Stimulate documentation and links

Stimulate is basic fMRI software. It can be used to compute maps using either a t-test or correlation approach, but it is best used for viewing previously computed BOLDfold maps. Stimulate is also useful for picking out Talairach coordinates, but has no capacity for intersubject averaging. With large datasets, Stimulate can be slow to display the images. Another drawback to stimulate is that it requires an 8-bit display to work. No modern computers have 8-bit display as a default setting any more so it may be tricky to get stimulate to run.

Before the February 2002 MRI upgrade, data from our fMRI experiments were converted to Stimulate's sdt format on the Siemen's MRI console before being transferred to akasha. After a session of 6 to 8 experiments with one subject, it was simply not practical to transfer 10,000 individual EPI images by ftp to akasha (it took about 3 hours to transfer files that way). Concatenating data into 6 to 8 sdt files allowed the data to be transfered to akasha in about 15 minutes. After the MRI upgrade, the data are first transfered to akasha in DICOM format, then converted to stimulate format for use with the BOLDfold program which will output both stimulate and AFNI format data header files (the data files themselves are identical for stimulate and AFNI format).

The sdt format actually consists of two files, the data proper (we use the short data format) in a file with an sdt extension and a header file with an spr extension. The spr header format is extremely simple and contains all the necessary positional and geometrical information about the images in the sdt file. The spr and sdt files were written by the program fmrisdt (a local program written by G.E. Sarty) on the old MRI console. The fmrisdt program, which used proprietary C libraries provided by Siemens, converted the image spatial coordinates from the x,y,z MRI coordinate system to the x,y,z coordinate system used by Stimulate. The details of the coordinate transformation flash by on the screen when fmrisdt is run.

In the old format, the high resolution anatomical images are transfered directly from the MRI console to akasha. These images are in Siemens proprietary format and have the ima filename extensions. The anatomical images in the old format may be converted to Stimulate and AFNI format on akasha with the program anatsdt, a program that also uses the Siemens proprietary C libraries and with works very similarly to fmrisdt.

Normally, as an fMRI experimenter, the fmrisdt and anatsdt will have already been run for you by Jennifer Hadley and the anatomical files will be ready to look at using either Stimulate or AFNI. Jennifer will also compute the activation maps on akasha using the locally written bfold BOLDfold software. The bfold software writes out maps in both Stimulate (sdt and spr) and AFNI (BRIK and HEAD) format. So the basic activation maps will also be there for you to view using Stimulate or AFNI.

Start Stimulate by typing stimulate at the Unix command prompt.

NOTE: Older versions of Stimulate only work with 8-bit displays. So you will need to create an 8-bit display using vnc through the following steps:

  1. Start a vnc server this way: % vncserver -depth 8 -cc 3 and note the x-windows number (assume it is 1 here).
  2. Start a vnc viewer: % vncviewer yourhost:1.
  3. Start a terminal in the viewer.
  4. Start Stimulate by typing stimulate in the terminal.
A brand new 24-bit display version of Stimulate has been released:
ftp://ftp.cmrr.umn.edu/users/strupp/stimulate_Linux_6.0

Many many thanks to John Strupp for upgrading Stimulate!!

Links:

  1. You can find most of what you need at the Stimulate site including online Stimulate Documentation.
  2. The stimulate manual is also available locally in html, postscript or pdf format.
  3. Also look at The Utter Buffoon's Handbook on working with STIMULATE. This local guide, written by Greg Kraushaar, is available in pdf format.