ACRIN-6689 - MRS data acquisition and Raw Data Handling Instructions

1
ACRIN-6689 - MRS data acquisition and Raw Data
Handling Instructions For Siemens Data

2
In vivo MR Spectroscopy
Representative MRS of a normal human brain _at_3T
NAA
Cho
Cr
Lipids, macromolecules
Glu/ Gln
MI
3

• Proton MRS is able to detect the following
  metabolites
• N-Acetyl Aspartate (NAA) at 2 ppm Marker of
  neuronal density and viability
• Creatine (Cr) at 3 ppm Energy metabolism,
  generation of ATP
• Choline (Cho) at 3.2 ppm Pathological
  alterations in membrane turnover, increased in
  tumors
• Lipids (Lip) between 0.8 1.5 ppm Breakdown of
  tissue, elevated in brain tumors - lipids
  indicate necrosis

4

• Lactate (Lac) at 1.3 ppm, inverted at 144ms
  produced by an anaerobic metabolism, found in
  tumor containing zones of necrosis

5
The Sequence

• 3D chemical shift imaging using a Point-resolved
  spectroscopy (PRESS) excitation pulse sequence.
• 3D Volumetric Spectroscopy preferred 2D CSI
  Spectroscopy is acceptable

6
Optimal Voxel Placement

• The ROI will be placed at the center of the
  enhancing tumor covering the lesion and the
  normal brain as much as possible but excluding
  the subcutaneous fat and sinuses.

7
Suboptimal Voxel Placement

• Proximity to sinuses can result in signal
  broadening and susceptibility artifacts
• Proximity to scull can result in contaminating
  lipid signal

8
3D MRSI Parameters

• TE 144 ms, TR 1140 ms,
• FOV gt 160 mm2,
• Phase encoding arrays 12 x 12 x 8
• Numbers of Acquisitions 1
• Spatial zero-filling to 16 x 16 x 8 phase
  encoding arrays will result in an individual
  voxel size of 1 x 1 x 1 cm3.
• Approximate imaging time 6 min utilizing
  elliptical k-space sampling k-space sampling
• Manual shimming is recommended before the
  acquisition to obtain the best magnetic field
  homogeneity.

9
Shimming

• Shimming adjusting the magnetic field to make
  it more homogeneous
• 1.5T Signal line width or full width at half
  maximum (FWHM) lt15 Hz for 3D MRSI
• 3 T FWHM lt 25 Hz for 3D MRSI

• Better signal separation, thus better
  quantification of metabolites
• Better water suppression

• Suboptimal shimming

10
Shimming on Siemens
11
Manual Shimming on Siemens
Hit the Show tab Then Invalidate All Adjust
All Wait a couple of minutes until it says
Adjustments finished
12
Hit the Interactive Shim tab Then hit Measure
(1) Numbers will begin to scroll on the above
white box (2) You can alter the shim by changing
Z, then Y, then X. Do this slowly, only a couple
of increments at a time, then start with z again
Stop (3) and Apply (4)
2.
1.
3.
4.
13
Saturation Bands

• Click SAT and place up to 10 SAT bands around the
  voxel to suppress signals from lipid/fat

14
Saving the Data in .rda format
15

• The spectrum appears in one of the quadrants
• Note if another window appears asking you to
  select a protocol for the spectrum, just select
  any of the protocols listed and click OK.

16
BTW Please select Single Dataset Mode!
17
Go to the top of the screen Click on Patient
Dropdown menu will appear Save data
18

• Select first option, Selected results and 3
  reference images (shown above)
• This will save the spectrum and corresponding
  images in a DICOM format

19
Go to a difference slice and repeat the process
20
In order to use a different slice Right click on
the Image A scroll down window will appear
Select 3D CSI Selection
21
Under 3D CSI Selection Choose Plane number
22
Saving the Data in .rda format

• Click on Options export raw data (shown above).

23
Saving the Data in .rda format

• The previous command (Options-export raw data),
  will open this new window. By default the
  directory is C\Temp (leave default)
• .Save File name as ACRINcase_timepointXweeks
• Example case09_16weeks.rda
• Click Export

24
Sending P-Files to ACRIN

• Be sure the rda file is named Case_ Timepoint
• For example 4200_case15_baseline.rda or
  4200_case09_week16.rda
• Again, this MUST be the ACRIN CASE NUMBER
  assigned at registration.
• Login to ACRIN via ftp
• On your web browser, go to ftp//xray.acrin.org
• User Name (CONTACT ACRIN FOR USERNAME)
• Password (CONTACT ACRIN FOR PASSWORD)
• (If not prompted, click file, Login As)
• Find your folder
• It will be identified by your ACRIN Institution
  Name
• Contact Jim Gimpel at ACRIN at jgimpel_at_acr-arrs.or
  g for assistance
• Store your file in the folder
• (BE SURE YOU HAVE NAMED IT as Case_Timepoint)