Merge pull request #19 from HealthBioscienceIDEAS/4-further-changes-to-nifti-nibabel

4 - further changes to nifti nibabel

Author: mxochicale

.gitignore

@@ -9,6 +9,9 @@ episodes/*html
 site/*
 !site/README.md
 
+## Temporal files for ITK-SNAP registration
+**Untitled.txt
+
 # History files
 .Rhistory
 .Rapp.history

README.md

@@ -23,14 +23,15 @@ git clone git@github.com:HealthBioscienceIDEAS/Medical-Image-Registration-Short-
 ```
 
 ## Maintainers
+This project exists thanks to all mainteners. Sort list by last name (alphabetically). 
 * [Dave Cash](https://github.com/davecash75)
 * [Jamie Mcclelland](https://github.com/jamie-mcclelland)
 
 ## Contributors
-This project exists thanks to all the people who contribute.
+This project exists thanks to all the people who contribute. Sort list by last name (alphabetically). 
 * [Dave Cash](https://github.com/davecash75)
-* [Jamie Mcclelland](https://github.com/jamie-mcclelland)
 * [Milan Malfait](https://github.com/milanmlft)
+* [Jamie Mcclelland](https://github.com/jamie-mcclelland)
 * [Zakaria Senousy](https://github.com/zsenousy)
 * [Stephen Thompson](https://github.com/thompson318)
 * [Miguel Xochicale](https://github.com/mxochicale)

episodes/data/README.md

@@ -1,4 +1,4 @@
-# Demo data
+# Medical Data Imaging 
 
 ## CT-vs-PET-Ventilation-Imaging
 CT Ventilation as a Functional Imaging Modality for Lung Cancer Radiotherapy from [TCIA](https://www.cancerimagingarchive.net/collection/ct-vs-pet-ventilation-imaging/).
@@ -39,7 +39,12 @@ Data paths look like these:
 ```
 
 
-### Data is converted using:
+### Citations & Data Usage Policy
+Data Citation Required: Users must abide by [the TCIA Data Usage Policy and Restrictions](https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/). 
+Attribution must include the following citation, including the Digital Object Identifier:
+> Eslick, E. M., Kipritidis, J., Gradinscak, D., Stevens, M. J., Bailey, D. L., Harris, B., Booth, J. T., & Keall, P. J. (2022). CT Ventilation as a functional imaging modality for lung cancer radiotherapy (CT-vs-PET-Ventilation-Imaging) (Version 1) [Data set]. The Cancer Imaging Archive. https://doi.org/10.7937/3ppx-7s22
+
+### Data is converted from DICOM to nifti using `dicom2nifti`:
 ```
 from pathlib import Path 
 import dicom2nifti 
@@ -50,5 +55,5 @@ dicom2nifti.convert_directory(dicoms, ".", compression=True, reorient=True)
 
 ## Demons Image Registration Exercise Data
 
-Please check `data` folder inside `episodes` for accessing `cine_MR_img_1.png`, `cine_MR_img_2.png`, and `cine_MR_img_3.png` that are used for demonReg.py and `exampleSolution3.py`.
+Please check [`data`](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/tree/main/episodes/data) folder inside `episodes` for accessing `cine_MR_img_1.png`, `cine_MR_img_2.png`, and `cine_MR_img_3.png` that are used for [`demonReg.py`](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/blob/main/src/mirc/utils/demonsReg.py) and [`exampleSolution3.py`](https://github.com/HealthBioscienceIDEAS/Medical-Image-Registration-Short-Course/blob/main/src/mirc/examples/exampleSolution3.py).
 

episodes/excthreesteps.Rmd

@@ -25,6 +25,20 @@ Open terminal, activate `mirVE` environment and run python
 conda activate mirVE
 python
 ```
+:::::::::::::::::::::::::::::::::::::: spoiler
+
+## How to avoid `ModuleNotFoundError: No module named VARIABLE`?
+
+You need to export relative imports, using the following notation for either linux or windows (might be similar to mac)
+
+```bash
+#WINDOWS
+set PYTHONPATH=%PYTHONPATH%;C:\path\to\your\project\
+#LINUX
+export PYTHONPATH="${PYTHONPATH}:/path/to/your/project/"
+```
+
+::::::::::::::::::::::::::::::::::::::
 
 This document explains the implementation of a 2D image registration algorithm using the Demons algorithm. The implementation includes visualisation updates within a single window containing three panes for easier comparison of source, target, and warped images.
 
@@ -460,4 +474,4 @@ demonsReg(cine_MR_img_1, cine_MR_img_2)
 <video width="800" height="450" controls>
     <source src="fig/final_results_vid.mp4" type="video/mp4">
     Your browser does not support the video tag.
-</video>
+</video>