Pre-release

@DerOrfa DerOrfa released this Dec 21, 2018 · 33 commits to master since this release

Fixed

Many small bugs - refer to commits for details...

Added

  • DICOM import for Philips data:
    Properly accounts for the rescaling factor for quantitative analysis
    (see Chenevert et al. 2014).

  • Tracking Matlab version number in the JSON metadata.

Changed

  • MT saturation map file name from *_MT to *_MTsat.
Assets 2
Pre-release

@DerOrfa DerOrfa released this Nov 20, 2018 · 90 commits to master since this release

Fixed

Many small bugs - refer to commits for details...

Added

  • Rescaling factor to pre-processed B1:
    To deal with B1 maps that are not in p.u. of the nominal flip angle.
    Percent units expected by the hMRI-toolbox, but...
    The current BIDS proposal is to have B1 maps scaled so that a value of 1 corresponds to the nominal flip angle.
    To be continued...

  • Logging processing messages:
    In order to review and keep track of info, warnings and other messages coming up during data processing, all messages are logged using the hmri_log.m script.
    Various options available (pop-up messages, messages logged to the Matlab Command Window, messages saved into a log file).
    Improved tracking and readability of the messages, with more explicit descriptions and improved uniformity of the used format.

Changed

  • Imperfect spoiling correction disabled by default:
    To avoid confusion and resulting mistake (applying correction coefficients to the wrong sequence).
    With the publication of "standard MPM protocols", it is likely to have new protocols implemented with sequences other than the customised sequences for which the correction coefficients have been calculated.
    Therefore the TR and FA criteria are not sufficient any longer to identify the right set of correction coeficients to be used unambiguously.
Assets 3
Pre-release

@DerOrfa DerOrfa released this Nov 23, 2018 · 125 commits to master since this release

Fixed

Many small bugs - refer to commits for details...

Added

  • Single echo VFA approach:
    Implemented with a default minimum number of echoes for R2* calculation of 4.
    The number of echoes used is logged and a general warning informs the user about data interpretation when R2* map derived from only a few echoes.

  • Metadata & processing parameters:
    Bunch of modifications to improve the readability and completeness of the metadata, for each output image as well as for the processing parameters.

  • UNICORT-generated R1 and B1 to calculate PD and MT maps:
    This option has not been thoroughly tested.
    Made available under "ADVANCED USERS ONLY": the option to use the R1-UNICORT-derived B1 map for B1 transmit bias correction in PD and MT maps can only be enabled by an advanced user implementing customized defaults.

  • Example files: For defaults customization and toolbox configuration examples.

  • New option to disable the coregistration steps:
    Coregistration shouldn't be disabled but it can be convenient in specific cases (simulated data, phantom data).
    Option made available under "ADVANCED USERS ONLY", i.e. can only be modified by an advanced user implementing customized defaults.
    When enabled (defaults), all input images to hmri_create_MTProt.m (transmit and receive fields, T1w and MTw images) are coregistered to the PDw average (or TE=0 fit) image (see hmri_create_MTProt.m).

Changed

  • Options for RF sensitivity bias field correction:
    The available options are now None, Unified Segmentation(default), Single and Per contrast.
    Beware that the previously implemented Noneoption corresponds to the current Unified Segmentation!!!
    Batch files saved with the previous version are not fully compatible with the current version and must be adapted.
Assets 3
Pre-release

@DerOrfa DerOrfa released this Nov 23, 2018 · 190 commits to master since this release

First public beta-version of the hMRI-toolbox.

Modular structure including the following modules:

  • Configure toolbox
  • DICOM Import
  • Auto-Reorient
  • Create hMRI maps
  • Process hMRI maps
Assets 2

@DerOrfa DerOrfa released this Nov 23, 2018 · 573 commits to master since this release

First stable version of the VBQ toolbox,
considered as mainstream among the various sites taking part in the project
and starting point for the hMRI-toolbox development.

Assets 2