BITC - Resources

Biomedical Imaging Technology Center

Resources and Facilities [Home] [Resources]
The Biomedical Imaging Technology Center (BITC) at Emory University is housed in approximately 3000 square feet of space. BITC is a core facility of the School of Medicine at Emory University. It was established to focus on the development and application of imaging technology, particularly magnetic resonance imaging.

BITC is equipped with a 3 Tesla Siemens Magnetom Trio^TM whole-body MR system, and a 9.4T/21-cm Bruker animal MR imaging/spectroscopy system dedicated to research. In addition, a research agreement was reached with Siemens Medical System such that we have full access to sequence programming software, technical details for data manipulation, and necessary technical support. This MRI system will be used for MR studies proposed in the project.

A state-of-art computing facility consisting of a Linux-based nineteen nodes computational cluster, disk RAIDs with a capacity of 21 TB, and an automated backup system, is established in the BITC. It is Sun Grid Engine powered for maximum data processing efficiency. This state-of-the-art hardware setup is augmented with a number of software packages including Matlab, FSL, AFNI, Hammer, SPM5/8, IDL, LCMODEL, and Stimulation.

In addition to the MRI system and computing facility, peripheral equipment, including computers and software for paradigm generation, setup for stimulus presentation, devices for recording behavioral data recording and monitoring physiological activities such as respiration and heart-beat, are also available in our center.

RF coils

CP_Head coil [Siemens]
8-channel head array coil [Siemens]
8-element Cardiac Array coil [Siemens]
CP Extremity Coil (Knee coil) [Siemens]
CP Wrist Coil [Siemens]

Managed Peripheral Equipments

Invivo Vital Sign Monitor (MRI compatible) -- ECG, SpO₂, EtCO₂, and HR (heart bit rate); also (upgraded to) provide external trigger signal and synchronized vital signal digital recording.
Home-made respiration bilt monitoring/recording setup.
Home-made visual stimulation setup -- support computer video display mode 640x480 up to 1280x1024. 800x600 is default.
Home-made LED goggle -- visual stimulation.
Avotec Silent Scan^TM Audio System -- PI-patient communication and acoustic stimulation.
Applied Science Laboratories eye-tracker -- pupil tracking.
Current Designs, Inc. optical button box -- non-audio patient response.
Home-made single large button -- simple response.
Home-made buzzer -- tactile stimulation.

Third Party Peripheral Equipments

Biopac MP100 -- GSR recorder.

BITC Cluster softwares available to users

Function	Command	Vendor	Note
For Office Usage
Web Browsing	firefox	Mozilla.org	Known best Web Browser
PDF Viewing	acroread	Adobe Acrobat Reader
Image Editing	gimp	GIMP	Open source image editor, compatible with most image format. Photoshop alternative.
Fast Image View and Convert	ImageMagick		Open source image editor, compatible with most MRI image format. See HERE for a brief user guide.
Word Processing	ooffice	OpenOffice.Org	Microsoft Office alternative, compatible with MSOffice files
Personal Event Calendar	evolution	GNOME Evolution Project
Text Editing (GUI)	gedit
Text Editing (text mode)	nano
Calculator	gcalctool
Ghost Script Viewer	kghostview
For MRI data processing
fMRI data processing	afni	AFNI
fMRI/DTI data processing	fsl	FMRIB Software Library
MRI image converter/viewer	startmricro	MRIcro
fMRI data processing for animal image	stimulate	Stimulate
Generic Scientific Calculation
	matlab	The Mathworks
System Utilities
to check your disk space	du -sh		We do not enforce quota, however, you should consider clean up if your disk usage get over 100GB for BITC staff/students or 20GB for users. BITC system administrator may delete your big files in case needed.
to check overall available space of your home directory	df -h .		If the available space goes below 100GB, BITC system administrator will start clean up procedure. You may be asked to remove files.
to find a file under your home directory	find ~ -name "your file name"
to check memory usage	free -m		If the used swap memory get over 1000M, please do not start new MRI analysis or Matlab. You may greatly slow down the whole server and your process may be killed for server performance. Always check this beforr running large process.
to look at most active procedures	top		You are recommended to check this while your are running big process. If the CPU usage and/or memory usage is already very high, you are recommended to hold launching large processes.
to change your password	passwd		A good password is more than 8 characters long, contain both numbers, lower case and upper case letters, and special charecters. We periodically hunt for weak password. Once found, your account will be locked. Hint: do not use single English word, your initial plus a yymmdd date, and all number passwords. They are very easy to be hacked.
Recommended Windows Softwares for connecting to the cluster
data transfer	WinSCP	WinSCP	Use the standalone application
text mode remote login	Putty	Putty	Need 3rd party x-server to use graphical interface.
GUI remote login	cygwin	cygwin	Remote X interface could be very slow. Alternative commercial x-server for windows: X-Win32, HummingBird Exceed. unix box and Macintosh has built x-server. Just use ssh