====== Introduction ======

I have written a tcl script, ''ResultViewer.hx'', based on work from Steffen Prohaska that allows 

  - visualisation in Amira of affine registered brains compared with a template
  - selection of what kind of affine (9dof, ght etc)
  - selection of a template brain (FC6475, FCWB)
  - calculation of surface-based affine registration

There is also a related simpler script [[software:amira:stackviewer|StackViewer]] which simply allows rapid scanning through a directory of confocal scripts.
====== Install ======

  - You need the Amira mesh toolbox (on gjac or gj8c) or [[zib_amira|ZIB Amira]] for surface based affine registrations
  - Lives at https://bitbucket.org/jefferis/resultviewer/
  - ''git clone git@bitbucket.org:jefferis/resultviewer.git'' somewhere sensible
  - This also lives on JData here ''/Volumes/JData/JPeople/Steffen/2011-07-29_InitBrainPosGHT''
  - Make sure that you have a template brain called ''TemplateStem.surf'' in the hx subfolder
    - use a downsampled brain to make this and aim for ~ 20k faces in the surface model
  
====== Configuring ======

  - make downsampled versions of your images in a folder called ''images4um'' that is next to the folder containing registrations e.g.
    * MyBigRegistrationFolder
      * images4um
      * Registration
        * warp
        * affine 
  - Make a keylist file, a text file which contains the **key** for one brain per line
    - TCL will look for the registration folders like this: ''${refbrain}_${brainkey}_${chan}_${regtype}.list''
    - so make sure that the key corresponds to everything between the name of the refbrain and the channel
    - so for a registration folder called ''IS2_AABD4-1_01_9dof.list'' the **key** would be ''AABD4-1''
    - the script currently assumes that the reference (nc82) channel will be channel 1
  - Double click/drag and drop ''src/ResultViewer.hx'' onto Amira to get started
    - This lives at ''/Volumes/JData/JPeople/Steffen/2011-07-29_InitBrainPosGHT/src/ResultViewer.hx'' if you are using the JData version.
  - You will get a blue node in your object pool
  - Click on it
  - Choose the Reg root dir e.g. ''/Volumes/JData/JPeople/Aaron/YourRegistrationFolder/Registrations/IS2/Registration''
  - Choose the key list file e.g. ''/Volumes/JData/JPeople/Aaron/YourRegistrationFolder/Registrations/IS2/Registration/mynicebrains.txt''
    - the key list can be called anything and the location doesn't matter
  - Choose your reg type e.g. **9dof** or **ght**
    - this must be eveything between the last underscore after the channel number and ''.list'' (''${refbrain}_${brainkey}_${chan}_${regtype}.list'')
  - Choose your Ref Brain e.g. FCWB
  - Tick **Save registration at CMTK** if you want to save in CMTK format
    - if you want to use this as an initial affine registration (to feed into image based affine) then you should save as XXX_ght.list and use ''munger.pl'''s ''-H'' switch
    - if you want to use this as an affine to pass to the warp program then you should save as XXXX_9dof.list

====== Resampling Brains ======
  * You should have some resampled brains as input
  * This script expects them to live in a folder called ''images4um'' (though you can choose any voxel size you want within reason)
  * Voxel dimensions in the range 2x2x2 um to 4x4x4 um are sensible
  * In R with AnalysisSuite you can use ''NrrdResample(<infile>,<outdir>,voxdims=c(2,2,2))''
  * See [[using_showclones]] for a longer example
====== Selecting brains ======
  * move the brain num slider to move the brains in a list (FIXME there must be 2 or more at the moment)
  * Tick **selected** to choose a brain
  * Click **SaveSelected** button to save your selected brains 
    * if your input was ''mynicebrains.txt'' this will make a file called ''mynicebrains.txt-sel.txt''
    * if you already had a file called ''mynicebrains.txt-sel.txt'' it will make a backup called ''mynicebrains.txt-sel.txt.bak''
    * if you already had a backup file called ''mynicebrains.txt-sel.txt.bak'' it will be overwritten
  * Save at least every few hundred brains (it seems to crash after ~ 1000)
  * If you want to restart with an existing selection click **LoadSelected**

====== Calculating Affine Registrations ======
If the existing registration is poor (or non-existent) you can often make a good one using Amira's surface based registration

  * Click **SetupReg**
  * a red surface model should appear 
    * Turn off ''curbrainview'' (volume rendering) so you can see more clearly
  * Click on ''curbrain.surf''
    * Click on the **Transform editor** (4th icon along)
    * Choose **Manipulator ... Tab Box**
    * Make sure that you have the arrow selected (top left icon in viewer pane)
    * Drag the red surface model on top of your reference
    * Either click on ''curbrain.AlignSurfaces''
      * choose Trafo ''rigid''
      * Hit **Surfaces**
      * choose Trafo ''rigid + unifiorm scale''
      * Hit **Surfaces**
      * choose Trafo ''affine''
    * OR scale it using the green corners if the size is different
      * then click on ''curbrain.AlignSurfaces''
      * choose Trafo ''affine''
      * Hit **Surfaces**
    * You now have an affine that can be used to initialise either an image based affine or a warping registration
    * Go back to ResultViewer.hx
    * Hit **SaveReg**

====== ToDo ======
  - <del>Make affine directories if they don't exist (so that one can make surface based registrations from scratch)</del>
  - <del>Add a surface for IS2</del>
  - make it possible to look at reformatted images directly (rather than applying registration to original image)
  - resample images