gin commit from rMBP-15-Malthe.local

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Example/README_EXAMPLE.md

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+# Example of the runner.py
+How to run:
+In the commandline type in
+```sh
+bash runner_example.sh
+```
+
+The program will run the program with the sample file and output the correct
+files in a new directory inside this one named after the file name of the
+brainslice.

Example/README_EXAMPLE.txt

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-In this folder an example of the automatic segementation program shown.
-
-
-By running one of the two shell scripts the program starts and segments a
-brainslice with the segmentation and template files. There are two diffrent
-scripts, one for MacOS and one for Linux. The only difference between the two is
-in the nameing of the python instalation. The program only works with python
-3.7+ and the default macOS instalation of python is 2.7. You are able to check
-the version of your python instalation by typing 'python --version' in the
-command line. If the version installed is python 2.7 the python 3 package is
-often installed as 'python3' instead 
-
-How to run:
-In the commandline type in 'bash runner_example.sh'
-
-The program will run the program with the sample file and output the correct
-files in a new directory inside this one named after the file name of the
-brainslice.

Example/runner_example.sh

@@ -1,3 +1,4 @@
 #!/bin/bash
-python runner.py ./Example/Brain_example.tif ./data/dapi_template.nii.gz ./data/dapi_template_segmentation_full.nii.gz 0.15 ./ --dapi 1
+# cd ..
+python3 ../runner.py ./Brain_example.tif ../data/dapi_template.nii.gz ../data/dapi_template_segmentation_full.nii.gz 0.15 ./ --dapi 1
 

Example/runner_example_macOS.sh

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-#!/bin/bash
-# cd ..
-python3 ../runner.py ./Brain_example.tif ../data/dapi_template.nii.gz ../data/dapi_template_segmentation_full.nii.gz 0.15 ./ --dapi 1
-