Merge pull request #34 from jkosciessa/updated

Merge of PRESTUS feature updates

Author: jkosciessa

.gitignore

@@ -80,4 +80,4 @@ $RECYCLE.BIN/
 .directory
 .Trash-*
 core.*
-
+.Rhistory

.gitmodules

@@ -0,0 +1,12 @@
+[submodule "toolboxes/export_fig"]
+	path = toolboxes/export_fig
+	url = https://github.com/altmany/export_fig
+[submodule "toolboxes/xml2struct"]
+	path = toolboxes/xml2struct
+	url = https://github.com/joe-of-all-trades/xml2struct
+[submodule "toolboxes/k-wave"]
+	path = toolboxes/k-wave
+	url = https://github.com/ucl-bug/k-wave.git
+[submodule "toolboxes/FEX-minimize"]
+	path = toolboxes/FEX-minimize
+	url = https://github.com/rodyo/FEX-minimize.git

README.md

@@ -24,9 +24,30 @@ cp /opt/prestus/example_data/PRESTUS_example_data.zip ${HOME}
 
 Download and install these tools:
 
-- [SimNIBS 4](https://simnibs.github.io/simnibs/build/html/index.html#simnibs-4)
-- [k-Wave 1.4](http://www.k-wave.org/download.php) (should be installed in the 'toolbox' folder of PRESTUS or be added automatically on MATLAB startup if you use HPC)
-- toolboxes included in this repository
+- MATLAB (R2022b)
+- [SimNIBS 4](https://github.com/simnibs/simnibs)
+- toolboxes included as submodules if this repository is cloned (must be added on MATLAB startup)
+    - [k-Wave (1.4)](https://github.com/ucl-bug/k-wave.git)
+    - [export_fig](https://github.com/altmany/export_fig)
+    - [FEX-minimize](https://github.com/rodyo/FEX-minimize.git)
+    - [xml2struct](https://github.com/joe-of-all-trades/xml2struct)
+
+Tested on MATLAB 2022b, set up to work on Donders HPC (can work on a local PC as well). 
+
+Before using the package, you need to have some libraries on your path. Major dependencies are included as submodules in the toolbox folder. If you clone this repository, you can retrieve the submodules as follows:
+```
+git clone --recurse-submodules https://github.com/Donders-Institute/PRESTUS.git
+```
+
+If you cloned this repository in the past, and updated it, you can retrieve submodules as follows:
+```
+cd PRESTUS
+git submodule init
+git submodule update
+```
+You additionally need to install SimNIBS (https://simnibs.github.io/simnibs/build/html/index.html#simnibs-4).
+
+*Note: If you do not clone this repository, you must manually download and add the toolboxes specified above.*
 
 Example data: We are currently working on a solution to make the example dataset available for users outside the DCCN.