SECTION
8:
MRI COMPUTER AND WORKSTATION RESOURCES
Facility
Manager: Larry Dougherty, Ph.D.
215-349-5274
doughel@uphs.upenn.edu
Equipment
Software
Scanner Software
Procedures
MR Image and
Raw Data Retrieval
Pulse Sequence
Approval
Equipment
The MRI section has three workstations available for
general use: "SiemensPC" which is a Dell
PC; "barnacle" - SUN Ultra; and "lxsg"
- a SGI Octane. The main research workstation is "SiemensPC".
User accounts are available to anyone in the section.
Users are expected to backup their own directories,
the manager only backs-up the system and general use
files. Contact Memo Isaac (isaac@rad.upenn.edu, 662-6671)
for account infornmtion.
Software
The principal use of SiemensPC is pulse sequence development
for the HUP5/HUP6 scanner platforms. The IDEA (Siemens)
sequence development environment is available from
the Start menu. An online programmer's manual is available
for more details. The ICE reconstruction tools and
the "Pulsetool" RF development software
are also available from within the same menu. Researchers
may run this development package on their own PCs
by obtaining a license "dongle " from Larry
Dougherty. To run this package on their own PCs, users
must also obtain a copy of Visual C++.
Siemens
source code is provided on an as needed basis by asking
Larry Doughetry or Memo Isaac..
For
sequence development on the GE LX platform, the EPIC
software package resides on "lxsg". Additionally,
IDL is available on all three workstations.
Scanner
Software Procedures
HUP5* and HUP6* are the designated research scanners.
The advanced user options are available on these machines
only. Users must be approved by the individual facility
manager in order to load pulse sequences. Try not
to overload the disk with old sequences. System software
should not be loaded or modified by anyone other than
Siemens service. Sequences to be used for human use
must be approved by CAMRIS prior to use on any human
subjects.
HUP
1,2,3,4 are in general not accessible for research.
Arrangement to use these systems made be made depending
on need and availability.
*
The designated research scanners may be subject to
change. Whichever scanners are being used for research,
the same user account and the responsibilities of
the user described here, will be in effect.
MR Image
and Raw Data Retrieval
Images are most easily retrieved from HUP5 or HUP6
by using the "Archive to Disk" option. This
will load the images onto a CD using the DICOM format.
There
are multiple ways to save and retrieve raw data ("measurement
data" in Siemens speak). For low volume studies
use the following method:
Start
(taskbar) -> Run... and type " ideacmdtool".
In cmd tool. Select 3 (Switches)
Select 4 (MeasData2Disk)
This saves a meas.out and MrPort.asc. to Q:\SimMeasData.
Data must be renamed immediately since the next sequence
loaded dumps out this data to the same file.
Please
make sure to set Data2Disk to "OFF" and
exit MATE before leaving
the scanner. Also, it's a good thing to delete the
simulation data after
it has been transferred.
The
data can be ftp transferred to another computer. Additionally,
SIEMENSPC is cross-mounted withh the scanner so that
certain folders are available on the SIEMENSOC desktop.
An
alternative method is to write a custom reconstruction
(ICE routine) that can simply save the data or even
transfer it and start a remote reconstruction.
Pulse Sequence
Approval
All
research pulse sequences that are to be used on human
subjects must be approved by the CAMRIS committee
prior to human use. Formal approval from the CAMRIS
committee or its designee is required before use of
a research sequence on any volunteer, including the
researchers themselves. Research pulse sequences include
those written at HUP or any other institution or corporation.
The only sequences that are exempted are those provided
by the manufacturer as product and are used within
the parameters and protocols for which they were developed.
Overriding the design of a product sequence using
"control variables" requires CAMRIS approval.
Modification of any aspect of an approved sequence
requires CAMRIS re-approval before human use is allowed.
Additionally, disabling of the RF power monitor is
prohibited.
We
anticipate that the approval process will only require
the documentation of steps that are already being
performed by researchers in the development of their
sequences, so this process should not represent a
burden. Our goal is to formalize and document these
procedures. The approval procedure requires the following
documents to be submitted to the CAMRIS committee:
1.
A brief description of the sequence, paying particular
attention to the RF pulse parameters and duty cycle.
Include in this description the method of the SAR
estimation. SAR may be calculated using the RF pulse
structure and code within the pulse sequence, or may
be calculated separately. Comparing the new sequence
to an existing approved sequence can be a helpful
approach.
2.
A copy of the actual pulse sequence source code on
diskette.
3.
A timing diagram of the pulse sequence. This diagram
should be generated by the sequence development tools
on the workstations. This will document the expected
sequence output.. If sub sequences are used (for example,
pre-saturation pulses), provide a timing diagram for
each sub-sequence. Please use sufficient resolution
so as to discern areas of interest (for example, gradient
rise times) and turn on axis labeling. Multiple pages
may be required to show sufficient detail.
4.
A phantom image using the new sequence.
5.
The imaging protocol for human use. This may include
a range of values to allow flexibility.
When
naming the sequences, use a numeric extension that
increments on each revision (for example, fgre0, fgre1,
… fgreN) so that modifications and their subsequent
approval can be documented. Each revision will require
CAMRIS approval. Many revisions may qualify for expedited
approval as described below.
Documents
will be submitted for approval at the CAMRIS meeting
following their submission. Sequence changes that
do not significantly alter the dB/dt or RF may be
reviewed by Larry Dougherty, Hee Kwon Song in an expedited
fashion and then presented at the next CAMRIS meeting.
.
2-24-04 LD/ak
