Merge pull request #268 from Image-X-Institute/better_workflow_figure

Add files via upload

README.md

@@ -5,24 +5,7 @@ This code enables characterization, reporting, and correction of geometric disto
 
 The workflow steps are below. All steps have well defined input/output so you can use any part of this code independently from the other parts. For an example of our automated reporting template see [here](https://image-x-institute.github.io/mri_distortion_toolkit/_static/MR_QA_report_20_05_2022.html)
 
-```mermaid
-flowchart LR
-
-AA[Phantom Design]
-
-A[Marker <br>Extraction]--->B[Marker <br>Matching]
-B[Marker <br>Matching]--->C[Field <br> Calculation] & E[Automated <br>reporting]
-C[Field <br> Calculation]-->D[Spherical Harmonic <br>Analysis]
-D[Spherical Harmonic <br>Analysis]-->E[Automated <br>reporting];
-D[Spherical Harmonic <br>Analysis]-->F[Distortion Correction]
-
-click AA "https://image-x-institute.github.io/mri_distortion_toolkit/phantom_notes.html"
-click A "https://image-x-institute.github.io/mri_distortion_toolkit/marker_extraction.html"
-click B "https://image-x-institute.github.io/mri_distortion_toolkit/marker_matching.html"
-click C "https://image-x-institute.github.io/mri_distortion_toolkit/field_calculation.html"
-click D "https://image-x-institute.github.io/mri_distortion_toolkit/fit_spherical_harmonics.html"
-click E "https://image-x-institute.github.io/mri_distortion_toolkit/reporting.html"
-```
+![](docsrc/__resources/Brendan_Phantom.png)
 
 
 

docsrc/index.rst

@@ -7,25 +7,7 @@ MRI Distortion QA
 =================
 `This code <https://github.com/image-x-institute/mri_distortion_toolkit>`_ enables characterization and reporting of geometric distortion in Magnetic Resonance Imaging. The basic end-to-end workflow is below, but all steps have well defined input/output so you can use any part of this code independently from the other parts. For a tutorial on each step, click on the diagram below.
 
-.. mermaid::
-
-   flowchart LR
-
-   AA[Phantom Design]
-
-   A[Marker <br>Extraction]--->B[Marker <br>Matching]
-   B[Marker <br>Matching]--->C[Field <br> Calculation] & E[Automated <br>reporting]
-   C[Field <br> Calculation]-->D[Spherical Harmonic <br>Analysis]
-   D[Spherical Harmonic <br>Analysis]-->E[Automated <br>reporting];
-   D[Spherical Harmonic <br>Analysis]-->F[Distortion Correction]
-
-   click AA "https://image-x-institute.github.io/mri_distortion_toolkit/phantom_notes.html"
-   click A "https://image-x-institute.github.io/mri_distortion_toolkit/marker_extraction.html"
-   click B "https://image-x-institute.github.io/mri_distortion_toolkit/marker_matching.html"
-   click C "https://image-x-institute.github.io/mri_distortion_toolkit/field_calculation.html"
-   click D "https://image-x-institute.github.io/mri_distortion_toolkit/fit_spherical_harmonics.html"
-   click E "https://image-x-institute.github.io/mri_distortion_toolkit/reporting.html"
-
+.. image:: __resources/Brendan_Phantom.png
 
 
 .. toctree::