updated course flow images to match name changes

carpentries-incubator · Jun 2, 2021 · f8e28de · f8e28de
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diff --git a/README.md b/README.md
@@ -31,10 +31,10 @@ The primary goals of this workshop are:
 | Time | Episode | Question(s) Answered |
 | ---  | ---     | ---                  |
 ||Setup|Download files required for the lesson|
-| 00:00 | 1. sMRI Modalities | How is MR image acquired? What anatomical features do different modalities capture?  |
+| 00:00 | 1. sMRI Acquisition and Modalities | How is MR image acquired? What anatomical features do different modalities capture?  |
 | 00:30 | 2. sMRI Clean-up | How do we remove intensity artifacts and extract brains? |
 | 01:15 | 3. sMRI Spatial Normalization | What are "coordinate spaces", "templates", "atlases"? What is image registration? |
-| 02:00 | 4. sMRI Quantification | How do we delineate brain anatomy and quantify phenotypes? |
+| 02:00 | 4. sMRI Segmentation and Parcellation | How do we delineate brain anatomy and quantify phenotypes? |
 | 02:45 | 5. sMRI Quality-control | How do we identify image preprocessing failures? |
 | 03:15 | 6. Statistical Analysis | How to compare regional anatomical differences in case-control groups? |
 | 04:00 | 7. Reproducibility Considerations | How sensitive are the findings to your MR pipeline parameters? |

diff --git a/episodes/02-Image_Cleanup.md b/episodes/02-Image_Cleanup.md
@@ -132,17 +132,17 @@ _Source: FSL Introduction to Brain Extraction_
 
 > ## Brain extraction quiz
 >
-> Apart from stripping off non-brain tissue, what can brain-mask be used for?
+> Can we use this brain-mask as an estimate for brain volume?
 >
 > > ## Solution
-> > Brain mask offers information about total brain volume - which can be used for quality control (i.e. identifying algorithm failures) as well as for brain-specific correction (normalization) for downstream statistical models. Althugh intracranial volume is better and more commonly used measure for the latter purpose. 
+> > Brain mask at this stage only offers a crude estimate about total brain volume. It can be used for quality control (e.g. detecting preprocessing algorithm failures). More accurate estimates of total brain and intracranial volumes are calculated in subsequent steps, which are used as covariates or normalzing factors in statistical analysis. 
 > > 
 > > 
 > {: .solution}
 {: .challenge}
 
 
-#### Side-note: [ANTs](http://stnava.github.io/ANTs/) is a software comprising several tools and image processing algorithms. ANTs can be run independently or we can import ANTs scripts in python using [nypype](https://nipype.readthedocs.io/en/latest/) library. 
+#### Side-note: [ANTs](http://stnava.github.io/ANTs/) is a software comprising several tools and image processing algorithms. ANTs can be run independently or we can import ANTs scripts in python using [nipype](https://nipype.readthedocs.io/en/latest/) library. 
 
 ~~~
 from nipype.interfaces.ants.segmentation import BrainExtraction

diff --git a/episodes/04-Image_Quantification.md b/episodes/04-Image_Quantification.md
@@ -1,5 +1,5 @@
 ---
-title: "sMRI Segmentation and Quantification"
+title: "sMRI Segmentation and Parcellation"
 teaching: 30
 exercises: 15
 questions:
@@ -10,9 +10,9 @@ objectives:
 - "Visualize cortical surface meshes (vertex spaces)"
 - "Visualize and differentiate pathologies in MR images" 
 keypoints:
-- "Whole-brain quantification of brain anatomy is a first step towards more specific analysis"
-- "sMRI pathology measures can have significant impact in diagnosis, treatment planning, and surgery"
+- "Whole-brain quantification of brain anatomy is a first step towards biological analysis"
 ---
+
 ## You Are Here!
 ![course_flow](../fig/episode_4/Course_flow_4.png)
 

diff --git a/episodes/04-Image_Quantification_long.md b/episodes/04-Image_Quantification_long.md
@@ -1,5 +1,5 @@
 ---
-title: "sMRI Segmentation and Quantification"
+title: "sMRI Segmentation and Parcellation"
 teaching: 30
 exercises: 15
 questions:
@@ -10,8 +10,7 @@ objectives:
 - "Visualize cortical surface meshes (vertex spaces)"
 - "Visualize and differentiate pathologies in MR images" 
 keypoints:
-- "Whole-brain quantification of brain anatomy is a first step towards more specific analysis"
-- "sMRI pathology measures can have significant impact in diagnosis, treatment planning, and surgery"
+- "Whole-brain quantification of brain anatomy is a first step towards biological analysis"
 ---
 ## You Are Here!
 ![course_flow](../fig/episode_4/Course_flow_4.png)

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diff --git a/fig/episode_4/Course_flow_4.png b/fig/episode_4/Course_flow_4.png
diff --git a/fig/episode_5/Course_flow_5.png b/fig/episode_5/Course_flow_5.png
diff --git a/fig/episode_6/Course_flow_6.png b/fig/episode_6/Course_flow_6.png
diff --git a/fig/episode_7/Course_flow_7.png b/fig/episode_7/Course_flow_7.png
diff --git a/fig/index/Course_flow_0.png b/fig/index/Course_flow_0.png