Running BIC applications under MS Windows

Preamble

Just so you know, I'm not a MS Windows expert - by any stretch of the imagination. In Unix, I use tcsh (and bash under Linux). But, at my place of work, we're mainly a M$ Windows shop. Rather than become the local Unix/Linux help desk, I chose to install some BIC tools that have been ported to Windows. This has been a learning experience for me and I have created this page in order to document what I have learned - and to avoid having to tell the story over and over again. :^)

If you have a contribution to make, please let me know! That includes comments on the setup of this page and the usefulness of the content.

So far, I've installed and run register and Display for Windows on the machine in my office, the particulars of which are given below:

     OS Name        Microsoft Windows 2000 Professional
     Version        5.0.2195 Service Pack 2 Build 2195

     Processor      AMD Athalon 1GHZ

     VideoCard      ASUS AGP-V7700 DDR SGRAM v5.33
     Adapter Type   GeForce2 GTS, ASUSTek compatible
     Resolution     1024 x 768 x 60 hertz
     Bits/Pixel     32

Getting the programs

If you want to download the BIC applications that have been ported to Windows, you can find them at Frank Morales' web site. In addition to the visualization software register and Display, Frank has a version of the EMMA toolbox for Matlab that you can download. And, Prof. Keith Worsley has a version of the fmristat toolbox (again for Matlab) available for download.

The EMMA and fmristat toolboxes need to be installed in the same directory as the other Matlab toolboxes

The other BIC applications can be installed anywhere, but for the sake of convention, should be installed in c:\Program Files. I leave it to you to decide whether to put them in one folder or separate ones. At this time, the "installation" process consists of decompressing the *.zip files and putting the folder (which contains the precompiled binaries) in the appropriate location.

Official Documentation

For more info about Display, register and other BIC applications, follow these links:

Setting up Windows

FWIW, I got the info. on modifying Windows for tab completion from Bill Allison's web site.

from the Start/Run menu, run "regedt32"
in the "HKEY_LOCAL_MACHINE on Local Machine" window, look for:
- HKEY_LOCAL_MACHINE/Software/Microsoft/Command Processor
  - Double clicking on the file icon (e.g. HKEY_LOCAL_MACHINE or Software) will display the sub-folders, if they are not already visible.
- Double click on the key "PathCompletionChar", and in the "Dword editor" dialogue box that pops up, change the value to 9.
  - The numbering displayed in the Registry window is hexa-decimal, but 9 is 9 in that numbering system, so you don't have to translate it.
- Then click on "okay" and close the Registry. You don't have to save anything; it is automatically updated.
When you are ready to use the command shell use the Start/Run menu and invoke "cmd" instead of "command" (or, select Start/Programs/Accessories/Command Prompt from the Start menu.
- You should verify which executable file is used by your system. Do this by right-clicking on the Command Prompt icon and examining its properties; specifically, look at the "Target:" and look for: %SystemRoot%\system32\cmd.exe.

Caveat emptor!

Tab completion under Windows doesn't work quite as intelligently as in Unix/tcsh. Rather than stopping at the last common character when there is more than one file or command that starts with a string like ab_cd., tab-completion in Windows will fill in the word/string that it first encounters.
Use register -rgb rather than the command "register" alone.
Invoke register from the directory where your minc files live. Trying to find image files from the register directory gave me some trouble.
At the moment, I don't know how to get Display to load the full menu when I invoke it from the image file directory. More on this later... for now, you have to be in the display directory in order to get full menu functionality. You should be able to call the image files using tab-completion from the display directory. Let me know if this fails, please.

Other helpful hints

You can use the mouse to cut and paste file names in Windows! Use the left mouse button and double click on the file name of interest to copy it to the mini-buffer. Use the right mouse button and double click to paste the file name on the command line.
You can list the contents of a directory with the dir command (not ls!). And, you can search for files containing certain strings (eg. dir *blind*stat*mnc will list all minc files containing the strings "blind" and "stat").