Merge pull request #14 from Konohana0608/dev/fix_image_paths

fixing all image paths to work with online manual.

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>

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>
 
 <!--

docs/material_methods/anatomical_refs.md

@@ -6,22 +6,22 @@ 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.
 IXI025, the female model, is characterized by 43 individually segmented tissues. Conversely, IXI208, the male model, contains 50 segmented tissues. The difference in the number of tissues included in the two head models is due to the segmentation of deep brain structures in the male model.
 
 <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

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_.

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**
@@ -16,19 +16,19 @@ 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/>
    Use this option for a one-time purchase. After specifying the amount and entering credit card details, the credits will immediately be added to your balance.
 
 <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>
@@ -45,13 +45,13 @@ 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**
 
 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>

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>
 
 

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>
 
 

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:

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).

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>

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>

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>

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:

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

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>