2/19/15 

The VSyncFSCAN Zip file contains links to download the latest 
distribution of fScan.  There are separate Zip files for: 
  Windows  (64-bit) 
  Linux (32-bit) 
  Linux (64-bit) 
  Macintosh (64-bit) 

FSCAN and related software are distributed using the VSync software 
version synchronization program.  VSync organizes groups of software 
files into projects stored at a central web-site. Running VSync at a 
remote site will compare all local files to the most recent versions 
on the web-site and then download any files that need updating. For 
more information on VSync, see: 

   http://wiki.biac.duke.edu/jvs:vsync 

The Zip file contains a copy of the VSYNC program and an XML file 
called "vsync_project.xml" that tells VSync which projects to 
download. The Zip file also has a copy of this README file. 

To use VSync you must have your computer connected to the Internet. 
If your machine is not connected to the web you will need to load 
this onto some other computer that is, and then transfer your files 
locally. 

Installing fScan on WINDOWS: 
=========================== 
 0) Decide where you want to install the software on your computer. 
    You will only need ~4Mb of disk space for fScan but if you want 
	to download its atlas and sample data you will need nearly a gigabyte 
	of disk space. 

    Where you install these files on your computer shouldn't really 
    matter, but I suggest you avoid installing it too far down your 
    directory tree.  Something like: 

     C:\Program Files\JVS 
    or 
     C:\Documents and Settings\MyAccount\JVS 

    should be fine. Keep in mind that if you want multiple users to have 
    access to the software you should put it where then can all find it. 

    I use the abbreviation JVS (Jim V software) but you can call 
    this folder anything you like. 
	 
 1) Create an empty folder (e.g. "JVS") to hold the software. 
 2) Put the contents of the Zip file to your new folder (e.g. "JVS"). 
 3) Double click the "VSync.exe" program.  This should pop up a dialog 
    for project "FSCAN" (VSync gets its project information from 
    the vsync_project.xml file). 
 4) Click the "Download" button in the dialog. 
    When it asks you a question, answer YES. 
    This will copy the rest of fScan from Duke's website. 
    Close the log file and Exit VSync when it's done. 
 5) Before you run fScan you will need to modify its configuration 
    file to tell fScan where you have put all its files. 
	To find the configuration file go to the subfolder: 
	    lib\FSCAN2 
	There you should see the file: 
		config.txt 
	Double-click that file to open it using Notepad or Wordpad. 
	(Do not open it with Word -- or if you do, save it as text-only.) 
	 
	The second line in CONFIG.TXT is where you specify the JVSHOME 
	parameter. By default it will be something like: 
		C:/Programs/JVS 
	which is almost certainly not the path to your 'JVS' folder. 
	Change the path to match wherever you ran VSync from. 
	Note: Windows usually uses '\' between folder names but fScan 
	      prefers it if you use '/' instead of '\' in path names. 
	Important: When you modify the JVSHOME parameter make sure you 
	      only change what is between the '>' and '<' characters. 
		  The beginning and end of that line must be: 
		      <uservarb name="jvshome">      </uservarb> 
 6) Once you have specified your JVSHOME path, save and close config.txt. 
 7) To make it easy to run fScan, you should associate it with the "WDF" 
    file extension.  WDF is the suffix used for Workspace Definition Files, 
	which are simply XML text files that fScan uses to open one or more 
	image files. (If you already use the WDF suffix for some other type 
	of file you should skip this step.) 
	To associate WDF files with fScan simply double-click the file: 
		Test\test.wdf 
	If WDF is not already used, your computer should ask you how you 
	want to use to open test.wdf. 
	  Click: Select a program from a list of installed programs 
	  Click: OK 
	Next you want to choose fScan.exe, so: 
	  Click:  Browse... 
    and then navigate to the your JVSHOME folder and then into its 
	Windows subfolder.  There you should select: 
	    fscan.exe 
	  then click: Open 
	So that Windows will always use fScan to open WDF files, 
	  Check: Always use the selected program to open this kind of file 
	  Click: OK 

	fScan should then start running. If the brain image does not appear 
	automatically, click the "brain" entry in the fScan window. 
	To close fScan, 
	  Click: Exit 

Running fScan 
============= 
Now you should be able to use fScan simply by clicking any WDF file. 
You can also use it by creating a shortcut to fScan.exe and putting it 
on your desktop, or launch bar, or copying the shortcut to wherever you 
have image data files. 

If you do create a fScan shortcut, before you use it you should open 
its "properties (right click the shortcut and select Properties) and 
delete anything that is in the "Start in" field.  That way if you use 
the shortcut fScan will read and write files in your data folder instead 
of in the folder where fScan.exe is located. 

Updating software 
================= 
Anytime you want to download updates to any VSync project (e.g. 
FSCAN or VSYNC) you can simply double-click the VSync icon in the 
appropriate folder and select the "Status" option to see if there 
is anything new on the central website. 

If your files are not all "up-to-date", select "Download" and 
VSync will automatically copy whatever files are needed to bring 
you up to date.  Hopefully this will make subsequent upgrades 
pretty trivial.  All changes are recorded in the log file and 
a backup copy of any existing file that is overwritten will be 
saved in a "VSync_bkup" folder. Older numbered software versions 
are also stored on the website, so if you don't like a new 
version you can go back to an older one if you want. 

When downloading fScan updates, be careful about overwriting your 
   config.txt 
file, or else you will need to fix your JVSHOME path again. 
(I will need to come up with a better way to specify the path 
on Windows). 

Jim Voyvodic