Merge pull request #21 from Konohana0608/updates/cindys_feedback

changed image with same numbers, and clarified stuff about atlas sele…

docs/services/fiducials_placement.md

@@ -2,7 +2,7 @@
 
 **_Summary_**:
 
-Import the generated anatomical 3D model into the GUI by selecting ```Import``` and loading the model file from the ```inputs/input_1``` directory. Place the fiducial points Nz, Iz, LPA, and RPA by selecting ```Sketch``` then ```Point``` in the GUI, rename them using ```F2```, and export them to the ```outputs/output_1``` directory with the .sab extension.
+Import the generated anatomical 3D model into the GUI by selecting ```Import``` and loading the model file from the ```inputs/input_1``` directory. Place the fiducial points Nz, Iz, LPA, and RPA by selecting ```Sketch``` then ```Point``` in the GUI, rename them using ```F2```(have to be called Nz, Iz, LPA and RPA exactly), and export them to the ```outputs/output_1``` directory with the .sab extension.
 
 ----
 

docs/services/file_picker.md

@@ -8,7 +8,7 @@ To ensure the highest quality of the head models, please adhere to the following
 
 1. **File Format**
    - Ensure your MRI data is in the NIfTI file format (`.nii.gz`).
-   - Only a T1 weighted scan is needed. Please make sure the file name contains "t1" somewhere.
+   - Only a T1 weighted scan is needed. **Please make sure the file name contains "t1" somewhere.**
 
 2. **Data Integrity**
    - The MRI scans should be free from artifacts and implants.
@@ -48,4 +48,16 @@ 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">
-</p>
+</p>
+
+### Q: What to do if your DTI data contains PA / AP acquisitions?
+
+**A:** AP / PA refer to the polarity of the phase encoding direction of the acquired sequences. AP / PA volumes are acquired to offer a way to correct the distortions that typically appear in EPI sequences, so they are used at the preprocessing stage, prior to fitting your (e.g. DTI) model. 
+
+So, you do not fit your local model into them separately; they are used at the preprocessing stage in order to get a single DWI volume where the relevant distortions have been corrected to the extent that is possible.
+
+DIPY by itself does not offer a method to correct such distortions, so you will need to use third-party tools for that purpose. One very well-known and widely used tool is **FSL**. You can read more about how to use the tools FSL offers for this purpose [here](https://www.fmrib.ox.ac.uk/primers/intro_primer/ExBox20/IntroBox20.html).
+
+There are a few packages out there that perform dMRI data preprocessing steps in a principled way, calling the required FSL methods under the hood and transparently to the user. You can find a comparison of such packages [here](https://qsiprep.readthedocs.io/en/latest/comparisons.html).
+
+*Source*: [dipy discussions](https://github.com/dipy/dipy/discussions/3289)

docs/services/personalizer.md

@@ -59,7 +59,8 @@ The interface has the following elements:
    The radius of the cylindrical electrodes is selected here. This can only be changes as long as no simulations have been started in [Step 4: EM Simulations](/docs/services/simulator.md).
 
 2. **Select Atlas to Register** <br/>
-   If a detailed atlas should be registered to the brain, select the according option. This is a multi-select list. Please make sure that ```None``` is not selected together with the atlas to register because the registration will always be skipped if ```None``` is selected.
+   By defailt, the model prediction already contains a couple of targets. These are listed in the logger (4) in the image above. If these are sufficient, you can leave this setting at ```None```.
+   If not, a detailed atlas can be registered to the brain. Select the according option. Since this is a multi-select list, please make sure that ```None``` is not selected together with the atlas to register, because the registration will always be skipped if ```None``` is selected.
 
 3. **Progress Overview** <br/>
    Shows the progress of each individual step in the model generation. ```10-10``` will only be done if the [Step 2: Fiducials Placement](/docs/services/fiducials_placement.md) already has been done.