Merge pull request #163 from FZJ-INM1-BDA/documentation

Documentation
FZJ-INM1-BDA · Mar 27, 2023 · 5a9704f · 5a9704f
2 parents b898784 + 0d1992d
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Showing 18 changed files with 5 additions and 6 deletions.
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -28,6 +28,7 @@ nav:
   - About voluba: 'index.md'
   - 'requirements.md'
   - 'acknowledgement.md'
+  - 'examples.md'
   - Workflow:
     - 'input.md'
     - 'views.md'
@@ -37,8 +38,6 @@ nav:
   - Tutorials:
     - 'tutorial.md'
     - 'video.md'
-  - Examples:
-    - 'examples.md'
   - How to:
     - NIfTI conversion: 'nifti_conversion.md'
   - Contact us:

diff --git a/user_docs/alignment.md b/user_docs/alignment.md
@@ -15,7 +15,7 @@ The axis orientations and the voxel scaling can be modified using the **Transfor
 
 ![snippet](images/transformation.png)
 
-If you didn't specify the voxel resolution in your NIfTI header, voluba assumes 1 mm voxel resolution. In this case, you need to scale the volume to its actual resolution. For example, if the resolution of the incoming volume is 100 μm, scale it down by 0.1. You can also adjust the scale for each axis separately by ticking off `Isotropic`.
+If you didn't specify the voxel resolution in your NIfTI header, voluba assumes 1 mm voxel resolution. In this case, you need to manually specify the actual resolution in the **Resolution** section. As the resolution and the scale are related to each other, the values change when either one is modified. This means you can also influence the resolution by scaling the volume. You can adjust the scale for all axes or for each axis separately by ticking off `Isotropic`.
 
 Whenever you want to secure a transformation parameter, click on the lock. This locks the value so that it cannot be changed, for example by interactive manipulation. You can also fix all settings by clicking the lock on the top right next to the volume filters. It is useful to prevent you from accidentally changing the transformation parameters when inspecting the alignment.
 

diff --git a/user_docs/gifs/tutorial_explorer.gif b/user_docs/gifs/tutorial_explorer.gif
diff --git a/user_docs/gifs/tutorial_landmarks.gif b/user_docs/gifs/tutorial_landmarks.gif
diff --git a/user_docs/gifs/tutorial_transform.gif b/user_docs/gifs/tutorial_transform.gif
diff --git a/user_docs/gifs/tutorial_view.gif b/user_docs/gifs/tutorial_view.gif
diff --git a/user_docs/images/history.png b/user_docs/images/history.png
diff --git a/user_docs/images/landmarks1.png b/user_docs/images/landmarks1.png
diff --git a/user_docs/images/landmarks2.png b/user_docs/images/landmarks2.png
diff --git a/user_docs/images/overlay_mode.png b/user_docs/images/overlay_mode.png
diff --git a/user_docs/images/results.png b/user_docs/images/results.png
diff --git a/user_docs/images/teaser.png b/user_docs/images/teaser.png
diff --git a/user_docs/images/transformation.png b/user_docs/images/transformation.png
diff --git a/user_docs/images/tutorial_filter.png b/user_docs/images/tutorial_filter.png
diff --git a/user_docs/images/tutorial_history.png b/user_docs/images/tutorial_history.png
diff --git a/user_docs/images/two_pane_mode.png b/user_docs/images/two_pane_mode.png
diff --git a/user_docs/images/views.png b/user_docs/images/views.png
diff --git a/user_docs/tutorial.md b/user_docs/tutorial.md
@@ -43,7 +43,7 @@ Open the **Edit Landmarks** dialog by clicking on the pin icon on the left. To a
 
 ![gif](gifs/tutorial_landmarks.gif)
 
-By switching back to overlay mode, you can inspect the resulting alignment. If you are not satisfied with the result, you can always roll back to any state of the previous alignment steps by using the history browser. 
+By switching back to overlay mode, you can inspect the resulting alignment. If you are not satisfied with the result, you can always roll back to any state of the previous alignment steps by using the history browser. Open the browser by clicking the gray history icon on the left.
 
 ![snippet](images/tutorial_history.png)
 
@@ -52,13 +52,13 @@ By switching back to overlay mode, you can inspect the resulting alignment. If y
 You can now for example download and reuse the parameters of the affine transformation matrix or view the anchoring result in the interactive atlas viewer siibra-explorer. Click on the **Save/Share Transformation Results** and select the brain icon to open siibra-explorer.
 
 ![gif](gifs/tutorial_explorer.gif)
-s
+
 ## Essential information
 
 As seen from the tutorial, there is some information that is essential to anchor the volume as precisely as possible. When aligning your own imaging data, the anchoring process is facilitated when the following details are known about your data:
 
 * **Resolution of the incoming volume**  
-_If you don't specify the voxel resolution, you will need to scale your incoming volume accordingly._
+_If you don't specify the voxel resolution in the NIfTI header of your incoming volume, you will need to set it manually in voluba._
 * **Hemisphere and cytoarchitectonic area/region of extraction**  
 _You will need this information to find a corresponding location in reference space._
 * **Slicing direction of the incoming volume**