diff --git a/docs/images/hOc1.png b/docs/images/hOc1.png new file mode 100644 index 0000000..ba8dcb4 Binary files /dev/null and b/docs/images/hOc1.png differ diff --git a/docs/images/loaded_volume.png b/docs/images/loaded_volume.png deleted file mode 100644 index 2f37901..0000000 Binary files a/docs/images/loaded_volume.png and /dev/null differ diff --git a/docs/images/start.png b/docs/images/start.png deleted file mode 100644 index 1872a3c..0000000 Binary files a/docs/images/start.png and /dev/null differ diff --git a/docs/images/teaser.png b/docs/images/teaser.png index d1fb72b..1a46d64 100644 Binary files a/docs/images/teaser.png and b/docs/images/teaser.png differ diff --git a/docs/images/tutorial.png b/docs/images/tutorial.png new file mode 100644 index 0000000..b864bde Binary files /dev/null and b/docs/images/tutorial.png differ diff --git a/docs/images/warped.png b/docs/images/warped.png deleted file mode 100644 index 475a844..0000000 Binary files a/docs/images/warped.png and /dev/null differ diff --git a/docs/images/workflow.png b/docs/images/workflow.png index 9efe0a6..b33738f 100644 Binary files a/docs/images/workflow.png and b/docs/images/workflow.png differ diff --git a/docs/tutorial.md b/docs/tutorial.md index 9e24f20..d2f4716 100644 --- a/docs/tutorial.md +++ b/docs/tutorial.md @@ -3,16 +3,14 @@ In this tutorial, you will warp an example MRI scan to ICBM MNI152 2009c nonlinear asymmetric space and assign a region to a point in the input space. For this example, we use a NIfTI file from the publicly available [NFBS Skull-Stripped Repository](http://preprocessed-connectomes-project.org/NFB_skullstripped/). We choose the T1-weighted MRI scan `sub-A00028185_ses-NFB3_T1w.nii.gz` of patient `A00028185`. 1. Download the NFBS skull-stripped images from [here](http://preprocessed-connectomes-project.org/NFB_skullstripped/). -2. Unpack the .tar.gz archive. We recommend using [7zip](https://www.7-zip.org). +2. Unpack the .tar.gz archive. 3. Choose `C:/Users/your_username/Downloads/NFBS_Dataset/A00028185/sub-A00028185_ses-NFB3_T1w.nii.gz` as Input NIfTI. You can either copy and paste this path or you can choose this file from the file explorer by clicking .... -4. Leave the Output folder at the default location `C:\Users\your_username\voluba-mriwarp`. +4. Leave the Output folder at the default location `C:/Users/your_username/voluba-mriwarp`. 5. Click Warp input to MNI152 space to warp patient `A00028185`'s brain to ICBM MNI152 2009c nonlinear asymmetric space. The progress bar indicates that the calculation is still running. When the registration is finished, a green checkmark will appear next to the button. -6. Double-click a location in the input space to assign brain regions to it. We select a point in Hippocampus. In the side panel on the left every listed region is indeed part of the Hippocampus. -7. Click :fa-external-link: to get more details about a specific region in siibra-explorer. We choose the most probable brain region for this point, which is DG (Hippocampus) left. +6. Double-click a location in the input space to assign brain regions to it. We select a point in the visual cortex. In the side panel on the left every listed region is indeed part of the visual cortex. -

Video tutorial

+ ![image](images/tutorial.png) - -
+7. Click :fa-external-link: to get more details about a specific region in siibra-explorer. We choose the most probable brain region for this point, which is Area hOc1 (V1, 17, CalcS) left. + + ![image](images/hOc1.png) diff --git a/docs/video_tutorial.md b/docs/video_tutorial.md new file mode 100644 index 0000000..ee826c0 --- /dev/null +++ b/docs/video_tutorial.md @@ -0,0 +1,8 @@ +# Video tutorial + +This tutorial shows the functionalities of _voluba-mriwarp_ with an example dataset. Note, that paths may differ on you computer. + + +
\ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 7a8c90d..d2a0b02 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -29,6 +29,7 @@ nav: - 'acknowledgement.md' - Tutorials: - 'tutorial.md' + - 'video_tutorial.md' - Contact us: - Support: 'mailto:support@ebrains.eu?subject=[voluba-mriwarp]' - GitHub Issues: 'https://github.com/FZJ-INM1-BDA/voluba-mriwarp/issues'