From add8b399344757a58cd22761b47d8b304e50d31a Mon Sep 17 00:00:00 2001
From: Konohana0608 <mesteiner@student.ethz.ch>
Date: Mon, 15 Jul 2024 13:17:20 +0200
Subject: [PATCH] fixing all image paths to work with online manual.

---
 README.md                                     |  2 +-
 .../quantities_of_interest.md                 | 16 ++++++------
 docs/material_methods/anatomical_refs.md      |  8 +++---
 docs/plan/create_new_plan.md                  |  2 +-
 docs/platform_introduction/billing_center.md  | 12 ++++-----
 docs/platform_introduction/dashboard.md       |  4 +--
 docs/platform_introduction/data.md            |  2 +-
 docs/platform_introduction/overview.md        |  2 +-
 docs/services/electrode_placement.md          |  2 +-
 docs/services/electrode_selector.md           |  6 ++---
 docs/services/fiducials_placement.md          |  6 ++---
 docs/services/file_picker.md                  |  4 +--
 docs/services/personalizer.md                 |  4 +--
 docs/services/post_processing.md              | 26 +++++++++----------
 docs/services/s4l_post_processing.md          |  2 +-
 docs/services/simulator.md                    |  2 +-
 16 files changed, 50 insertions(+), 50 deletions(-)

diff --git a/README.md b/README.md
index b1cbfa1..9c6dff5 100644
--- a/README.md
+++ b/README.md
@@ -4,5 +4,5 @@ Welcome to the *TI Planning Tool* (TIP) user manual. This document provides back
 
 <br>
 <p align="center">
-  <img width="350" height="150" src="../../assets/logo.svg">
+  <img width="350" height="150" src="assets/logo.svg">
 </p>
diff --git a/docs/background/electromagnetic_modeling/quantities_of_interest.md b/docs/background/electromagnetic_modeling/quantities_of_interest.md
index 45b39c8..965d2fe 100644
--- a/docs/background/electromagnetic_modeling/quantities_of_interest.md
+++ b/docs/background/electromagnetic_modeling/quantities_of_interest.md
@@ -6,7 +6,7 @@ For classic TI (two channels), the total field is obtained as:
 
 
 <p align="center">
-  <img width = "390" src="../../assets/equations/eq1w2.png">
+  <img width = "390" src="assets/equations/eq1w2.png">
 </p>
 
 <!--
@@ -15,10 +15,10 @@ $$
 $$
 -->
 
-where <img width = "30" src="../../assets/equations/E12w2.png"> are the fields of the two channels and ω<sub>1,2</sub> are their angular frequencies (initial phases are set to zero without loss of generality). Its projection along a direction of interest <img width = "12" src="../../assets/equations/nvecw2.png"> (e.g., the principal axis of a pyramidal neuron, or the principal axis of the local diffusion tensor; <img width = "52" src="../../assets/equations/n1w2.png"> ) is obtained as:
+where <img width = "30" src="assets/equations/E12w2.png"> are the fields of the two channels and ω<sub>1,2</sub> are their angular frequencies (initial phases are set to zero without loss of generality). Its projection along a direction of interest <img width = "12" src="assets/equations/nvecw2.png"> (e.g., the principal axis of a pyramidal neuron, or the principal axis of the local diffusion tensor; <img width = "52" src="assets/equations/n1w2.png"> ) is obtained as:
 
 <p align="center">
-  <img width = "520" src="../../assets/equations/eq2w2.png">
+  <img width = "520" src="assets/equations/eq2w2.png">
 </p>
 
 <!--
@@ -27,10 +27,10 @@ $$
 $$
 -->
 
-The modulation envelope magnitude (MEM) along <img width = "12" src="../../assets/equations/nvecw2.png">  can easily be obtained as
+The modulation envelope magnitude (MEM) along <img width = "12" src="assets/equations/nvecw2.png">  can easily be obtained as
 
 <p align="center">
-  <img width = "340" src="../../assets/equations/eq3w2.png">
+  <img width = "340" src="assets/equations/eq3w2.png">
 </p>
 
 <!--
@@ -41,7 +41,7 @@ $$
 As TI-exposure quantity, the modulation envelope magnitude (MEM) has been chosen, which is computed according to the formula from [[5]](/docs/background/references.md):
 
 <p align="center">
-  <img width = "800" src="../../assets/equations/eq4w2.png">
+  <img width = "800" src="assets/equations/eq4w2.png">
 </p>
 
 <!--
@@ -55,7 +55,7 @@ $$
 -->
 
 
-where α denotes the angle between <img width = "30" src="../../assets/equations/E12w2.png">. This metric has been chosen because it reproduces empirical observations, such as the neurons responding to the demodulated exposure and stimulation target moving towards the channel carrying less current when the current ratio is adapted.
+where α denotes the angle between <img width = "30" src="assets/equations/E12w2.png">. This metric has been chosen because it reproduces empirical observations, such as the neurons responding to the demodulated exposure and stimulation target moving towards the channel carrying less current when the current ratio is adapted.
 
 To assess the quality of a TI exposure condition, three key metrics have been defined:
 
@@ -68,7 +68,7 @@ Typically, it is not possible to find exposure conditions that simultaneously op
 In addition to the TI-relevant MEM distribution, **high-frequency** exposure can also be of interest (e.g., to analyze potential high frequency stimulation or conduction blocking). For this, the peak field magnitude is used, which is obtained as:
 
 <p align="center">
-  <img width = "470" src="../../assets/equations/eq5w2.png">
+  <img width = "470" src="assets/equations/eq5w2.png">
 </p>
 
 <!--
diff --git a/docs/material_methods/anatomical_refs.md b/docs/material_methods/anatomical_refs.md
index f34de7d..ec93f9e 100644
--- a/docs/material_methods/anatomical_refs.md
+++ b/docs/material_methods/anatomical_refs.md
@@ -6,7 +6,7 @@ TIP is designed such that it supports different head models. While the initial r
 
 <br>
 <p align="center">
-  <img width="500" src="../../assets/methods/MIDAHead.png">
+  <img width="500" src="assets/methods/MIDAHead.png">
 </p>
 
 * Shifting focus to the IXI head models, we introduce two new additions: IXI025, representing a female head model, and IXI208, corresponding to a male head model. These two models have been generated from MR images of the IXI Dataset, which contains 600 scans of healthy subjects [[8]](/docs/background/references.md). Each subject's dataset includes T1, T2, and PD-weighted images, as well as MRA images and diffusion-weighted images with 15 directions. All images were resampled to an isotropic resolution of 0.5 mm during segmentation.
@@ -14,14 +14,14 @@ IXI025, the female model, is characterized by 43 individually segmented tissues.
 
 <br>
 <p align="center">
-  <img width="500" src="../../assets/methods/IXI_male_model.png">
+  <img width="500" src="assets/methods/IXI_male_model.png">
 </p>
 
 * The newly introduced mouse model has been segmented from high-resolution structural magnetic resonance imaging (MRI) data obtained from the Animal Imaging Center of the Institute of Biomedical Engineering, a joint institution of the ETH Zurich and the University of Zurich. This model represents a 3-week-old male mouse and comprises a total of 67 detailed segmented tissues and organs. The model was introduced to enable researchers engaged in rodent studies, to also use TIP for the planning. Further technical details can be explored through the comprehensive documentation accessible at [[9]](/docs/background/references.md).
 
 <br>
 <p align="center">
-  <img width="500" src="../../assets/methods/mouse_model.png">
+  <img width="500" src="assets/methods/mouse_model.png">
 </p>
 
 In version 3.0, users can generate personalized head models based on a T1-weighted MR images. The tissue segmentation is automatically generated using a U-Net, which is able to delineate 29 tissues, eight of which are subcortical regions.
@@ -78,7 +78,7 @@ Since the model is trained on healthy subjects without implants/lesions/atrophy,
 
 <br>
 <p align="center">
-  <img width="500" src="../../assets/methods/personalized_head.png">
+  <img width="500" src="assets/methods/personalized_head.png">
 </p>
 
 In addition to that, users have to option to provide diffusion tensor imaging data. Based on that, an inhomogeneous, anisotropic conductivity map can be extracted using a linear relationship which has been described by D.S. Tuch [citation ...]. To use this feature, users need to provide a preprocessed DTI nifty (.nii.gz), a .bval and .bvec file. The bval file lists the b-value for each volume in the series, the bvec file the gradient direction, with one column per volume
diff --git a/docs/plan/create_new_plan.md b/docs/plan/create_new_plan.md
index ae72dd2..0000548 100644
--- a/docs/plan/create_new_plan.md
+++ b/docs/plan/create_new_plan.md
@@ -3,7 +3,7 @@
 The setup of new TI Plan can easily be initiated by clicking on the large ```New Plan``` icon on the ```Dashboard```. 
 
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/newplanv2.png">
+  <img width="90%" src="assets/quickguide/newplanv2.png">
 </p>
 
 Three different kinds of planning studies can be initialized, which correspond to the [three modes](/docs/background/modes.md): _classic TI_, _multi-channel TI_, and _phase-modulation TI_.
diff --git a/docs/platform_introduction/billing_center.md b/docs/platform_introduction/billing_center.md
index 93d5fde..95516f8 100644
--- a/docs/platform_introduction/billing_center.md
+++ b/docs/platform_introduction/billing_center.md
@@ -3,7 +3,7 @@
 The **Billing Center** provides the following sub-menus: ```Credit Accounts```, ```Payment Methods```, ```Transactions``` and ```Usage``` (1.).
 
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/billing_center/credit_accounts.png">
+  <img width="90%" src="assets/quickguide/billing_center/credit_accounts.png">
 </p>
 
 **Credit Accounts**
@@ -16,7 +16,7 @@ Here users can ```Buy Credits```, set up ```Auto-recharge``` or ```Share``` thei
    If you would like to automatically recharge your account with a specified amount of credits once it gets low.
 
 <p align="center">
-<img width="30%" src="../../assets/quickguide/billing_center/auto_recharge.png">
+<img width="30%" src="assets/quickguide/billing_center/auto_recharge.png">
 </p>
 
 4. **Buy Credits** <br/>
@@ -24,11 +24,11 @@ Here users can ```Buy Credits```, set up ```Auto-recharge``` or ```Share``` thei
 
 <div style="display: flex; justify-content: space-between;">
     <div style="flex: 1; text-align: center;">
-        <img src="../../assets/quickguide/billing_center/credits_amount_select.png" alt="Image 1" style="width: 100%; max-width: 300px;"/>
+        <img src="assets/quickguide/billing_center/credits_amount_select.png" alt="Image 1" style="width: 100%; max-width: 300px;"/>
         <p>Select purchase amount</p>
     </div>
     <div style="flex: 1; text-align: center;">
-        <img src="../../assets/quickguide/billing_center/credit_card.png" alt="Image 2" style="width: 100%; max-width: 300px;"/>
+        <img src="assets/quickguide/billing_center/credit_card.png" alt="Image 2" style="width: 100%; max-width: 300px;"/>
         <p>Enter Credit Card details</p>
     </div>
 </div>
@@ -45,7 +45,7 @@ If you would like to save your credit card details for further purchases or for
 In this menu, all of your transactions are summarized. Receipts of purchases can be downloaded as a PDF if needed.
 
 <p align="center">
-<img width="90%" src="../../assets/quickguide/billing_center/transactions.png">
+<img width="90%" src="assets/quickguide/billing_center/transactions.png">
 </p>
 
 **Usage**
@@ -53,5 +53,5 @@ In this menu, all of your transactions are summarized. Receipts of purchases can
 Here a list with all the simulation runs that have been submitted is displayed. It is sortable and can be filtered to specific time intervals. The list also shows the credits used per simulation and is exportable.
 
 <p align="center">
-<img width="90%" src="../../assets/quickguide/billing_center/usage.png">
+<img width="90%" src="assets/quickguide/billing_center/usage.png">
 </p>
\ No newline at end of file
diff --git a/docs/platform_introduction/dashboard.md b/docs/platform_introduction/dashboard.md
index 36dde1b..936db03 100644
--- a/docs/platform_introduction/dashboard.md
+++ b/docs/platform_introduction/dashboard.md
@@ -3,7 +3,7 @@
 The **Dashboard** hosts the two principal views: ```Studies``` and ```Data``` (1.).
 
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/dashboard.png">
+  <img width="90%" src="assets/quickguide/dashboard.png">
 </p>
 
 
@@ -27,7 +27,7 @@ on the **Dashboard**. Clicking this icon will bring you directly to the update m
 versions of each Service and where you can update them either individually or all together.
 
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/settings_service.png">
+  <img width="90%" src="assets/quickguide/settings_service.png">
 </p>
 
 
diff --git a/docs/platform_introduction/data.md b/docs/platform_introduction/data.md
index 4d78155..803cb21 100644
--- a/docs/platform_introduction/data.md
+++ b/docs/platform_introduction/data.md
@@ -3,7 +3,7 @@
 The second tab available on the top of the **Dashboards** screen is the ```Data``` tab.
 
 <p align="center">
-  <img width="90%"  src="../../assets/quickguide/data.png">
+  <img width="90%"  src="assets/quickguide/data.png">
 </p>
 
 
diff --git a/docs/platform_introduction/overview.md b/docs/platform_introduction/overview.md
index 8698431..3c38888 100644
--- a/docs/platform_introduction/overview.md
+++ b/docs/platform_introduction/overview.md
@@ -1,7 +1,7 @@
 ### Landing Page
 
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/landingpage_v2.png">
+  <img width="90%" src="assets/quickguide/landingpage_v2.png">
 </p>
 
 The Landing Page currently serves primarily for user authentication. Two-factor authentication is required:
diff --git a/docs/services/electrode_placement.md b/docs/services/electrode_placement.md
index 00ad476..96145c7 100644
--- a/docs/services/electrode_placement.md
+++ b/docs/services/electrode_placement.md
@@ -16,7 +16,7 @@ It is important to note that if the fiducial were misplaced, or the imported hea
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/fiducial_placement_3.png">
+  <img width="90%" src="assets/quickguide/fiducial_placement_3.png">
 </p>
 
 You can now click to the arrow on the right side of the browser to move to [**_Step 4: EM Simulations_**](/docs/services/simulator.md).
\ No newline at end of file
diff --git a/docs/services/electrode_selector.md b/docs/services/electrode_selector.md
index d5a0c79..4f8a393 100644
--- a/docs/services/electrode_selector.md
+++ b/docs/services/electrode_selector.md
@@ -12,7 +12,7 @@ If you are using the personalized classic TI mode, the model selection will be e
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/electrode_selector/setup.png">
+  <img width="90%" src="assets/electrode_selector/setup.png">
 </p>
 
 The **_Setup_** interface has the following elements:
@@ -22,7 +22,7 @@ The **_Setup_** interface has the following elements:
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/electrode_selector/species.png">
+  <img width="90%" src="assets/electrode_selector/species.png">
 </p>
 
 2. **_Select Target Structure_** <br/>
@@ -42,5 +42,5 @@ Once you are finished with the setup, you can press ```Finish set up```. This wi
 You can now click to the arrow on the right side of the browser to move to [**_Optimal Configuration Identification_**](/docs/services/post_processing.md).
 
 <p align="center">
-   <img src="../../assets/quickguide/electrode_selector_2.gif" width="900" height="578" />
+   <img src="assets/quickguide/electrode_selector_2.gif" width="900" height="578" />
 </p>
diff --git a/docs/services/fiducials_placement.md b/docs/services/fiducials_placement.md
index b4290e0..edc02b5 100644
--- a/docs/services/fiducials_placement.md
+++ b/docs/services/fiducials_placement.md
@@ -10,7 +10,7 @@ Now that the anatomical 3D model is generated, it needs to be imported into the
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/fiducial_placement_1.png">
+  <img width="90%" src="assets/quickguide/fiducial_placement_1.png">
 </p>
 
 The **Fiducials Placement** interface has the following elements:
@@ -23,7 +23,7 @@ The **Fiducials Placement** interface has the following elements:
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/fiducial_placement_2.png">
+  <img width="90%" src="assets/quickguide/fiducial_placement_2.png">
 </p>
 
 Users are asked to create 4 points, representing positions Nz (nasion), Iz (inion), LPA and RPA (left/right pre-auricular). These points should be properly renamed according to their position (Nz, Iz, LPA, RPA). This can be done using the shortcut ```F2```. Once created, points need to be exported by selecting them and clicking ```Export Selected``` in the top ribbon to put them in the ```outputs/output_1``` directory. Please specify the file extension ```.sab``` in the file name.
@@ -38,5 +38,5 @@ Users are asked to create 4 points, representing positions Nz (nasion), Iz (inio
    When selecting an entity from the model tree, this section of the UI will display information and editable settings.
 
 <p align="center">
-   <img src="../../assets/quickguide/electrode_selector.gif" width="740" height="578" />
+   <img src="assets/quickguide/electrode_selector.gif" width="740" height="578" />
 </p>
\ No newline at end of file
diff --git a/docs/services/file_picker.md b/docs/services/file_picker.md
index 572e873..c87cc13 100644
--- a/docs/services/file_picker.md
+++ b/docs/services/file_picker.md
@@ -26,7 +26,7 @@ To ensure the highest quality of the head models, please adhere to the following
 
 <br>
 <p align="center">
-  <img width="60%" src="../../assets/quickguide/TIP_v3_files-MRI.png">
+  <img width="60%" src="assets/quickguide/TIP_v3_files-MRI.png">
 </p>
 
 ### DWI Data Quality Requirements
@@ -47,5 +47,5 @@ Providing DTI data is only necessary, if you would like to use anisotropic condu
 
 <br>
 <p align="center">
-  <img width="60%" src="../../assets/quickguide/TIP_v3_files-DTI.png">
+  <img width="60%" src="assets/quickguide/TIP_v3_files-DTI.png">
 </p>
\ No newline at end of file
diff --git a/docs/services/personalizer.md b/docs/services/personalizer.md
index 7622bf0..655cf67 100644
--- a/docs/services/personalizer.md
+++ b/docs/services/personalizer.md
@@ -29,7 +29,7 @@ As the initial step for personalization, the user is asked to provide, in the fi
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/file_picker.png">
+  <img width="90%" src="assets/quickguide/file_picker.png">
 </p>
 
 1. **Data Instructions**
@@ -48,7 +48,7 @@ Once uploaded, the user can specify the geometry of the electrode, and if the he
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/personalizer.png">
+  <img width="90%" src="assets/quickguide/personalizer.png">
 </p>
 
 The interface has the following elements:
diff --git a/docs/services/post_processing.md b/docs/services/post_processing.md
index 390b6ce..63a61ff 100644
--- a/docs/services/post_processing.md
+++ b/docs/services/post_processing.md
@@ -33,7 +33,7 @@ xxx review the below xxx
     <br>
 
     <p align="center">
-      <img width="90%" src="../../assets/postpro/classic_ti_three_metrics_numbered.png">
+      <img width="90%" src="assets/postpro/classic_ti_three_metrics_numbered.png">
     </p>
 
 * **Report** <br/>
@@ -55,7 +55,7 @@ To facilitate the search for an ideal setup, the table summarizing the results o
 
 <br>
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/classic_ti_three_metrics_numbered.png">
+  <img width="90%"  src="assets/postpro/classic_ti_three_metrics_numbered.png">
 </p>
 
 The sorting can be done using the scaling sliders on top (1.), where the weight (importance) of each metric can be set. The table is then sorted according to the score resulting from this weighting. The score is also shown in the last table column. For additional information regarding these metrics, check the [**Background**](/docs/background/background.md) section. Alternatively, the table can be sorted according to a single metric by clicking on the column name (2.). 
@@ -68,11 +68,11 @@ Once that sweep is complete, all the viewers in the lower half of the screen are
 
 <br>
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/analysis_slicer_numbers_v2_classic_ti.png">
+  <img width="90%"  src="assets/postpro/analysis_slicer_numbers_v2_classic_ti.png">
 </p>
 
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/classic_ti_quantitative_analysis.png">
+  <img width="90%"  src="assets/postpro/classic_ti_quantitative_analysis.png">
 </p>
 
 1. **Main Controls** <br/>
@@ -106,17 +106,17 @@ Once that sweep is complete, all the viewers in the lower half of the screen are
 
 Metrics table:
 <p align="center">
-  <img width="90%"  src="../../assets/quickguide/postpro_gui_1.gif">
+  <img width="90%"  src="assets/quickguide/postpro_gui_1.gif">
 </p>
 
 Slice Viewers:
 <p align="center">
-  <img width="90%"  src="../../assets/quickguide/postpro_gui_2.gif">
+  <img width="90%"  src="assets/quickguide/postpro_gui_2.gif">
 </p>
 
 Reporting:
 <p align="center">
-  <img width="90%"  src="../../assets/quickguide/postpro_gui_3.gif">
+  <img width="90%"  src="assets/quickguide/postpro_gui_3.gif">
 </p>
 
 #### Multichannel TI and Phase-Modulation TI
@@ -126,15 +126,15 @@ For the non-classic TI modes, the settings are similar, except for the fact that
 Multichannel TI:
 
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/multichannel_ti_settings.png">
+  <img width="90%"  src="assets/postpro/multichannel_ti_settings.png">
 </p>
 
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/multichannel_ti_visual_analysis.png">
+  <img width="90%"  src="assets/postpro/multichannel_ti_visual_analysis.png">
 </p>
 
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/multichannel_ti_quantitative_analysis.png">
+  <img width="90%"  src="assets/postpro/multichannel_ti_quantitative_analysis.png">
 </p>
 
 
@@ -143,15 +143,15 @@ Multichannel TI:
 Phase-Modulation TI:
 
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/phase_modulation_ti_settings.png">
+  <img width="90%"  src="assets/postpro/phase_modulation_ti_settings.png">
 </p>
 
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/phase_modulation_ti_visual_analysis.png">
+  <img width="90%"  src="assets/postpro/phase_modulation_ti_visual_analysis.png">
 </p>
 
 <p align="center">
-  <img width="90%"  src="../../assets/postpro/phase_modulation_ti_quantitative_analysis.png">
+  <img width="90%"  src="assets/postpro/phase_modulation_ti_quantitative_analysis.png">
 </p>
 
 ### Report
diff --git a/docs/services/s4l_post_processing.md b/docs/services/s4l_post_processing.md
index 73d6be5..b8dc0ae 100644
--- a/docs/services/s4l_post_processing.md
+++ b/docs/services/s4l_post_processing.md
@@ -10,5 +10,5 @@ _In addition to the predefined exposure visualizations of the second step, free
 To perform an interactive exposure analysis, you need to generate the .cache file of the setup of interest by clicking the ```Export to S4L``` as explained in [**Analysis**](/docs/services/post_processing.md). Once the pipeline detects a .cache file, it will be loaded into Sim4Life web's workbench automatically. Now, all of Sim4Life's analysis capabilities are available to you. 
 
 <p align="center">
-  <img width="90%"  src="../../assets/quickguide/postpro_s4l.gif">
+  <img width="90%"  src="assets/quickguide/postpro_s4l.gif">
 </p>
\ No newline at end of file
diff --git a/docs/services/simulator.md b/docs/services/simulator.md
index c462cb9..927de15 100644
--- a/docs/services/simulator.md
+++ b/docs/services/simulator.md
@@ -14,7 +14,7 @@ When all the simulations are done, users can hit the ```Export``` button which d
 
 <br>
 <p align="center">
-  <img width="90%" src="../../assets/quickguide/simulator.png">
+  <img width="90%" src="assets/quickguide/simulator.png">
 </p>
 
 The **_Setup_** interface has the following elements: