itksnap #35: adds mircrop dataset for a new fig, adds desktop script …

…(not working now but for future work)

itk-snap/README.md

@@ -1,4 +1,5 @@
-# ITK-SNAP Medical Image Segmentation Tool 
+# ITK-SNAP Medical Image Segmentation Tool #35
+> ITK-SNAP is a free, open-source, multi-platform software application used to segment structures in 3D and 4D biomedical images. It was originally developed at the University of North Carolina by student teams led by Guido Gerig (NYU Tanden School of Engineering), who envisioned a tool that would be easy to learn, with a limited feature set centered specifically on the task of image segmentation. Current ITK-SNAP development is led by Paul Yushkevich, Jilei Hao, Alison Pouch, Sadhana Ravikumar and colleagues at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania. http://www.itksnap.org/pmwiki/pmwiki.php 
 
 ## Download and Install
 ``` 
@@ -13,33 +14,42 @@ du -sh itksnap-4.*
 
 ## Datasets
 Site for datasets http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.Data
+* MRI-crop.zip #3D brain MRI for the SNAP 2.x tutorial 64MB
 * Multi-modal brain tumor MRI [Zip archive (9.1 MB)] 
 * Brain diffusion MRI dataset  [Zip archive (10.6 MB)]
 ```
-bash download-datasets.bash
+bash get-datasets.bash
 ```
 
 ## Usage
-* `itksnap-4*`
+* Launch `itksnap-4*`
 ```
 cd $HOME/Downloads/itksnap/itksnap-4.0*/bin
 cd $HOME/Downloads/itksnap/itksnap-4.2*/bin
 ./itksnap
 ```
 
-* `itksnap-4*` with `diffusion.itksnap`
+* `itksnap-4*` with `diffusion.itksnap`   
 ![app](app.png)
 
+
+* `itksnap-4*` with `MRIcrop` dataset
+Open `MRIcrop-orig.gipl` as the main image and `MRIcrop-seg.gipl` as segmentation image to then click update!   
+![mri-crop](mri-crop.png)
+
+
 ## Source code 
 * https://github.com/pyushkevich/itksnap 
 * https://sourceforge.net/p/itk-snap/src/ci/master/tree/  
 * https://sourceforge.net/projects/itk-snap/files/  
 * https://sourceforge.net/projects/itk-snap/files/itk-snap/4.2.0/
 
 
+## References
+* http://www.itksnap.org/docs/fullmanual.php
+
+
 ## Issues 
 ### 01: error while loading shared libraries: libpng12.so.0 with itksnap-3.8.0-20190612-Linux-x86_64.tar.gz
 Not sorted but only with the use of /repositories/ITK-SNAP/itksnap-4.0.0-alpha.3-20220203-Linux-gcc64/bin
 
-
-

itk-snap/download-installation.bash

@@ -1,6 +1,9 @@
 # USAGE
 # bash download_installation.bash
 
+## REFERENCES
+# http://www.itksnap.org/pmwiki/pmwiki.php?n=Documentation.TutorialSectionInstallation
+
 ## LATEST VERSION
 # https://sourceforge.net/projects/itk-snap/files/itk-snap/
 # https://sourceforge.net/p/itk-snap/activity/
@@ -9,7 +12,7 @@
 # itksnap-3.8.0-20190612-Linux-x86_64.tar.gz
 # itksnap-4.0.1-20230320-Linux-gcc64.tar.gz
 # itksnap-experimental-vtk9qt6-Linux-gcc64.tar.gz
-#FILENAME=itksnap-nightly-rel_4.0-Linux-gcc64.tar.gz  #Length: 200943059 (192M) [application/x-gzip]
+# FILENAME=itksnap-nightly-rel_4.0-Linux-gcc64.tar.gz  #Length: 200943059 (192M) [application/x-gzip]
 
 #VERSION=4.0.2
 #FILENAME=itksnap-4.0.2-Linux-gcc64.tar.gz
@@ -23,4 +26,3 @@ wget https://sourceforge.net/projects/itk-snap/files/itk-snap/${VERSION}/${FILEN
 tar -xvzf ${FILENAME}
 rm ${FILENAME}
 
-

itk-snap/get_datasets.bash

@@ -1,14 +1,17 @@
 ##USAGE
-# bash download-datasets.bash
+# bash get-datasets.bash
 # Site for datasets http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.Data
 
 FILENAME0=diffusion.zip # Brain diffusion MRI dataset  [Zip archive (10.6 MB)]
 FILENAME1=braintumor.zip # Multi-modal brain tumor MRI [Zip archive (9.1 MB)] 
+FILENAME2=MRI-crop.zip #3D brain MRI for the SNAP 2.x tutorial 64MB
 
 cd ~/Downloads/
 mkdir -p itksnap && cd itksnap
 wget https://www.nitrc.org/frs/download.php/6161/$FILENAME0 -O $FILENAME0
 wget http://www.nitrc.org/frs/download.php/6176/$FILENAME1 -O $FILENAME1
+wget http://www.nitrc.org/frs/download.php/720/$FILENAME2 -O $FILENAME2
 unzip $FILENAME0
 unzip $FILENAME1
+unzip $FILENAME2
 

itk-snap/itksnap.desktop

@@ -0,0 +1,11 @@
+#REF
+#https://askubuntu.com/questions/1237042/desktop-files-not-launching-from-desktop-in-ubuntu-20-04-lts
+[Desktop Entry]
+Type=Application
+Encoding=UTF-8
+Name=ITK-SNAP
+Exec=/home/mxochicale/Downloads/itksnap/itksnap-4.2.0-20240422-Linux-gcc64/bin/itksnap
+Icon=/path/to/eclipse/icon
+Exec=application
+Type=Application
+Categories=Development;