This page contains a list of Frequently Asked Questions and their answers.

• How do I download Stimulate via anonymous ftp?
• How are K-space and Image-space filtering related?
• How do I download the GNU split files for Stimulate?
• How do I determine my workstation's hostid ?
• How do I determine my workstation's hostname ?
• How do I view the User's Guide in html locally?
• What does the error "fatal: libxview.so.3" mean?
• Why do I get a "Numerical Recipes run-time error"?
• What Operating System does my workstation have?
• Why do I get "Permission denied" when I try to run Stimulate?
• How do I renew my authorization?
• Which Stimulate executable should I use?

Stimulate is available at: ftp.cmrr.umn.edu
In the directory: /pub/stimulate/stimulate_v5.0 

Here is an example download session with user input
shown in red.


unix> ftp ftp.cmrr.umn.edu 
Connected to ftp.
220 ftp FTP server (Version wu-2.4(6) Thu Jul 7 18:29:45 CDT 1994) ready.
Name (ftp.cmrr.umn.edu:strupp): anonymous
331 Guest login ok, send your complete e-mail address as password.
Password: user@host.domain 
230-
230-                    Welcome to the
230-        Center for Magnetic Resonance Research
230-               University of Minnesota
230-  
230 Guest login ok, access restrictions apply.
ftp> cd /pub/stimulate/stimulate_v5.0
250 CWD command successful.
ftp> binary
200 Type set to I.
ftp> get stimulate_Solaris.Z
200 PORT command successful.
150 Opening BINARY mode data connection for stimulate_Solaris.Z (519657 bytes).
226 Transfer complete.
local: stimulate_Solaris.Z remote: stimulate_Solaris.Z
519657 bytes received in 0.68 seconds (7.4e+02 Kbytes/s)
ftp> quit
221 Goodbye.

unix> uncompress stimulate_Solaris.Z
unix> chmod +x stimulate_Solaris

The low-pass gaussian filter available as a load option
is done as a K-space multiplication prior to the FFT
with a radius_k.  This is equivalent to a convolution 
on an NxN matrix in image space with a kernel of radius_i, 
where radius_i = 0.22 (N / radius_k).  The FWHM is simply 
twice the radius: FWHM_i = 2 * radius_i.

See FWHM for details.

The Stimulate executables and user's guide are available in
a set of consecutively numbered/lettered sections generated
by GNU split.  These files are intended for downloading by
users who have slow internet connections that experience
occasional (or regular) interruptions.  Thus only those
sections interrupted during the ftp download need to be
retransmitted.

The files are located at: ftp.cmrr.umn.edu 
In the directory: /pub/stimulate/stimulate_v5.0/split 

For example, to reconstruct stimulate_Solaris.Z
retrieve all the files sections:
      stimulate_Solaris.Z.aa
      stimulate_Solaris.Z.ab
      stimulate_Solaris.Z.ac

Then:
   unix> cat stimulate_Solaris.Z.* > stimulate_Solaris.Z
   unix> uncompress stimulate_Solaris.Z
   unix> chmod +x stimulate_Solaris
   unix> rm stimulate_Solaris.*

   Use the unix command: "hostid"

   Example> hostid
          0x80654ef1

   Use the unix command: "uname -n"
   where the option switch is as follows:
      -n Prints the hostname or nodename.

   Example> uname -n
          dagny

1) Download the usersGuide.tar.Z file to some directory.
(e.g. /usr/local )

2) unix> zcat usersGuide.tar.Z | tar xvf -

3) Then in the netscape Location field type:
   file:/usr/local/stimUsersGuide/usersGuide.html

The reason you may receive one or both of the following
messages when trying to run Stimulate is that your
LD_LIBRARY_PATH environment variable is not set or is set
incorrectly.

   fatal: libxview.so.3: can't open file: errno=2
   fatal: libolgx.so.3:  can't open file: errno=2

The installation script puts the following command into the
stimulate script which is used to invoke the stimulate
executable:

   setenv LD_LIBRARY_PATH /usr/openwin/lib

This is the default location for openwin.  However, if your
System Administrator has installed openwin at a different
location, you must edit the stimulate script.

Another reason you may get these errors is that you did
not run the installation script "stimInstall.sh."

The following error occurs when generating a t-Test map
with that has no (i.e. 0.0) variance in either the control
or stim periods.

   Numerical Recipes run-time error...  
   a or b too big, or TMAX too small in BETACF 
   ...now exiting to system... 

Here at the CMRR always have a bit of noise in our images
so this rarely or never happens to us.  However, I'll fix
this sometime soon and release a version 5.0.1.

You can probably work around this problem by generating a
mask to eliminate evaluation of pixels with no variance.


 Generate a stat map of StdDev type (see Section 9.2.4)
 Generate a "bin" mask of the StdDev map via a threshold 
 GT 0.0 (see Section 15.1)
 Do your t-test with the "Mask" option selected. 
 (see Figure 20, Button 10).

   Use the unix command: "uname -s -r"
   where the option switches are as follows:
      -r Prints the operating system release level.
      -s Prints the name of the operating system.

   Example> uname -s -r
          SunOS 5.5.1
   
   Note that for Sun workstations the SunOS release level
   corresponds to the Solaris version as follows:
      SunOS 4.1 == Solaris 1.1
      SunOS 5.3 == Solaris 2.3
      SunOS 5.4 == Solaris 2.4
      SunOS 5.5 == Solaris 2.5

The "Permission denied" unix error message means that the
the file mode of the Stimulate executable isn't set
correctly.  It can be corrected with the "chmod" command.

unix> ls -l stimulate
-rw-r--r-- 1 strupp  nmr   583 Oct 27 19:23 stimulate

unix> chmod +x stimulate
unix> ls -l stimulate

-rwxr-xr-x 1 strupp  nmr   583 Oct 27 19:23 stimulate*

If you get a message ``Your authorization code has expired.''
You can simply get a new authorization code. 

Your new code will be valid for one year from the date you
obtain it.  You'll need to go through the same process next
year, but by then there will almost certainly be a newer 
version of Stimulate to download anyways.

The purpose of the authorization expiration is that we want
to keep a track of the number of sites actually using
Stimulate on an on-going basis.

For SGI workstations use the Stimulate_IRIX executable
which was compiled under IRIX 5.3 and has been successfully
tested under IRIX 5.3, 6.1 and 6.2.

Stimulate_SunOS was compiled under SunOS 4.1.3 and
Stimulate_Solaris was compiled under Solaris 2.5, thus for
Sun workstations running:

      SunOS 4.1 == Solaris 1.1 use Stimulate_SunOS
      SunOS 5.3 == Solaris 2.3 use Stimulate_SunOS 
      SunOS 5.4 == Solaris 2.4 use Stimulate_Solaris
      SunOS 5.5 == Solaris 2.5 use Stimulate_Solaris