diff --git a/_episodes/introduction.md b/_episodes/introduction.md index 651908cf..2b1008a5 100644 --- a/_episodes/introduction.md +++ b/_episodes/introduction.md @@ -39,10 +39,9 @@ brain tissue. DWI has been used extensively to diagnose stroke, assess white matter damage in many different kinds of diseases, provide insights into the white matter connectivity, and much more! -![fiber_configurations] -({{ relative_root_path }}/fig/introduction/diffusion_direction_new.png) -\Diffusion along X, Y, and Z directions. The signal in the left/right oriented -corpus callosum is lowest when measured along X, while the signal in the ++![Diffusion along different directions]({{ relative_root_path }}/fig/introduction/diffusion_directions.png) \ +\Diffusion along X, Y, and Z directions. The signal in the left/right oriented +corpus callosum is lowest when measured along X, while the signal in the inferior/superior oriented corticospinal tract is lowest when measured along Z. ## b-values & b-vectors @@ -71,8 +70,7 @@ properties. The DWI acquisition process is thus: For the rest of this lesson, we will make use of a subset of a publicly available dataset, ds000221, originally hosted at [openneuro.org](https://openneuro.org/datasets/ds000221/versions/1.0.0). The dataset is structured according to the Brain Imaging Data Structure -([BIDS](https://bids-specification.readthedocs.io/en/etable/)). Please check -the [the BIDS-dMRI Setup page](https://carpentries-incubator.github.io/SDC-BIDS-dMRI/setup.html) +([BIDS](https://bids-specification.readthedocs.io/en/etable/)). Please check the [BIDS-dMRI Setup page](https://carpentries-incubator.github.io/SDC-BIDS-dMRI/setup.html) to download the dataset. Below is a tree diagram showing the folder structure of a single MR subject and diff --git a/_episodes/preprocessing.md b/_episodes/preprocessing.md index f27b2d3c..c6872792 100644 --- a/_episodes/preprocessing.md +++ b/_episodes/preprocessing.md @@ -52,9 +52,9 @@ lesson. ### Brainmasking The first step to the preprocessing workflow is to create an appropriate -brainmask from the diffusion data! Start by first importing the necessary modules and -reading the diffusion data along with the coordinate system (the affine)! We will also grab -the anatomical T1w image to use later on, as well as the second inversion from the anatomical +brainmask from the diffusion data! Start by first importing the necessary modules and +reading the diffusion data along with the coordinate system (the affine)! We will also grab +the anatomical T1w image to use later on, as well as the second inversion from the anatomical acquisition for brainmasking purposes. ~~~ @@ -128,7 +128,7 @@ differs. Typically, this is done using two acquisitions acquired with opposite phase-encoding directions, which results in the same field creating distortions in opposing directions. -![blips]({{ relative_root_path }}/fig/preprocessing/blip_up_blip_down.png) +![Blip up and blip down pairs]({{ relative_root_path }}/fig/preprocessing/blip_up_blip_down.png) \ Opposite phase-encodings from two DWI Here, we will make use of the two opposite phase-encoded acquisitions found in diff --git a/code/introduction.ipynb b/code/introduction.ipynb index 85f6a099..8433ad40 100644 --- a/code/introduction.ipynb +++ b/code/introduction.ipynb @@ -28,7 +28,7 @@ "diagnose stroke, assess white matter damage in many different kinds of diseases, \n", "provide insights into the white matter connectivity, and much more!\n", "\n", - "![fiber_configurations](../fig/introduction/diffusion_direction_new.png) \\\n", + "![[Diffusion along different directions](../fig/introduction/diffusion_directions.png) \\\n", "Diffusion along X, Y, and Z directions. The signal in the left/right oriented \n", "corpus callosum is lowest when measured along X, while the signal in the \n", "inferior/superior oriented corticospinal tract is lowest when measured along Z." diff --git a/code/preprocessing.ipynb b/code/preprocessing.ipynb index e470d0d7..e724b126 100644 --- a/code/preprocessing.ipynb +++ b/code/preprocessing.ipynb @@ -150,7 +150,7 @@ "phase-encoding directions, which results in the same field creating distortions\n", "in opposing directions.\n", "\n", - "![blips](../fig/preprocessing/blip_up_blip_down.png)\\\n", + "![Blip up and blip down pairs](../fig/preprocessing/blip_up_blip_down.png)\\\n", "Opposite phase-encodings from two DWI\n", "\n", "Here, we will make use of the two opposite phase-encoded acquisitions found in\n", diff --git a/fig/introduction/diffusion_direction_new.png b/fig/introduction/diffusion_directions.png similarity index 100% rename from fig/introduction/diffusion_direction_new.png rename to fig/introduction/diffusion_directions.png