Gannet Quick Start Guide: Again

0.   Get Matlab with Optimisation and Statistics Toolboxes

1.       Get the code from github and add these files to your matlab path

Assuming familiarity with Matlab, make sure all the files downloaded from github are in your matlab path; (i.e.use “add with subfolders”). If you are not familiar with matlab, someone else in your group probably is.

 The Link top left for Gannet 2.0 BETA takes you to github.

2.       What do I type?

Gannet is currently run from two commands – GannetLoad and GannetFit.  This section will cover the load and processing of a single data file. Replace the filename with the actual name of your file.

2.1.    GE data

P files contain a water reference internally, so:

MRS_struct  = GannetLoad({‘GE_data1.7’});

MRS_struct  = GannetFit(MRS_struct);

2.2.    Philips .sdat files

If no water reference data have been collected:

MRS_struct  = GannetLoad({‘Philips1.sdat’});

MRS_struct  = GannetFit(MRS_struct);

If water reference data have been collected:

MRS_struct  = GannetLoad({‘Philips1.sdat’},{‘Philips1_water.sdat’});

MRS_struct  = GannetFit(MRS_struct);

2.3.    Philips .data files

If no water reference data have been collected:

MRS_struct  = GannetLoad({‘Philips1.data’});

MRS_struct  = GannetFit(MRS_struct);

If SEPARATE water reference data have been collected:

MRS_struct  = GannetLoad({‘Philips1.data’},{‘Philips1_water.data’});

MRS_struct  = GannetFit(MRS_struct);

For newer patch versions, the water data is in the same .data file, so use the first option.
MRS_struct  = GannetLoad({‘Philips1.data’});
MRS_struct  = GannetFit(MRS_struct);

2.4.    Siemens .rda files (saved as OFF and ON rda files separately)

MRS_struct  = GannetLoad({'Siemens1_OFF.rda' 'Siemens1_ON.rda'});

MRS_struct  = GannetFit(MRS_struct);
If water reference data have been collected:
MRS_struct  = GannetLoad({ 'Siemens1_OFF.rda' 'Siemens1_ON.rda' },{'Siemens_water.rda'});
MRS_struct  = GannetFit(MRS_struct);

       2.5.   Siemens .dat files (assumes Jamie Near's implementation)
             MRS_struct = GannetLoad({'Siemens1.dat'});
             MRS_struct = GannetFit(MRS_struct);
             If water reference data have been collected:
             MRS_struct = GannetLoad({ 'Siemens1.dat'},{'Siemens1_water.dat'});

             MRS_struct = GannetFit(MRS_struct);


3.       Data Formats

GE, Philips and Siemens data formats are supported. Vendor is chosen according to file endings, so make sure your data files end .7 .rda .sdat or .data.

4.       Assumptions

The formatting of data within the data files is assumed to be the  same as for ‘our’ implementations on Philips and GE, whereas we handle Siemens outputted data that have already been processed into a single data file.  If you are using this software to process your own implementation of GABA-edited MRS, please contact us.

5.       Batch Processing

If you want to batch process files, simply add more that one filename string into the cell arrays, e.g.:

MRS_struct=GannetLoad({'gaba1.dat' 'gaba2.dat'},{'water1.dat' 'water2.dat');

GABAMRS discussion list on jiscmail

As mentioned below, one of the outcomes of the Cardiff meeting was the GABAMRS jiscmail group. This has the advantage of thread being searchable and archived by a UK-based university service. It is accessible to all.
To subscribe to the list:

• Send an email to listserv@jiscmail.ac.uk 

               Subject: BLANK Message: SUBSCRIBE GABAMRS Firstname Lastname

Hopefully, this will become a discussion forum for any issues of data acquisition, processing and interpretation, and participation will be as open as it was during the symposium.

Cardiff symposium talks and Jiscmail group

Two main requests that came out of the symposium were for access to talks and an online discussion forum.

  

We are implementing access to talks bit-by-bit as speakers opt in.  Take a look at the program at :  

https://sites.google.com/site/gabamrssymposium/meeting-schedule

in which titles will either link to downloadable talk or the submitted abstract if speakers have allowed it.  Some speakers are delaying providing talks, but will do so at a later date, so do keep checking (or perhaps even contact speakers directly if you have a special interest).

Following Gareth Barker's excellent suggestion, we have started the GABAMRS jiscmail group - this has the advantage of thread being searchable and archived by a UK-based university service.  It is accessible to all.  To subscribe to the list: 

Send an email to listserv@jiscmail.ac.uk Subject: BLANK Message: SUBSCRIBE GABAMRS Firstname Lastname

Hopefully, this will become a discussion forum for any issues of data acquisition, processing and interpretation, and participation will be as open as it was during the symposium.

Frequency correction revisited

In Gannet, frequency and phase correction of individual dynamics is performed by fitting the Cr signal in the frequency domain to estimate the frequency and phase shift (as per Waddell et al. MRI 2007).  This approach has at least two limitations.  Firstly, there is some similarity (over a small frequency range) between a small frequency shift and a small phase shift, leading to ambiguity in the fitting parameters.  Secondly, the approach is SNR-restrictive because it focuses in on one peak (of many) to figure out the frequency and phase.  For this reason, the correction will fall over below a certain voxel size (separate from the question of whether the final GABA signal is of good SNR through averaging).

Therefore we are in the process of implementing a new time-domain algorithm discussed by Jamie Near at ISMRM 2013, which estimates frequency and phase shifts by using all of the available signal.  This approach seems to result in substantially improved correction, as typified by the example below.

Comparison of GannetLoad output using the old frequency correction (left) and the new Spectral Registration algorithm (right).  The post-correction spectrum has substanitally smaller subtraction artefacts using Spectral Registration, and the frequency-correction output below shows much improved consistency between spectra post-alignment.

Algorithm courtesy of Jamie Near; Figure courtesy of Ashley Harris.

Gannet: the paper

As papers go, it was a struggle, but I am delighted to say that the official peer-reviewed reference for Gannet is now in press at Journal of Magnetic Resonance Imaging.  I will update this as things progress, but with teh current astronomical lag at JMRI that won't be soon.  For now, if you use Gannet, please reference:

Gannet: a batch-processing tool for the quantitative analysis of GABA-edited MRS spectra
RAE Edden, NAJ Puts, AD Harris, PB Barker and CJ Evans, J Magn Reson Imag, DOI: 10.1002/jmri.24478.

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UPDATE: The paper is now available in Early View at: http://onlinelibrary.wiley.com/doi/10.1002/jmri.24478/pdf
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And as our reviewer very graciously suggested:

Plan it, Scan it, Gannet.

2nd Cardiff International Symposium on GABA MRS

I would like to thank the speakers, organising committee and all attendees for making the symposium such a successful event.  The quality and breadth of the presentations was particularly impressive.  Several people have remarked upon the positive and collaborative atmosphere and the excellent interchange between "technical and "applications" people - thank you all.

Next steps that I have taken away:

• re-contacting presenters to ask about making presentations available.
• setting up a jiscmail-type list for exchange of ideas.
• doing it all again in a couple of years.

Once again, the scedule can be found here.

Cardiff GABA Symposium: Early Registration Deadline July 31st

This exciting meeting will feature international leaders in the field, presenting recent work on clinical and basic neuroscience applications, as well as technical developments.

Click here to register.

2nd Cardiff International Symposium on GABA MRS

When: 12-13 September 2013
Where: Cardiff University, Wales, UK.
Early Registration (before July 23rd): 65 GBP
Late Registration (before July 23rd): 100 GBP

We are happy to announce that registration is open; more information can be found HERE.

Gannet at ISMRM 2013

Finally, there is an abstract number to cite for Gannet: Proc. ISMRM 2013, 2041.  I am really hoping putting the poster together will energize me to write the paper.

The current draft version of the poster is here.  If you want to drop by, it is Thursday 10:30.

Gannet Output Structure

If you have ever puzzled over the multitudinous attributes stored in the GAnnet MRS_struct output structure, you might like this summary.

2nd Cardiff International Symposium on GABA MRS

After an interesting meeting in 2011, we are going again on September 12th-13th 2013 in Cardiff. If you are interested in attending, please email gabasymposium at gmail.com for more information. Click the poster below for a pdf-version.

Field Drift and fMRI

Some scanners suffer from rather large field drifts after fMRI acquisitions, due to heating of passive shims and other metal in the scanner.  We are working on the extent to which this impacts measurements. Dr Benjamin Glaubitz in Bochum acquired this data showing the dramatic field drift caused by a single 10-minute fMRI run. Gannet seems to do a reasonable job of correcting the drift (although whether it removes all the effects of the drift is not yet clear).

 Clearly there are some studies which require fMRI to be performed before GABA-MRS< but if you can avoid it, we'd suggest leaving fMRI (or DTI) until after the GABA scans.

A GABA paper review of 2012

Mainly to stop the promise of Gannet 2.0 from haunting me in the most recent post, I thought I'd do a quick look-back over 2012.  Some of this is shameless plugging, some is poorly focused musings...  either way, here is a quick review with links to some of our (and other people's) GABA MRS papers from 2012).

December 2012
For me, the highlight was the acceptance of our "Current Pracice in GABA MRS" review paper that came out of the 2011 Cardiff Symposium.  Paul Mullins did a great job of keeping it moving and it should be out in the new year in a special edition on GABA MRS.

November 2012

Dikoma Shungu's groups published a few GABA papers this year, this paper in OCD and also two AGP papers (!) earlier in the year in Schizophrenia and Depression.

September 2012
Charlie Stagg in Oxford has done some great work manipulating the GABA system with TMS and tDCS, and here she asks the million-dollar question "What are we measuring with GABA MRS?". A very interesting question and paper.

August 2012
Linking in great with the "What are we measuring?" question are a few genetic studies that relate brain, or in this case CSF, GABA to genetic variants.

July 2012
It was great to see a couple of long-term collaborations come to fruit in July, with James Stone publishing his Ketamine challenge study in Molecular Psychiatry, and my ADHD collaboration with Stewart Mostofsky in AGP.

June 2012
The role of GABA in sleep is an interesting area and a few groups have started to look at Insomnia.

May 2012
Speaking of collaborations baring fruit, Brad Foerster and the UMichigan group have published a pilot in ALS, with a follow-up of a larger cohort in press at JAMA Neurology.

Feb 2012
Graeme Mason's group showed that ethanol decreases brain GABA, maybe a counter-intuitive result, but one that fits with a 'more GABA, better performance' trend in individual difference studies.

Jan 2012
While doing reading for a grant submission in 2010, I let myself get waylaid by writing a review of the same material.  This kicked off a productive (in papers terms) 2012 for us, and a second paper for my postdoc Nick Puts.  The first paper also came out that applied GABA MRS to Parkinson's Disease - an area where the technique is very relevant, if only we can get things to work well subcortically.

If your paper isn't up here, I probably missed it - no slight intended!