Merge remote-tracking branch 'refs/remotes/origin/master'

README.md

@@ -22,58 +22,32 @@ For detailed parameter and output description go to the [automatic segmentation
 ## How to setup the environment
 Below is a quick guide to setup the enviroment on a UNIX (Mac and Linux) system
 
-* The program requires Python 3.7+. You can get the newest version of python by installing Anaconda (https://www.anaconda.com). To check your version of python, type
-  ```sh
-  python --version
-  ```
-
-* Install or update all packages listed in `requirements.txt`. All packages can be installed/updated using `pip`. To install a package, e.g. nibabel:
-
-  ```sh
-  pip install nibabel
-  ```
-
-  To check the version of a package
-  ```sh
-  pip freeze | grep nibabel
-  ```
-* Install ANTs, preferably using precompiled binaries, available (for Mac/Linux) at  
-  https://github.com/ANTsX/ANTs/releases/tag/v2.1.0
-
-* Create ANTSPATH and add it to your path. This is done by editing the config file for the terminal shell. The config-file is often named
-  ```sh
-  ~/.bashrc
-  ```
-  or
-  ```sh
-  ~/.bash_profile
-  ```
-
-  In the config-file add the following lines
-  ```sh
-  export ANTSPATH=usr/local/bin/ANTs
-  export PATH=$PATH:$ANTSPATH
-  ```
-  Here, ANTs was installed in `/usr/local/bin/ANTs`
-
-  After adding this to the config-file, restart the terminal and test if the
-  path was added correctly by typing
-  ```sh
-  which antsRegistration
-  ```
-  The correct path should then be printed.
-
-
-* if permission is denied, the file needs to be made executable - this is done using the command
-  ```sh
-  chmod +x <...>/antsRegistration
-  ```
-
-  
+* The program requires Python 3.7+. You can get the newest version of python by installing Anaconda (https://www.anaconda.com). To check your version of python, type ```python --version```
+* Install or update all packages listed in `requirements.txt`. All packages can be installed/updated using `pip`. To install a package, e.g. nibabel: ```pip install nibabel```. To check the version of a package ```pip freeze | grep nibabel```
+* Install ANTs, preferably using precompiled binaries, available (for Mac/Linux) at [https://github.com/ANTsX/ANTs/releases/tag/v2.1.0](https://github.com/ANTsX/ANTs/releases/tag/v2.1.0)
+* Create ANTSPATH and add it to your path. This is done by editing the config file for the terminal shell. *The config-file is often named ```~/.bashrc``` or ```~/.bashprofile```*. In the config-file add the following lines
+    ```sh
+    export ANTSPATH=usr/local/bin/ANTs
+    export PATH=$PATH:$ANTSPATH
+    ```
+    Here, ANTs was installed in ```/usr/local/bin/ANTs```.
+    
+    After adding this to the config-file, restart the terminal and test if the path was added correctly by typing
+    ```sh
+    which antsRegistration
+    ```
+    The correct path should then be printed. If permission is denied, the file needs to be made executable - this is done using the command ```chmod +x <...>/antsRegistration```
+
+
+
 ## Prerequisites  
 * A high-resolution, DAPI modality TIFF image of a coronal mouse brain slice. Can have multiple channels.  
 * The DAPI template file (.nii or .nii.gz)  
-* A segmentation of the DAPI template  (.nii or .nii.gz)  
-  
+* A segmentation of the DAPI template  (.nii or .nii.gz)
+
+
+
 ## Usage  
-Use runner.py to preprocess and output a segmentation registred to the slice. For detailed parameter and output description go to the [automatic segmentation program](./automatic_segmentation_program).
+Use runner.py to preprocess and output a segmentation registred to the slice. For detailed parameter and output description go to the [automatic segmentation program](./automatic_segmentation_program).
+
+