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Brain picture
Beauchamp Lab


How to Scan

next step is Getting raw data from the scanner

About the UT Philips Scanner

Our scanner is a 3 T whole-body Philips scanner with 16 parallel RF channels. It is a hybrid Intera (older) and Achieva (newer). Slice acquisition is set to the default order, with the time maximized between adjacent slices. Slice acquisition order seems to be from bottom to top, based on the raw DICOM images (where the first image is the most inferior) and real-time view seen during scanning (where the most inferior images are display first, sometime most superior aren't displayed at all before the next TR starts). The scanner technologist (Vips Patel) will run the scanner for you.

About the BCM CAMRI Siemens Scanners

The BCM CAMRI has 3 whole-body Trios and 1 head-only Allegra (as well as a decommissioned Allegra). We usually use 3T-5, one of the Trios. David Ress' former student Andrew Florens examined the acquisition time stamps and found that axial slices are collected from Superior to Inferior (head to foot). If an odd number of slices is acquired, the slice order is

 1, 3, 5, 7, etc.
 2, 4, 6, 8 etc.

If an even number of slices is acquired, the slice order is reversed:

 2, 4, 6, 8, etc.
 1, 3, 5, 7, etc.

See Krista to have your badge activated.

More details on the BCM scanners

  1. Stimuli on the 3T-5 are displayed on an LCD screen. Link to manual here: Cambridge Research Systems BOLD Screen User Guide

The BOLDScreen has a built-in color profile that can make images appear too dark. Instead, use the default color profile as follows:

  1. On the Mac laptop stimulus computer, Click on the Apple, Open "System Preferences"
  2. click on "Displays", select the "Color" Tab
  3. Select the "Color LCD" profile for the second display (the BOLDscreen)

Responses are recorded with a fORP system. Link to Jung Hwan's user guide here: fORP Configuration For Beauchamp Lab experiments, do the following:

  1. Push in fORP front button
  2. Go to changes modes, select YES
  3. Select Autoconfigure
  4. Scroll down to HID NAR BYGRT, Select
  5. Confirm that Mode is 002 in top right of display

This gives a trigger as a T rather than a 5. An extra step needs to be taken to make sure that the right USB device is selected in Matlab (from the three possibilities).

To access pulse sequences, Click on Ctrl-Esc and select the "Advanced User" program. Type in the password (meduser1). Then go back, and open a Windows Explorer window. The pulse sequences are located under


The diffusion vectors are stored in the file


If the real-time is not working, make sure you are using the correct pulse sequence (VB17rt EPI). Also check the tabs computer (MacPro):

  1. Change user to admin_local
 $ su admin_local
  1. Kill afni:
 $ kill -9 'cat /Uses/tabs/tabs/var/'
  1. If that does not help reboot tabs
  2. You can check the log on the scanner for hints:
 Type logviewer from the command prompt.

Image information in Trios: 76.5 cm from screen to eyeball height of screen is 13.7 in = 34. 8 cm

width of screen is 34.8 * (1024/768) = 46.4 cm atan(23.2/76.5) = 0.29 rad = 16.6 degrees ~30 degrees full width

More stuff on real-time:

  1. Register subject, open Patient Database
  2. Find subject, click on MP-RAGE first, "Send to TABS"
  3. Once AFNI is up, then run rt fMRI sequence (look on "Special card" )
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