Obsolate, stays for legacy reasons, use the new parallel GUI instead : https://github.com/sandorbx/Parallel-Fiji-CMTK-Registration

Fiji-CMTK-registration-runner-GUI Cross-platform Fiji-Imagej macro GUI to run CMTK-Munger image registration (https://www.nitrc.org/projects/cmtk/) . You can pass arguments to the script interactively, several registration instances can be started up after each other. The script will run on any generic pc from the last ten years I even tested it on a 8 year old thinkpad with acceptable performance. Works on Debian/Ubuntu, Windows 10 with WSL and macOS

Test data available here: https://www.dropbox.com/sh/n866kvoakscig4i/AAB-m1WzqgpkEwk5PV5vMbzEa?dl=0

Change log

2020-08-13

• Reformat at the affine level now works as intended

• Nicer datestamp

• Added some basic feedback on erroneous operation choice combinations

Main features:

-Cross platform, tested on macOS Catalina, Windows 10 WSL and Ubuntu 20.04

-Setup is fully automated and guided, Fiji, CMTK and the registration GUI works out of the box

-The right registration library structure is generated automatically, no need of copying around files

-All parameters can be set interactively, you don't have to worry about syntax

-The script calls CMTK-Munger registration through the native shell so it runs automatically after clicking ok

-You can spawn several different registration jobs quickly, just open the macro gui again, set, click and repeat

-Generates a log file with the commands an parameters

-The script is very simple just under 100 lines and written in Imagej script language, easy to understand and modify, especially adding imagej functions

Linux install

1. Install is fully automated (including CMTK and fiji), if you don’t have Fiji, the installer will set one up for you. Simply run the "linux_install.sh" bash file in the terminal. One way to do this is to download or clone the repo https://github.com/sandorbx/Fiji-CMTK-registration-runner-GUI.git. Extract the files if needed, right click on the folder and choose the "open terminal here" option, type in the terminal: bash linux_install.sh

2. If you need test data download this : https://www.dropbox.com/sh/n866kvoakscig4i/AAB-m1WzqgpkEwk5PV5vMbzEa?dl=0

3. In Fiji you can launch the registration GUI from the menu: plugins>macros>Fiji CMTK registration runner GUI

User Guide:

• for cmtk library with munger browse for the location in your fiji folder Fiji.app/lib/cmtk_munger_wsl_linux

• Very important to avoid any spaces or special characters in your files and folders names

• your data, refbrain and working directory can be wherever on your windows drives, you can browse for them from the gui, they will be in /mnt , (for example to go to your windows desktop folder /mnt/c/users/username/desktop)

• make sure that none of the file or directory names containing spaces

• registration directory with the right structure will be generated automatically and the script copies there your images to register

• almost everything is automatic the only prequisite that your images to register has to be contained in a separate folder and named by adding a number indicating the channel in the end of the filename separated by and underscore (yourpicturename_01;yourpicturename_02 and so on)

• You can choose whether the script should clean up after itself and just keep the reformatted images with the log. Be mindful when you specify the paths to files and folders(refbrain, reg dir, images)

• Set your parameters, if you click ok the registration script starts and the GUI will close, Fiji will display a log, in case you want to follow the progress of the actual commands in detail, open a task manager program.

Windows install:

1. Install linux subsystem for Windows as follows:

2. click into the windows search bar next to the startmenu icon, type powershell, select and start powershell with admin privileges.

3. Use the following command in powershell: Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux

4. Reboot pc when promted

5. install latest ubuntu 20.04 lts from the microsoft store then run ubuntu. Set your username and password. Type/paste in and run these commands to set up your environment:

sudo apt update

sudo apt upgrade

sudo apt install git

git clone https://github.com/sandorbx/Fiji-CMTK-registration-runner-GUI.git

bash ~/Fiji-CMTK-registration-runner-GUI/wslwin10_install.sh

6. Close ubuntu terminal, you need an xterminal emulator to run GUI in the linux subsystem. Download and install mobaxterm home installer edition : https://mobaxterm.mobatek.net/download-home-edition.html

7. Start mobaxterm, if prompted allow it in windows defender

8. From now work in mobaxterm, you can already start your WSL Ubuntu session by double clicking it on the left side under user sessions

9. You can start a graphical file manager from the terminal with the pcmanfm command, you can manipulate files here and start fiji and other apps graphically, your windows drives are in the location /mnt on the filesystem, you can reach it going up the directory structure and in the base look for mnt

10. You have to start fiji inside the mobaxterm terminal, use either the file manager above or the command ~/Fiji.app/ImageJ-linux64 . From fiji launch the registration GUI through the plugins>macros menu

macOS install

1. Download Fiji https://imagej.net/Fiji.html#Downloads , if finder not unzip it, do it manually, then drag and drop the Fiji package to the desktop. Right click on Fiji package choose open, macOS will complain, click cancel if just gives you the move to bin option and right click open it again now there should be the "open" button, click on it.

2. Close Fiji for now. Download the repo https://github.com/sandorbx/Fiji-CMTK-registration-runner-GUI.git to a convenient location

3. Download the folder with the cmtk binaries : https://www.dropbox.com/s/c2ijc5qzb732to0/cmtk_munger_mac.zip?dl=0 if anything needs to be unzipped don’t forget to do it

4. From the downloaded repo "Fiji-CMTK-registration-runner-GUI-master" copy the "Fiji_CMTK_registration_runner.ijm" file to your Fiji package plugins/Macros folder, to reach this destination right click on Fiji and choose "show package contents".

5. Copy the downloaded "cmtk_munger_mac" into your fiji package "lib" library. Again right click on the fiji package and choose show package content to open as a library

6. In Fiji you can launch the registration GUI from the menu: plugins>macros>Fiji CMTK registration runner GUI

7. For cmtk munger library browse for the folder in Fiji.app/lib/cmtk_munger_mac