Merge pull request #15 from Konohana0608/update/tip_v3_fixing

Update/tip v3 fixing

_sidebar.md

@@ -6,7 +6,7 @@
   * [Planning Steps](/docs/background/modeling_steps.md)
   * [TI modes](/docs/background/modes.md)
   * [Electromagnetic Modeling](/docs/background/electromagnetic_modeling.md)
-    * [Head Models](docs/material_methods/anatomical_refs.md)
+    * [Head Models](/docs/material_methods/anatomical_refs.md)
     * [Electrode Shapes and Placement](docs/material_methods/electrode_models.md)
     * [Electromagnetic (EM) Simulator](docs/material_methods/em_sim.md)
     * [Dielectric Tissue Properties](docs/material_methods/dielectric_properties.md)

docs/background/modeling_steps.md

@@ -2,7 +2,7 @@
 
 Starting from TIP v3.0, personalized optimizations are available. The personalized flavor allows the use of magnetic resonance and/or diffusion tensor images of choice, to obtain results tailored to an individual. Note that the precomputed flavors that were available in V2.0 are still supported.
 
-The planning process is described below for both approaches. Should the user proceed with the precomputed path, steps 1 to 5 can be disregarded and step 6 is considered the first step.
+The planning process is described below for both approaches. Should the user proceed with the precomputed path, steps 1 to 4 can be disregarded and step 5 is considered the first step.
 
 Personalized flavor only steps:
 - **Step 1 - Images processing**: The so-called personalizer, either uses a T1-weighted MR image for isotropic simulations only, or a T1 in combination with DTI data to enable simulations with anisotropic conductivity in the white matter of the brain as well. Based on this data, a tissue model is generated using our AI model and anisotropic conductivity is extracted if DTI was provided.

docs/background/references.md

@@ -20,3 +20,5 @@
 [8] [IXI Dataset](https://brain-development.org/ixi-dataset/). Accessed: 2021-11-15.
 
 [9] [ViZOO - 3 week male mouse](https://itis.swiss/virtual-population/animal-models/animals/3-week-male-mouse/). Accessed: 2023-08-11.
+
+[10] David S. Tuch, Van J. Wedeen, Anders M. Dale, John S. George, and John W. Belliveau. Conductivity tensor mapping of the human brain using diffusion tensor MRI, DOI: 10.1073, Sept 25, 2001

docs/material_methods/anatomical_refs.md

@@ -26,49 +26,49 @@ IXI025, the female model, is characterized by 43 individually segmented tissues.
 
 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.
 
-Here is a list of all the tissues which are segmented and their electric conductivity values which are taken directly from our material database:
+Here is a list of all the tissues which are segmented and their electric conductivity values which are taken directly from our material database [[4]](/docs/background/references.md):
 
 <table style="width: 100%; border-collapse: separate; border-spacing: 10%;">
 <tr>
 <td style="padding-left: 10%; vertical-align: top;">
 
-| Tissue Name       | Elec. Conductivity [S/m] | Density [kg/m^3]        |
-| ---------- | --- | ----------- |
-| Amygdala   | 0.419055  | 1044.5    |
-| Artery | 0.66246  | 1049.75 |
-| Brainstem| 0.35  | 1045.5     |
-| Caudate nucleus   | 0.419055  | 1044.5    |
-| Cerebellum gray matter | 0.419055  | 1044.5 |
-| Cerebellum white matter| 0.347954  | 1041     |
-| Cerebrospinal fluid   | 1.879  | 1007    |
-| Cerebrum gray matter | 0.419055  | 1044.5 |
-| Cerebrum white matter| 0.347954  | 1041     |
-| Dura   | 0.06  | 1174    |
-| Eyes | 2.16486  | 1004.5 |
-| Globus pallidus| 0.419055  | 1044.5     |
-| Hippocampus   | 0.419055  | 1044.5    |
-| Midbrain ventral | 0.35  | 1045.5 |
-| Mucosa | 0.461008  | 1102     |
+| Tissue Name       | Elec. Conductivity [S/m] |
+| ---------- | --- |
+| Amygdala   | 0.419055  |
+| Artery | 0.66246  |
+| Brainstem| 0.35  |
+| Caudate nucleus   | 0.419055  |
+| Cerebellum gray matter | 0.419055  |
+| Cerebellum white matter| 0.347954  |
+| Cerebrospinal fluid   | 1.879  |
+| Cerebrum gray matter | 0.419055  |
+| Cerebrum white matter| 0.347954  |
+| Dura   | 0.06  |
+| Eyes | 2.16486  |
+| Globus pallidus| 0.419055  |
+| Hippocampus   | 0.419055  |
+| Midbrain ventral | 0.35  |
+| Mucosa | 0.461008  |
 
 </td>
 <td style="vertical-align: top;">
 
-| Tissue Name       | Elec. Conductivity [S/m] | Density [kg/m^3]        |
-| ---------- | --- | ----------- |
-| Ocular muscle | 0.461008  | 1090.4    |
-| Nerve cranial II optic | 0.347954  | 1075 |
-| Nucleus accumbens| 0.419055  | 1044.5     |
-| Other tissues   | 0.0776213  | 911    |
-| Putamen | 0.419055  | 1044.5 |
-| Skin | 0.148297  | 1109     |
-| Skull cancellous | 0.0804595  | 1178.33    |
-| Skull cortical | 0.006302  | 1908 |
-| Spinal cord | 0.610954  | 1075     |
-| Thalamus   | 0.475  | 1044.5    |
-| Vein | 0.66246  | 1049.75 |
-| Ventricles | 1.879  | 1007     |
-| Vertebrae cancellous | 0.0804595  | 1178.33    |
-| Vetebrae cortical | 0.006302  | 1908 |
+| Tissue Name       | Elec. Conductivity [S/m] |
+| ---------- | --- |
+| Ocular muscle | 0.461008  |
+| Nerve cranial II optic | 0.347954  |
+| Nucleus accumbens| 0.419055  |
+| Other tissues   | 0.0776213  |
+| Putamen | 0.419055  |
+| Skin | 0.148297  |
+| Skull cancellous | 0.0804595  |
+| Skull cortical | 0.006302  |
+| Spinal cord | 0.610954  |
+| Thalamus   | 0.475  |
+| Vein | 0.66246  |
+| Ventricles | 1.879  |
+| Vertebrae cancellous | 0.0804595  |
+| Vetebrae cortical | 0.006302  |
 
 </td>
 </tr>
@@ -81,5 +81,5 @@ Since the model is trained on healthy subjects without implants/lesions/atrophy,
   <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
+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 [[10]](/docs/background/references.md). 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

@@ -1,20 +1,25 @@
 ## Create a New Plan
 
-The setup of new TI Plan can easily be initiated by clicking on the large ```New Plan``` icon on the ```Dashboard```. 
+The setup of a 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/newplanv3.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_.
+Via the pop-up, six 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, in both non-personalized and personalized form.
 
-Allow for some time for the study initiation. Once the study is ready, you will have access to the different planning steps and their views (note: some [TI modes](/docs/background/modes.md) only have two steps):
+Allow for some time for the study initiation. Once the study is ready, you will have access to the different planning steps and their views (note: the amount of steps necessary depends on the selected plan.):
+
+Personalized flavor only steps:
 
 * [Step 0: Preparing Your Data](/docs/services/file_picker.md)
 * [Step 1: Images Processing](/docs/services/personalizer.md)
 * [Step 2: Fiducials Placement](/docs/services/fiducials_placement.md)
 * [Step 3: Electrode Placement](/docs/services/electrode_placement.md)
 * [Step 4: EM Simulations](/docs/services/simulator.md)
+
+Global Steps
+
 * [Step 5: Setup](/docs/services/electrode_selector.md)
 * [Step 6: Optimal Configuration Identification](/docs/services/post_processing.md)
 * [Step 7: Exposure Analysis](/docs/services/s4l_post_processing.md)

docs/plan/start.md

@@ -1,14 +1,19 @@
 # Quick Start Guide
 
 This section starts with an [overview](/docs/platform_introduction/platform.md) of the TI Planning Tool.
-First, a brief introduction of the platform itself is given, then we show how to create a new plan and the next three sections describe the functionalities of the different services and their user interfaces within a plan.
-Then it provides step-by-step instructions on how to [create a new plan](/docs/plan/create_new_plan.md) by following the steps below (note: some [TI modes](/docs/background/modes.md) only have two steps):
+First, a brief introduction of the platform itself is given, then we show how to create a new plan and the next seven sections describe the functionalities of the different services and their user interfaces within a plan.
+Then it provides step-by-step instructions on how to [create a new plan](/docs/plan/create_new_plan.md) by following the steps below (note: the amount of steps necessary depends on the selected plan.):
+
+Personalized flavor only steps:
 
 * [Step 0: Preparing Your Data](/docs/services/file_picker.md)
 * [Step 1: Images Processing](/docs/services/personalizer.md)
 * [Step 2: Fiducials Placement](/docs/services/fiducials_placement.md)
 * [Step 3: Electrode Placement](/docs/services/electrode_placement.md)
 * [Step 4: EM Simulations](/docs/services/simulator.md)
+
+Global Steps:
+
 * [Step 5: Setup](/docs/services/electrode_selector.md)
 * [Step 6: Optimal Configuration Identification](/docs/services/post_processing.md)
 * [Step 7: Exposure Analysis](/docs/services/s4l_post_processing.md)

docs/platform_introduction/dashboard.md

@@ -1,14 +1,12 @@
 ### Dashboard
 
-The **Dashboard** hosts the two principal views: ```Studies``` and ```Data``` (1.).
+The **Dashboard** hosts the principal view: ```Studies``` (1.).
 
 <p align="center">
   <img width="90%" src="assets/quickguide/dashboard.png">
 </p>
 
-
-- Under ```Studies```, existing Plans (own Plans, or plans that have been shared by other users) can be accessed (3.) and managed (4.), and new Plans can be [created](docs/plan/create_new_plan.md). 
-- Under ```Data```, the existing data can be managed and downloaded (see [Data](/docs/platform_introduction/data.md)).
+Under ```Studies```, existing Plans (own Plans, or plans that have been shared by other users (6.)) can be accessed (3.) and managed (4.), and new Plans can be [created](/docs/plan/create_new_plan.md).
 
 In addition, buttons on the top right provide access to notifications, various support material/contact options, and a menu (5.) with the following entries:
 
@@ -21,16 +19,15 @@ In addition, buttons on the top right provide access to notifications, various s
 - _**License**_: Information about the TI Planning Tool license, as well as the licenses of the underlying technologies.
 - _**Log out**_: Logging out from the **TI Planning Tool**
 
-The user access more functionality such as **_Plan management_**, **_information_**, **_sharing_**, and **_Service overview and update_** (3.) through the three-dot menu (1.) icon (see the [o<sup>2</sup>S<sup>2</sup>PARC User Manual](https://docs.osparc.io/#/) for information on these functionalities as well as the locking states). 
+The user access more functionality such as **_Overview_**, [Study Files](/docs/platform_introduction/data.md), **Sharing**, and **_Services Updates_** (3.) through the three-dot menu (1.) icon (see the [o<sup>2</sup>S<sup>2</sup>PARC User Manual](https://docs.osparc.io/#/) for information on these functionalities as well as the locking states). 
 If Services within a Plan need updating, the small circular arrow sign will appear in the bottom right corner (2.) of the Plan
 on the **Dashboard**. Clicking this icon will bring you directly to the update menu where you see the current and newest available
-versions of each Service and where you can update them either individually or all together.
+versions of each Service and where you can update them either individually or all together (4.).
 
 <p align="center">
   <img width="90%" src="assets/quickguide/settings_service.png">
 </p>
 
-
 It is always possible to return to the _**Dashboard**_ by clicking the ```Dashboard``` button on the top left, which automatically saves the state of the currently opened plan.
 
 For more information, see the [o<sup>2</sup>S<sup>2</sup>PARC User Manual](https://docs.osparc.io/#/).

docs/platform_introduction/data.md

@@ -1,12 +1,12 @@
 ### Data
 
-The second tab available on the top of the **Dashboards** screen is the ```Data``` tab.
+The Data of a service can be accessed via the **Study Details** menu screen in the ```Study Files``` tab.
 
 <p align="center">
   <img width="90%"  src="assets/quickguide/data.png">
 </p>
 
 
-When changing to this section, you are presented with the file system of your account on o<sup>2</sup>S<sup>2</sup>PARC. You can navigate, delete, and download files, such as logs or the input/output data of Services. Two principal views are available: an icon and a list view - the latter provides additional information about the file size and the last modification date. Occasionally, it can be necessary to click the ```Reload``` button to refresh the file system tree.
+When changing to this section, you are presented with the file system of the selected Study (1.). By selecting a certain directory, the files within that folder will be displayed in the area to the right (2.). You can navigate, delete, and download files (3.), such as logs or the input/output data of Services. Two principal views are available: an icon and a list view - the latter provides additional information about the file size and the last modification date. Occasionally, it can be necessary to click the ```Reload``` button to refresh the file system tree.
 
 For more information, see the [o<sup>2</sup>S<sup>2</sup>PARC User Manual](https://docs.osparc.io/#/).

docs/platform_introduction/platform.md

@@ -4,12 +4,18 @@ The TI Planning Tool has the following principal views:
 * a [Landing Page](/docs/platform_introduction/overview.md), which currently serves primarily for user authentication
 * a [Dashboard](/docs/platform_introduction/dashboard.md) that provides an overview of a user's studies (plans) and permits to launch the creation of a [new plan](/docs/plan/create_new_plan.md)
 * an overview of the user's [Data](/docs/platform_introduction/data.md)
-* the step-by-step planning process that includes our two flavours {Personalized plan} and {Precomputed general plan}
+* the step-by-step planning process for the personalized and non-personalized [TI modes](/docs/background/modes.md)
+
+  Personalized flavor only steps::
+
   * [Step 0: Preparing Your Data](/docs/services/file_picker.md)
   * [Step 1: Images Processing](/docs/services/personalizer.md)
   * [Step 2: Fiducials Placement](/docs/services/fiducials_placement.md)
   * [Step 3: Electrode Placement](/docs/services/electrode_placement.md)
   * [Step 4: EM Simulations](/docs/services/simulator.md)
+
+  Global Steps:
+
   * [Step 5: Setup](/docs/services/electrode_selector.md)
   * [Step 6: Optimal Configuration Identification](/docs/services/post_processing.md)
   * [Step 7: Exposure Analysis](/docs/services/s4l_post_processing.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/electrode_selector.png">
 </p>
 
 The **_Setup_** interface has the following elements:
@@ -25,19 +25,19 @@ The **_Setup_** interface has the following elements:
   <img width="90%" src="assets/electrode_selector/species.png">
 </p>
 
-2. **_Select Target Structure_** <br/>
+1. **_Select Target Structure_** <br/>
    The brain structure that should be targeted by TI is specified here via the drop-down list. All the exposure quality metrics will be calculated according to the selected structure. 
 
-3. **_Select Electrode Shape_** <br/>
-   The shape of the electrode is selected here via the drop-down list. Currently the circular shape is available only.
+2. **_Select Electrode Shape_and Dimension** <br/>
+   The shape of the electrode is selected here via the drop-down lists. Currently the circular shape with an area of 3cm<sup>2</sup> is available only.
 
-4. **_Select Electrode Dimensions_** <br/>
-   The dimension of the electrode is set here via the drop-down list. Currently the area of 3cm<sup>2</sup> is available only.
-
-5. **_Electrode Pair Candidates_** <br/>
+3. **_Electrode Pair Candidates_** <br/>
    Electrode position candidates are interactively selected here. Click ```+``` button next to _Start selecting_ under each _Pair_ and then click on the location in the diagram to add. The selected electrode pair locations will be highlighted with the same color (Blue for _Pair 1_ and Yellow for _Pair 2_). Click the icon next to candidate electrode under _Pair_ list to unselect it. E*n* + and E*n* - correspond to candidate locations for the two electrodes that make up the *n*-th pair. All permutations of the candidates locations are then evaluated as part of the optimization process.
 
-Once you are finished with the setup, you can press ```Finish set up```. This will relay all the required information to the **Optimizer** for the evaluation. If settings are changed after submitting, the ```Finish set up``` button turns orange to indicate that the optimization results are outdated. Settings can then be resubmitted and the **Optimizer** is executed once more to update the pipeline, and the button color reverts to the standard color.
+4. **Finish set up** <br/>
+   Once you are finished with the setup, you can press this button. This will relay all the required information to the next step for the evaluation.
+
+ If settings are changed after submitting, the ```Finish set up``` button turns orange to indicate that the optimization results are outdated. Settings can then be resubmitted and the **Optimizer** is executed once more to update the pipeline, and the button color reverts to the standard color.
 
 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).
 

docs/services/fiducials_placement.md

@@ -35,8 +35,4 @@ Users are asked to create 4 points, representing positions Nz (nasion), Iz (inio
    Once points are placed on the 3D model, they appear in the model tree. Here they can be renamed, deleted or selected for export.
 
 3. **_Selection Details_** <br/>
-   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" />
-</p>
+   When selecting an entity from the model tree, this section of the UI will display information and editable settings.

docs/services/simulator.md

@@ -10,7 +10,7 @@ In this step, the generation of the field library, as described in the chapter [
 
 Once all the preparations are finished, the logging console will show the information that the window can be closed. Since the simulations will run for approximately 2.5 to 3 hours, users can come back later once the results are available.
 
-When all the simulations are done, users can hit the ```Export``` button which downloads all the results, and compiles all the necessary files which are needed to for the following steps. Once this step is done, users can either start another simulation run in case both anisotropic and isotropic flavors should be compared, otherwise they can proceed to the next step by clicking on the right arrow.
+When all the simulations are done, users can hit the ```Export``` button which downloads all the results, and compiles all the necessary files which are needed to for the following steps. Once this step is done, users can either start another simulation run in case both anisotropic and isotropic flavors should be compared.
 
 <br>
 <p align="center">