fixed readme

Author: dipterix

README.md

@@ -17,6 +17,11 @@
 * For function usage, check [Reference page](https://dipterix.github.io/threeBrain/reference/index.html)
 * Check [keyboard shortcuts](https://dipterix.github.io/threeBrain/shortcuts.html) here
 
+#### System Requirement
+
+* **Web Browsers**: the viewer uses `WegGL2` to render in browsers. Please check [this list](https://caniuse.com/?search=webgl2) to see compatible browsers. As of 2020, **Chrome** and **Firefox** have full supports.
+  - For **Safari** users, please enable this feature by going to `Safari` > `Preferences`, click `Advanced`, then select `Show Develop menu in menu bar`; then click `Develop` in the menu bar, go to `Experimental Features` > `WebGL 2.0`. This only needs to be done once. 
+
 ## A. Installation
 
 1. [`R`](https://cran.r-project.org/) and [`RStudio Desktop (Free Version)`](https://www.rstudio.com/products/rstudio/download/)
@@ -26,8 +31,8 @@ install.packages("threeBrain")
 ```
 If you want to install `dev` version from *Github*, then use:
 ```r
-install.packages("devtools")
-devtools::install_github("dipterix/threeBrain")
+install.packages("remotes")
+remotes::install_github("dipterix/threeBrain")
 ```
 3. (Optional) Setups: after installation, in `RStudio` console, type the following command
 ```r
@@ -37,39 +42,47 @@ and follow the instructions.
 
 ## B. Basic Brain Viewer
 
-Once finishing setting up of `threeBrain`, there will be a template subject `N27` (Collin's 27) created at
-```
-~/rave_data/others/three_brain/N27
+Once finishing setting up of `threeBrain`, there will be a template subject `N27` (Collin's 27) created locally. The location is platform-related. You can find it by running the following command:
+
+```r
+library(threeBrain)
+
+default_template_directory()
+#> [1] "/Users/dipterix/Library/Application Support/
+#> org.R-project.R/R/threeBrain/templates"
 ```
-`~` is your home directory. For example on my laptop, it's `/Users/dipterix/`. On Windows, it's `C:\Users\dipterix\`.
 
-Let's view this subject. The following commands all go to `RStudio` console.
+**N27** template folder resides inside of this directory.
+
+Let's view this subject using the `freesurfer_brain2` function.
 
 1. Import subject
 ```r
-# freesurfer_brain is deprecated, use freesurfer_brain2 instead
-n27 = freesurfer_brain2(
-    fs_subject_folder = '~/rave_data/others/three_brain/N27',
-    subject_name = 'N27',
-    surface_types = 'pial'
-)
+library(threeBrain)
+
+n27_path <- file.path(default_template_directory(), "N27")
+
+x <- freesurfer_brain2( fs_subject_folder = n27_path,
+  subject_name = 'N27', surface_types = 'pial')
 ```
 2. Visualize
 ```r
-plot(x)       # alternatively, you can use `x$plot()`
+plot(x)       # alternatively, you can use `n27$plot()`
 ```
 
-## C. Directory Setup
+## C. Subject Setup
 
-`~/rave_data/others/three_brain/N27` is a sample generated by `FreeSurfer` ([download](https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)). If you have any subjects processed by `FreeSurfer`, direct `fs_subject_folder` to your subject folder. 
+The sample subject (`N27`) is a sample generated by `FreeSurfer` ([download](https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)). If you have any subjects processed by `FreeSurfer`, use function `freesurfer_brain2` to visualize. 
+
+The `AFNI/SUMA` standard 141 brain is also supported. Please use terminal command `@SUMA_Make_Spec_FS -NIFTI -sid [subID]` to generate 141 brain. (Click [here](https://openwetware.org/wiki/Beauchamp:BuffyElectrodeNotes#Converting_Files_between_iELVis_and_AFNI/SUMA) for some hints)
 
 ## D. Add/Render Electrodes
 
 If you have electrode file, you can import it before calling `plot` function. Please make sure it's in `csv` format.
 ```r
 x$set_electrodes(electrodes = "[PATH to ELECTRODE FILE]")
 ```
-Here is an example of electrode csv file. Only the first five columns (**case-sensitive**) are mandatory: `Electrode (integer)`, `Coord_x`, `Coord_y`, `Coord_z`, and `Label (character)`. `Coord_*` is `RAS` location from `FreeSurfer` coordinates.
+Here is an example of electrode csv file. Only the first five columns (**case-sensitive**) are mandatory: `Electrode (integer)`, `Coord_x`, `Coord_y`, `Coord_z`, and `Label (character)`. `Coord_*` is `tkRAS` location from `FreeSurfer` coordinates.
 ```
 | Electrode| Coord_x| Coord_y| Coord_z|Label  | MNI305_x|  MNI305_y|  MNI305_z|SurfaceElectrode |SurfaceType | Radius| VertexNumber|Hemisphere |
 |---------:|-------:|-------:|-------:|:------|--------:|---------:|---------:|:----------------|:-----------|------:|------------:|:----------|
@@ -106,9 +119,11 @@ The electrode value file is also a csv like:
 
 If you have your own subjects with `FreeSurfer` output, for example, I have two subjects `YAB` and `YCQ`. To merge these two subjects and show them on `N27` template,
 ```r
+library(threeBrain)
+
 # yab = ... (see section B for import a single subject)
 # ycq = ...
-template_n27 = threeBrain::merge_brain(yab, ycq, template_subject = 'N27')
+template_n27 = merge_brain(yab, ycq, template_subject = 'N27')
 
 plot( template_n27 )
 ```
@@ -119,7 +134,7 @@ The viewer will be in `N27` template, and electrodes of these two subjects can b
 
 To cite threeBrain in publications use:
 
-> Magnotti, JF, Wang, Z, Beauchamp, MS. RAVE: comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data.
+> Magnotti, J. F., Wang, Z., & Beauchamp, M. S. (2020). RAVE: Comprehensive open-source software for reproducible analysis and visualization of intracranial EEG data. *NeuroImage, 223*, 117341.
 
 A BibTeX entry for LaTeX users: