Gannet supports Siemens Hermes data

Gannet now provides support for Hermes data acquired using Siemens 3T scanner. The acceptable format is .dat. Please note that it is beneficial to acquire metabolite data and water data using the same sequence for better coil combination. Below is the GannetLoad window displaying Siemens HERMES data before and after post-processing steps in Gannet.

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HERMES of GABA and GSH at 7T

Extending the multi-metabolite editing technique at high field scanner, we have developed HERMES of GABA and GSH at ultra-high field scanner. For this, M.G. Saleh and colleagues implemented semi-LASER (sLASER) voxel localizer and Hadamard encoding scheme (Figure a) at 7T to simultaneously edit GABA (at 3 ppm) and GSH (at 2.95 ppm) in half the scan time MEGA-sLASER takes to edit these metabolites sequentially (Figure b). HERMES of GABA and GSH will be presented at 27th Joint Annual Meeting of the ESMRMB-ISMRM, Paris, France, 2018.

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Provisional EDITINGSCHOOL schedule

Day 0 (Dec 3)

     Check-in, Opening Receptiopn/ Meet-the-Faculty

Day 1 (Dec 4)

     The MR Spectrum – Richard Edden

     Evolution of Spin Systems – Richard Edden

          Lunch

     The editable metabolites – Ashley Harris

     J-difference editing explained– Georg Oeltzschner

     Quantification – Paul Mullins

     Simulations and Data handling with FID-A – Jamie Near

Day 2 (Dec 5)

     Practicalities of Acquisition  - Nick Puts

     Practicalities of Acquisition  II - TBC

          Lunch

     Editable Metabolites in Psychiatric Disease – Laura Rowland

     Advanced Editing Methods – Richard Edden

     (MRS-relevant neurochemistry of GABA - TBC)

     Data Processing with Gannet – Mark Mikkelsen 

Day 3 (Dec 6)

   Morning Career Breakouts: maximizing your postdoc; early-career challenges; TBC.

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HERMES on Siemens

We are in the late stages of implementing HERMES for GABA/GSH on Siemens.  We are actively seeking collaborators who would like to apply this sequence, so get in touch and we can start the C2P paperwork.

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Gannet now listed on NITRC!

Gannet was recently added to the software catalogue of the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).

Please follow this link to visit the page.

We will be adding to this page in the coming weeks. Stay tuned for further exciting developments....

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Running a GSH-edited MEGA-PRESS dataset through Gannet 3.0

We have improved the data processing and quantification routines for GSH-edited MEGA-PRESS data in Gannet 3.0. Here is a quick "getting started" tutorial on running a GSH-edited MEGA-PRESS dataset:

  1. Download Gannet 3.0, placing the master folder at the top of your MATLAB's search path.
  2. Open GannetPreInitialise.m.
  3. Set MRS_struct.p.target to 'GSH' (MRS_struct.p.target2 can be ignored).
  4. Set MRS_struct.p.ONOFForder to 'offfirst' or 'onfirst' depending on the order of the ON/OFF editing pulses in your MEGA-PRESS acquisition (typically this should be 'offfirst' for Philips data and 'onfirst' for GE/Siemens data).
  5. Set MRS_struct.p.water_removal to 1 (this is the default) to remove residual water in the difference spectrum.
  6. Set MRS_struct.p.AlignTo to 'SpecRegHERMES'. (We recently published a novel frequency-and-phase correction algorithm for multiplexed edited MRS data [1]; this method also works well with GSH-edited data and is recommended.)
  7. Set MRS_struct.p.GSH_model to 'SixGauss' (recommended for long-TE MEGA-PRESS data).
  8. Save your changes.
  9. Change your working directory to where your GSH dataset is saved.
  10. To run GannetLoad on:
    1. GE data, run: MRS = GannetLoad({'GSH_MEGA_1.7'});
    2. Philips SDAT data (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1_act.sdat'});
    3. Philips SDAT data (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1_act.sdat'}, {'GSH_MEGA_1_ref.sdat'});
    4. Philips .data files (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1.data'});
    5. Philips .data files (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1.data'}, {'GSH_MEGA_1_water.data'});
    6. Siemens .rda data (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1_ON.rda', 'GSH_MEGA_1_OFF.rda'});
    7. Siemens .rda data (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1_ON.rda', 'GSH_MEGA_1_OFF.rda'},{'GSH_MEGA_1_water.rda'});
    8. Siemens TWIX data (no water reference), run: MRS = GannetLoad({'GSH_MEGA_1_metab.dat'});
    9. Siemens TWIX data (with water reference), run: MRS = GannetLoad({'GSH_MEGA_1_metab.dat'}, {'GSH_MEGA_1_water.dat'});
  11. Then run GannetFit: MRS = GannetFit(MRS);

 

1. Mikkelsen M, Saleh MG, Near J, et al. Frequency and phase correction for multiplexed edited MRS of GABA and glutathione. Magn. Reson. Med. 2017;0:1–8. doi: 10.1002/mrm.27027.

Running a HERMES dataset through Gannet 3.0

One of the new features of Gannet 3.0 is the ability to process and quantify edited MRS data acquired by HERMES (1–3). Here is a quick "getting started" tutorial on running a GABA-/GSH-edited HERMES dataset:

  1. Download Gannet 3.0, placing the master folder at the top of your MATLAB's search path.
  2. Open GannetPreInitialise.m.
  3. Set MRS_struct.p.target to 'GABAGlx' and MRS_struct.p.target2 to 'GSH' (these are the defaults).
  4. Set MRS_struct.p.ONOFForder to 'offfirst' if running a Philips HERMES dataset, or 'onfirst' if running a GE HERMES dataset.
  5. Set MRS_struct.p.water_removal to 1 (this is the default).
  6. Set MRS_struct.p.AlignTo to 'SpecRegHERMES'.
  7. Set MRS_struct.p.HERMES to 1.
  8. Save your changes.
  9. Change your working directory to where your HERMES dataset is saved.
  10. To run GannetLoad on:
    1. GE data, run: MRS = GannetLoad({'HERMES_1.7'});
    2. Philips data (with a water reference), run MRS = GannetLoad({'HERMES_1_act.sdat'},{'HERMES_1_ref.sdat'});
  11. Then run GannetFit: MRS = GannetFit(MRS);

 

1. Chan KL, Puts NAJ, Schär M, Barker PB, Edden RAE. HERMES: Hadamard encoding and reconstruction of MEGA-edited spectroscopy. Magn. Reson. Med. 2016;76:11–19. doi: 10.1002/mrm.26233.

2. Saleh MG, Oeltzschner G, Chan KL, Puts NAJ, Mikkelsen M, Schär M, Harris AD, Edden RAE. Simultaneous edited MRS of GABA and glutathione. NeuroImage 2016;142:576–582. doi: 10.1016/j.neuroimage.2016.07.056.

3. Chan KL, Saleh MG, Oeltzschner G, Barker PB, Edden RAE. Simultaneous measurement of Aspartate, NAA, and NAAG using HERMES spectral editing at 3 Tesla. NeuroImage 2017;155:587–593. doi: 10.1016/j.neuroimage.2017.04.043.

Gannet 3.0 released

Introducing Gannet 3.0! This new version includes a number of new data processing features (incl. handling of HERMES data), a revamped output MATLAB structure, slight improvements in speed and efficiency and many other changes and bug fixes.

Gannet 3.0 is available for immediate download at the following link: https://github.com/richardedden/Gannet3.0/archive/master.zip

Release notes:

MAJOR CHANGES

+ Added new puffin logo
+ Changes to output structure to accommodate multi-metabolite and multi-voxel datasets
+ Removed unused/redundant lines of code throughout Gannet
+ Removed historical/unused .m files in Gannet folder
+ Optimized code where possible, e.g.:
    - Removing loops and vectorizing instead
    - Simplifying code, e.g., using one-line logical indexing for frequency ranges
    - Pre-allocating memory by setting up variables with zeros
    - Removed ‘convergence’ loop in metabolite signal fitting (should be enough to first run lsqcurvefit followed by nlinfit with high enough max iterations/low enough tolerances)
+ A number of updates to ‘PhilipsRead.m’, ‘GERead.m’ and ‘SiemensTwixRead.m’, e.g.:
    - Almost all acquisition parameters now parsed from the header
    - For P-files and TWIX data, coil combination/pre-phasing is performed by signal-weighting method using unsuppressed water data (when available)
    - Complete revamping of ’SiemensTwixRead.m’; automatic determination of MEGA-PRESS sequence type and scanner software version; removed this parameter from ‘GannetPreInitialise.m’
    - For Philips HERMES data, only the averages where editing pulses do not affect residual water are used for pre-phasing (currently geared towards GABA-/GSH-edited data)
+ Added support for DICOM MRS data files
+ Added functions to de-identify GE P-files, Philips SDAT/SPAR files and Siemens TWIX files
+ SPM segmentation now called by either ‘CallSPM8segmentation.m’ or ‘CallSPM12segmentation.m’ depending on which version of SPM is installed

GannetLoad:
+ Data are now zero-filled to obtain a nominal spectral resolution of 0.061 Hz/point by default (to handle acquisitions with number of data points/spectral width other than 2048/2000 Hz); removed this parameter from ‘GannetPreInitialise.m’
+ HSVD water filter is applied to both GABA-/GSH-edited HERMES data, and to both pre- and post-aligned DIFF spectra
+ For filtered HERMES data, baseline correction performed by demeaning (real) signal between 9 and 10 ppm

Spectral_Registration:
+ Now only first n points of FIDs used for registration, where n is the last point where SNR > 3
+ By default, median across data points of all transients is used as the reference ‘FID’
+ Frequency/phase offset estimates now saved for each processed dataset
+ Transients are now rejected if their respective standardized mean square error (from the nonlinear regression routine) exceeds +/-3 stds.
+ Added ‘Spectral_Registration_HERMES.m’ for frequency/phase correction of HERMES data

GannetFit:
+ GABA+Glx model fitting now performed by weighted nonlinear regression, where observation weights are supplied in nlinfit to down-weight any Cho subtraction artifact and (for HERMES data only) co-edited(?) signals downfield of 3.7 ppm Glx signal (thanks to Alex Craven of University of Bergen for this idea)
+ Added fitting of residual water in MEGA-PRESS data to calculate water suppression factor
+ Added fitting of NAA signal in OFF spectrum


MINOR CHANGES

+ Lots of minor bug fixes
+ Renamed module output folders to ‘Gannet*_output’ (e.g., ‘GannetLoad_output’)
+ Renamed module output PDFs to ‘<filename>_*.pdf’ (e.g., ‘S01_GABA_load.pdf*)
+ Text in output figures aligned more cleanly
+ Addressed MATLAB warnings
+ Made code easier to read/understand by indenting lines and adding a header comment here and there at beginning of processing steps
+ Optimization options for lsqcurvefit and nlinfit now set consistently throughout Gannet
+ Renamed some variables for the sake of consistency
+ Output figures now open in center of screen regardless of screen resolution (figure pixel dimensions are fixed, however)
+ When batch-processing, each output figure is cleared rather than closed all together
+ Some useful acquisition parameters (e.g., edit pulse frequencies) are parsed from the data file headers (and saved in vendor-specific fields) where available

GannetLoad:
+ Fixed ON/OFF indices for GABA-/GSH-edited HERMES data (for ‘offfirst’ only); assumes ‘C B A D’ as per NeuroImage paper
+ Color of pre-/post-alignment spectra now fixed to red/blue regardless of user’s MATLAB version
+ Post-alignment spectra always plotted second so that they are displayed in the foreground (this is helpful for HERMES data)
+ Renamed ‘SiemensRead_RE.m’ to ‘SiemensRead.m’
+ Renamed ‘Gannetplotprepostalign.m’ to ‘GannetPlotPrePostAlign.m’

GannetFit:
+ Water-scaled ON and OFF spectra now saved along with water-scaled DIFF spectrum
+ Models always plotted second so that they are displayed in the foreground
+ Renamed ‘GaussModel_area’, ‘GABAGlxModel_area’, etc. to ‘GaussModel’, GABAGlxModel’, etc.
+ Renamed ‘MRSGABAinstunits’ to ‘CalcInstUnits’
+ Improved quantification of lactate

Thoughts on the GABA MRS symposium from James Prisciandaro, Ph.D., Assistant Professor at MUSC

"The Bi-Annual International GABA MRS Symposium has quickly become my favorite meeting. Though a rapidly growing field, proton MRS remains largely underrepresented at professional conferences. The GABA MRS Symposium has allowed me to keep up on the latest methods, present my findings to leaders in the field, and form and maintain collaborative relationships that otherwise would not have been possible. I look forward to the next meeting!"