====== Cross Platform GUI ======
We now recommend a Registration GUI that is distributed as a plugin for Fiji (see below for details of the Classic MacOSX GUI). Currently this provides a simple way to install CMTK, select input images and registration parameters and construct appropriate registration scripts. However it does not actually run the final registration script - you still have to go to your operating system and run the script directly.
===== Install =====
  * See https://github.com/jefferis/fiji-cmtk-gui
===== Run =====
    * Firstly ensure you have your folder structure set-up correctly. This is described in outline below. If you have trouble following any of the steps then please consult this detailed {{:warping_manual:readme_2012.pdf|README}} distributed with the classic MacOSX GUI (formerly available at flybrain.stanford.edu).
      {{ :warping_manual:cmtk_registration_folder_structure3.png?nolink&300 |}}
       * You will need:
          - a folder called e.g. ''yourregistrationfolder'' then within this folder
          - a folder for the image stacks to be registered ''images'', where each image should be named as follows<code>mystackmon_01.nrrd
mystackmon_02.nrrd
fredstack_01.nrrd
fredstack_02.nrrd
junestack_01.nrrd
junestack_02.nrrd</code> The important bit here is the presence of **''01.nrrd''** **''02.nrrd''** etc at the end of the file to ensure that the script can identify which channel is which. By default channel 1 will be used for the registration and up to 3 channels will be reformatted.
          - a folder containing your reference brain ''refbrain'' e.g. ''jfrc2.nrrd''
    * Run in Fiji via Plugins --> CMTK Registration --> CMTK Registration GUI
{{ :warping_manual:cmtk_registraion_gui2.png?nolink&600 |}}
    * Drag and drop requested files/folders onto the that appear
       * You want to drag and drop the folder containing the images to be processed ''~/yourregistrationfolder/images'' into the **Input Image or Image Directory** dialogue box, note the **Registation Folder** dialogue box automatically populates as ''~/yourregistrationfolder''.
       * You want to drag and drop ''~/yourregistrationfolder/refbrain/refbrain.nrrd'' into the **Reference Brain** dialogue box
{{ :warping_manual:cmtk_registraion_gui_dialog_boxes4.png?nolink&600 |}}
    * Ensure the **Registration Params** are set to **Cachero, Ostrovsky 2010**
{{ :warping_manual:cmtk_registraion_gui_reg_params.png?nolink&250 |}}
    * **Action** should be set to **Write Script**
{{ :warping_manual:cmtk_registraion_gui_action.png?nolink&140 |}}
    * Select how many cores of your computers processor you would like to dedicate to the registration (the plugin automatically selects half the total number of cores available to it).
    * Hit **OK** - this creates a small script in ''~/yourregistrationfolder/commands''
    * Navigate to the ''~/yourregistrationfolder/commands'' folder, you will find a new file called ''munger_<todays date>_<time file created>.command'', double click this to run the registration


===== Details =====

    * This is a jython script for fiji and in theory should run on all platforms that fiji supports. We have tested it on mac and it should run without any trouble on linux. I am not so sure about Windows, though there is not fundamental reason why it cannot be made to work.

====== Sample Data ======

  * 176 Mb test image data set available [[https://data.mrc-lmb.cam.ac.uk/weblinks/?id=46922a0880a8f11f8f69cbb52b1396be&filename=warpbench&path=warpbench_images.zip|here]]

====== Classic MacOSX GUI ======

For some time we have provided a simple MacOSX only registration GUI formerly available at http://flybrain.stanford.edu/GUI.

This is being distributed via the zenodo website. The latest version is always accessible using the https://doi.org/10.5281/zenodo.1193265. All released versions are saved on zenodo and can be referred to via their own unique DOIs.

Unzip and put this somewhere sensible e.g. ''/Applications/'' on a Mac.  Then **read the Readme (//carefully//)** to learn how to prepare your images and start the registration. For the **input images** you will need to **pay particular attention to file names**.

You will likely also need to install a copy of [[http://fiji.sc/wiki/index.php/Downloads|Fiji/ImageJ]] to save your images in the preferred input format ([[http://teem.sourceforge.net/nrrd/|nrrd]]) and then read the output (also in nrrd).