gin commit from rMBP-15-Malthe.local

New files: 4

Example/.gitignore

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+*.tif
+*.tiff
+*.nii
+/Brain_example

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

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+#!/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
+

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
+