Tips and Tricks

EPSI Data Acquisition

Positioning the head within the FOV

The FOV needs to cover the whole brain, including the scalp, in order for the image registration to work correctly. As shown in the figure, the VOI is co-aligned with and centrally positioned within the FOV. The top of the slab selection should include the top of the brain.

Saturation Slab

Angulation along the AC-PC line is commonly used. There has been some indication that an angulation of -15 deg may benefit shimming, but this will vary between systems.

Saturation Band

One regional saturation band is available (yellow band in the figure shown above) that should be located to suppress signal from the sinus and orbits. This saturation slab may be doubly-angulated to cover the orbits and the bottom of the brain in both dimensions.


Data Transfer

Measurements in Phantoms

For studies in phantoms it is recommended that the lipid inversion pulse be disabled. Because of the longer T1s in phantoms, the inversion pulse can significantly impact the metabolite spectrum. It should also be noted that the standard TR and Ernst angle excitation (71deg) will no longer be correct and longer TRs should be used.
An additional consideration when processing phantom studies is that the tissue segmentation will not work and the FAKESEGMASK utility should be used.

MIDAS Processing


Tissue segmentation is used in the SI processing to define the brain and lipid masks, and is also commonly used in the data analysis. The T1 MPRAGE sequence is always used for tissue segmentation, but as image quality and contrast can vary between sites the accuracy of the segmentation should always be checked when starting a new project. The first recommendation is to include the scanner option for "prescan normalize" to minimize the bias field in the MPRAGE image.
Common problems are incomplete brain extraction (done using BET) due to the effect of surgery or significantly altered image contrast in the presence of lesions. Options to be considered for segmentation problems are available in the IDLSEG program, and include changing the threshold used for BET and using SPM.


In situations where the MRI to SI registration has been found to be inaccurate it has been found that running the MSREG program twice can resolve the problem. This can be done from the GUI mode and checking the "Repeat if already done" option, or the process can be run twice in batch processing mode by using the "reprocess" command line option. See the help file for details.