diff --git a/README.md b/README.md index a35ff36..5c3a603 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Warping brain data to a standardized space like MNI152 enables anchoring of whol _voluba-mriwarp_ applies a set of predefined parameters to remove the skull and warp the input brain scan to MNI152 space. You can utilize the warping results in _voluba-mriwarp_ to interactively analyze points by making a probabilistic assignment of coordinates in the input space to brain regions of the [EBRAINS Human Brain Atlas](https://www.ebrains.eu/tools/human-brain-atlas). To get an overview of more information about a brain region, you can access [siibra-explorer](https://atlases.ebrains.eu/viewer/human) through the application. For further analysis, _voluba-mriwarp_ offers to export the anatomical assignments together with linked multimodal data features like receptor densities, cell distributions or brain connectivity. -![image](docs/images/teaser2.png) +![image](docs/images/teaser.png) ## Getting Started diff --git a/docs/images/EBRAINS_logo.png b/docs/images/EBRAINS_logo.png deleted file mode 100644 index 38a886d..0000000 Binary files a/docs/images/EBRAINS_logo.png and /dev/null differ diff --git a/docs/images/EU_logo.jpg b/docs/images/EU_logo.jpg deleted file mode 100644 index 3f68dd7..0000000 Binary files a/docs/images/EU_logo.jpg and /dev/null differ diff --git a/docs/images/FZJ_logo.png b/docs/images/FZJ_logo.png deleted file mode 100644 index a40518a..0000000 Binary files a/docs/images/FZJ_logo.png and /dev/null differ diff --git a/docs/images/HBP_logo.png b/docs/images/HBP_logo.png deleted file mode 100644 index 0d2c719..0000000 Binary files a/docs/images/HBP_logo.png and /dev/null differ diff --git a/docs/images/assignment_pane.png b/docs/images/assignment_pane.png deleted file mode 100644 index eeeef35..0000000 Binary files a/docs/images/assignment_pane.png and /dev/null differ diff --git a/docs/images/ca2.png b/docs/images/ca2.png deleted file mode 100644 index 63baf66..0000000 Binary files a/docs/images/ca2.png and /dev/null differ diff --git a/docs/images/pdf.png b/docs/images/pdf.png deleted file mode 100644 index 6b419bd..0000000 Binary files a/docs/images/pdf.png and /dev/null differ diff --git a/docs/images/teaser.png b/docs/images/teaser.png index 0e982a9..e88f915 100644 Binary files a/docs/images/teaser.png and b/docs/images/teaser.png differ diff --git a/docs/images/teaser2.png b/docs/images/teaser2.png deleted file mode 100644 index e88f915..0000000 Binary files a/docs/images/teaser2.png and /dev/null differ diff --git a/docs/images/tutorial.png b/docs/images/tutorial.png deleted file mode 100644 index b864bde..0000000 Binary files a/docs/images/tutorial.png and /dev/null differ diff --git a/docs/images/tutorial_assignment.png b/docs/images/tutorial_assignment.png index d3b5012..bdd5bef 100644 Binary files a/docs/images/tutorial_assignment.png and b/docs/images/tutorial_assignment.png differ diff --git a/docs/images/tutorial_assignment2.png b/docs/images/tutorial_assignment2.png deleted file mode 100644 index bdd5bef..0000000 Binary files a/docs/images/tutorial_assignment2.png and /dev/null differ diff --git a/docs/images/tutorial_warping.png b/docs/images/tutorial_warping.png index 09172e9..f636bd4 100644 Binary files a/docs/images/tutorial_warping.png and b/docs/images/tutorial_warping.png differ diff --git a/docs/images/tutorial_warping2.png b/docs/images/tutorial_warping2.png deleted file mode 100644 index f636bd4..0000000 Binary files a/docs/images/tutorial_warping2.png and /dev/null differ diff --git a/docs/images/warping_pane.png b/docs/images/warping_pane.png deleted file mode 100644 index aaedc78..0000000 Binary files a/docs/images/warping_pane.png and /dev/null differ diff --git a/docs/images/workflow.png b/docs/images/workflow.png index fda3d4d..b82ecde 100644 Binary files a/docs/images/workflow.png and b/docs/images/workflow.png differ diff --git a/docs/images/workflow2.png b/docs/images/workflow2.png deleted file mode 100644 index a989a44..0000000 Binary files a/docs/images/workflow2.png and /dev/null differ diff --git a/docs/images/workflow3.png b/docs/images/workflow3.png deleted file mode 100644 index 4d5ecab..0000000 Binary files a/docs/images/workflow3.png and /dev/null differ diff --git a/docs/images/workflow4.png b/docs/images/workflow4.png deleted file mode 100644 index b82ecde..0000000 Binary files a/docs/images/workflow4.png and /dev/null differ diff --git a/docs/index.md b/docs/index.md index e0b38a9..d74c54e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -15,6 +15,6 @@ Warping brain data to a standardized space like MNI152 enables anchoring of whol _voluba-mriwarp_ applies a set of predefined parameters to remove the skull and warp the input brain scan to MNI152 space. You can utilize the warping results in _voluba-mriwarp_ to interactively analyze points by making a probabilistic assignment of coordinates in the input space to brain regions of the [EBRAINS Human Brain Atlas](https://www.ebrains.eu/tools/human-brain-atlas). To get an overview of more information about a brain region, you can access [siibra-explorer](https://atlases.ebrains.eu/viewer/human) through the application. For further analysis, _voluba-mriwarp_ offers to export the anatomical assignments together with linked multimodal data features like receptor densities, cell distributions or brain connectivity. -![image_centered](images/teaser2.png) +![image_centered](images/teaser.png) [^1]: Isensee F, Schell M, Tursunova I, Brugnara G, Bonekamp D, Neuberger U, Wick A, Schlemmer HP, Heiland S, Wick W, Bendszus M, Maier-Hein KH, Kickingereder P. Automated brain extraction of multi-sequence MRI using artificial neural networks. Hum Brain Mapp. 2019; 1–13. [https://doi.org/10.1002/hbm.24750](https://doi.org/10.1002/hbm.24750) \ No newline at end of file diff --git a/docs/tutorial.md b/docs/tutorial.md index 4459f19..9b21402 100644 --- a/docs/tutorial.md +++ b/docs/tutorial.md @@ -26,7 +26,7 @@ You can choose this file from the file explorer by clicking .... * Click Warp input to MNI152 space to warp the brain of the subject to MNI152 space using the default registration method. This method is relatively fast but less accurate than the [advanced version](../warping/#advanced-settings). The progress bar indicates that the calculation is still running. When the registration is finished, a green checkmark will appear next to each step performed. - ![image](images/tutorial_warping2.png) + ![image](images/tutorial_warping.png) ## Analyze a point in the atlas context @@ -48,7 +48,7 @@ After successful warping _voluba-mriwarp_ can now use the resulting transformati * You should soon see the results of the anatomical assignment at the bottom of the side panel. As we specified a point uncertainty [different measures](../analysis/#results-of-the-analysis) for each assigned region are shown. Indeed, the region that correlates most with the selected point is **Area hOc1 (V1, 17, CalcS) left** which is part of the visual system. - ![image](images/tutorial_assignment2.png) + ![image](images/tutorial_assignment.png)

## Use the results diff --git a/docs/workflow.md b/docs/workflow.md index b4de179..16b91c0 100644 --- a/docs/workflow.md +++ b/docs/workflow.md @@ -14,4 +14,4 @@ The general workflow for _voluba-mriwarp_ can be summarized as follows: ![icon](images/5.png) Get a **quick overview** about an assigned brain region in [siibra-explorer](https://atlases.ebrains.eu/viewer/go/human). ![icon](images/6.png) **Export** assigned brain regions together with linked data features to a PDF report for extended analysis. -![image_centered](images/workflow4.png) \ No newline at end of file +![image_centered](images/workflow.png) \ No newline at end of file