Biomedical Imaging Technology Center
Resources and Facilities
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 PrismaTM whole-body MR system, and a 9.4T/20-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 computing and storage cluster consisting of a Linux-based 29 nodes computational
cluster, disk array with a capacity of 131 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, SPM5/8/12, 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.
- 64 channel Head-Neck array coil [Siemens]
- 24 channel Head-Neck array coil [Siemens]
- Spinal Matrix coil [Siemens]
- Flexible Body Matrix 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 visual stimulation setup -- support computer video display
mode 640x480 up to 1280x1024. 800x600 is default.
- Home-made LED goggle -- visual stimulation.
- Avotec Silent ScanTM
Audio System -- PI-patient communication and acoustic stimulation.
- Avotec RE-5721 Eye Tracker.
- 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 MP150.
Including: ECG100C-MRI (for ECG), RSP100C (for respiration), EDA100C-MRI (for skin conductivity), TSD160A (for animal respiration),
STM100C (for electrical stimulation), and DTU200/300 (for cardiac and respiration triggering).
BITC Cluster softwares available to users
|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|| |
|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.
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
||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
|Alternative GUI remote login||MobaXterm||MobaXterm
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