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Eddie Auerbach edited this page May 17, 2024 · 17 revisions

Welcome to the CMRR MB-EPI C2P sequence wiki!

The intent of this section is to provide additional documentation and supporting tools for "advanced" users.

Troubleshooting installation issues

  • Please carefully follow the installation instructions included with the sequence archive, and only attempt to install using the provided installer program.
  • Normally it is possible to upgrade or downgrade between different versions by simply running the installer program. If you encounter any strange issues, however, a cleanup tool is available to uninstall any previously installed versions. After running the cleanup tool proceed to running the installer for your desired version.
    Note the current version of the cleanup tool is only intended for use on VD/VE systems. https://www.cmrr.umn.edu/multiband/CLEAN_UNINSTALL_CMRR_MB_EPI.exe

Physiology log file format

  • Sample code for reading the new physiology log files [MATLAB, Python]
  • Support for reading the physiology data is also integrated in the BIDScoin toolbox

Extra shadowy shadow header parameters

Diffusion

In the "Phoenix" shadow header (text protocol), the following diffusion parameters are recorded (these are otherwise shown in a tooltip when editing a protocol):

  • sSpecPara.dSpecLipidSupprBandwidth: small delta (for monopolar scheme only)
  • sSpecPara.dSpecLipidSupprDeltaPos: big DELTA (for monopolar scheme only)
  • sSpecPara.dSpecWaterSupprBandwidth: estimated b-value of spoiler gradients (played for "b=0" scans)
  • sSpecPara.dSpecWaterSupprDeltaPos : (since R017pre9) maximum diffusion gradient amplitude allowed by the system
  • sSpecPara.dNOEFlipAngle: (since R017pre9) maximum diffusion gradient amplitude used in this protocol

MB RF phase scrambling

  • sIR.adFree[]: the inter-band phase offsets used if MB RF phase scrambling is enabled

Advanced sequence options

  • Some advanced sequence options can be unlocked by creating and editing a file named MBAdvancedSettings.ini in the customer sequence directory. This file uses the basic Windows ini-file syntax.

    Use these options at your own risk!

    • User-specified slice-GRAPPA kernel size

          [MultiBand]
    ManualGRAPPAKernelSize = 1

      Note: By default, the slice-GRAPPA kernel size is determined automatically. Enabling this ini-file option will unlock an option in the protocol UI for specifying the slice-GRAPPA kernel size on a per-protocol basis. Please refer to the UI tooltip for further details.

    • User-specified FoV shift factor (blipped-CAIPI, CAIPIRINHA)

        [MultiBand]
  ManualBlipFactorSL = 1

      Note: By default, the FoV shift factor is determined automatically. Enabling this ini-file option will unlock an option in the protocol UI for specifying the FoV shift factor on a per-protocol basis. Please refer to the UI tooltip for further details.

    • Slice multiplier factor (workaround for 128-slice limit of UI)

        [MultiBand]
  SliceMultiplier = 1

      Note: This option will automatically increase the number of acquired slices by the specified factor, otherwise keeping the slice FoV, TR, etc. constant. For example, to acquire 180 1mm slices, prescribe 90 2mm slices and set this parameter to 2. If the Mosaic matrix size limit is exceeded (4096x4096 on UHF; 2048x2048 otherwise), reconstruction will crash. This option is only unofficially supported for VB17A/UHF.

    • Allow "forbidden" options (R017 and newer)

        [MultiBand]
  AllowForbiddenOptions = 1

      Note: This option will open up options in the UI for features that are considered unstable. Be very careful when using this option: the "forbidden" options are disabled by default because they are strongly suspected of causing system instability—including but not limited to producing incorrect data, crashing the scanner, etc.

    • Additional "sparse TR" schemes

        [MultiBand]
  SparseTRSchemes = 1

      Note: When the "Sparse TR acq." option is in use, this option will allow for customizing the "sparse TR" or "silent" acquisition mode. The default option (0) is not entirely silent, but it best preserves the steady state (the slice select, slice refocus, and fat saturation spoiler gradients are still present and will make some noise). Option (2) disables all but the slice select gradient—this could result in image artifacts for some protocols. Option (1) is not recommended—it will disable everything during the "silent" period and not preserve the steady state.

    • Free(er) selection of RF pulse shapes

        [MultiBand]
  FreeRFPulseShape = 1

      Note: This option will open up additional options for the RF excitation and (if present) refocusing pulses, including user-defined sinc, HSN, and GOIA pulses. Please take great care with this option, as it is easy to define parameters here that will never be able to produce usable images.

    • Acquire noise reference scans (no RF excitation)

        [MultiBand]
  EPINoiseScan = 1

      Note: This will unlock the "EPI noise scans" option, which can be used to acquire a number of "noise reference" scans at the end of the series with no RF excitation. This parameter is not updated automatically when changing the number of measurements, so beware it can inadvertently be set in a way that only noise is acquired for an entire series.

    • Ignore clipped RF pulse warning

        [SeqDebug]
  IgnoreRFClipping = 1

      Note: This option will globally disable the "clipped RF pulse" warning popup. It is strongly recommended to not disable this popup, since multi-band pulses can easily exceed the available transmitter voltage, and in this case the system will silently run the acquisition at maximum voltage, which may yield a much lower flip angle than expected. Only use this option for testing, e.g. on UHF pTX systems.

    • Enable GPA balance model

        [SeqDebug]
  DisableGPABalance = 0

      Note: By default the GPA balance model checks are disabled. Setting this option to 0 will allow GPA balance model checks in the diffusion and spin echo modules on systems where the GPA balance model is supported. This will proactively reduce maximum gradient amplitude and increase TE/TR based on the specific protocol in an attempt to avoid GPA errors (possibly very conservatively).

  • Additional variant-specific advanced sequence options can be unlocked by creating and editing files named cmrr_mbep2d_bold.ini, cmrr_mbep2d_diff.ini, and cmrr_mbep2d_se.ini in the customer sequence directory. Settings added to these files will only apply to the named sequence variant. These files use the basic Windows ini-file syntax.

    Use these options at your own risk!

    • User-specified minimum base resolution (allowed values: 32-64)

          [Limits]
    MinBaseResolution = 32

      Note: By default (since R016), the minimum base resolution is 64. Any value lower than this seems to cause instabilities in the user interface such as not being able to select FOV phase % values of 100% for certain protocols. A value for this parameter outside of the range [32,64] will not be accepted.

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