for more details!
@@ -417,7 +417,7 @@Give me a hint
-
+
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 @@
TODO: Add the number of files and how you can tell
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?
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)
Figure 21
- the overlay list.
Figure 22
- {alt=“eye icon” height=‘24px’} ), or by double
+
+ ), or by double
clicking on the overlay name.Figure 23
@@ -648,9 +649,8 @@Figure 16
them.
Figure 17
-Select the MNI152_T1_1mm_brain from this list of files.
-
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 ( ), or by double
clicking on the overlay name.
Link overlay display properties with the chainlink button ( ).
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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
), or by double
clicking on the overlay name. ).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?
Duration: 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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
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?
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. 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.
+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.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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"
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"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"
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"profiles/learner-profiles.md" "5fe5bf7537072422b91ed393ada03f9a" "site/built/learner-profiles.md" "2024-06-23"
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diff --git a/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
Select the MNI152_T1_1mm_brain from this list of files.
-
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -756,7 +756,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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"
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-"episodes/structural-mri.Rmd" "3be352bd8438890b21ae5b208959c535" "site/built/structural-mri.md" "2024-06-23"
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+"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"
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"episodes/command-line.Rmd" "8733a1e565f18e6fee58edf75762ba6e" "site/built/command-line.md" "2024-06-23"
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"learners/reference.md" "527a12e217602daae51c5fd9ef8958df" "site/built/reference.md" "2024-06-23"
-"learners/setup.md" "0b2a8aac2aa65eb169e3ea584884eb95" "site/built/setup.md" "2024-06-23"
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"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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: add the solution of the three tissue volumes
BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -833,7 +833,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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"
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"episodes/pet-imaging.Rmd" "63836785bdc4085fb03ff16b8a04d151" "site/built/pet-imaging.md" "2024-06-23"
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"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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: Provide solution
BASH
Show me the solution
-
+
TODO: add key points to solution
diff --git a/md5sum.txt b/md5sum.txt
index b510aca..b8bc69d 100644
--- 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"
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+"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"
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"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/pkgdown.yml b/pkgdown.yml
index c351d37..e254fc9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
pkgdown: 2.0.9
pkgdown_sha: ~
articles: {}
-last_built: 2024-06-23T20:34Z
+last_built: 2024-06-23T20:47Z
diff --git a/structural-mri.html b/structural-mri.html
index 9cbcc19..f5255b6 100644
--- a/structural-mri.html
+++ b/structural-mri.html
@@ -641,7 +641,7 @@ Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
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
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: add key points to solution
Quality check
Select the MNI152_T1_1mm_brain from this list of files.
-
+
We can now check if our image is registered by flicking back and
forth between the MNI image and our image.
MNI152_T1_1mm_brain from this list of files.
-BONUS Exercise 1
Show me the solution
-
+
TODO: add the solution of the three tissue volumes
@@ -754,7 +754,7 @@ BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: add the solution of the three tissue volumes
BONUS Exercise 3
Show me the solution
-
+
TODO: Provide solution
@@ -831,7 +831,7 @@ BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: Provide solution
BASH
Show me the solution
-
+
TODO: add key points to solution
TODO: add key points to solution