There are two extremely common ways the analysis can fall over. And by 'extremely common', I just mean that I write more emails than I want to explaining the fixes. So here they are for posterity.
Both problems can be nicely summarized as "My spectra are negative".
If your GannetLoad output spectra look like this, the experiment is working fine, and one of two things have happened with the processing: either the data are phased negatively, or the ON and OFF spectra have been incorrectly identified.
Solution 1: spectra are phased negatively.
If the bottom-left panel from GannetLoad looks like this:
i.e. a cold (blue) stripe on a hot (red/yellow) background, then the spectra are phased negatively. This happens when the residual water signal is negative with respect to the rest of the spectrum (common using Philips-MOIST). The simple solution is to change the MRS_struct.p.WaterPositive parameter in GannetPreInitialise.m.
If you successfully do that and rerun the data, then they should look more like this:
i.e. a hot (red/yellow) stripe on a cold (blue) background. Your GABA difference spectra should now be positive.
Solution 2: ON and OFF are incorrectly identified.
If the creatine stripe is correct (red on blue; spectra phased positively) and the difference spectra are still negative, then the issue is the ordering of ON and OFF spectra. The simple solution is to change the MRS_struct.p.onofforder parameter in GannetPreInitialise.m. It is either 'onfirst' or 'offfirst' depending on the acquisition order.
So here's the summary:
"Gannet makes my GABA difference spectra negative".
"Are your creatine signals phased positively?".
If yes, change MRS_struct.p.onofforder; if no, change MRS_struct.p.WaterPositive.
There is a third scenario, which is probably not that bad, but is worth fixing anyway - that is, when both these parameters are set wrong. In that case, the GABA spectrum will be positive, but the Creatine stripes will appear negative. So flip 'onfirst'/'offfirst' and the WaterPositive setting.
Both problems can be nicely summarized as "My spectra are negative".
If your GannetLoad output spectra look like this, the experiment is working fine, and one of two things have happened with the processing: either the data are phased negatively, or the ON and OFF spectra have been incorrectly identified.
Solution 1: spectra are phased negatively.
If the bottom-left panel from GannetLoad looks like this:
i.e. a cold (blue) stripe on a hot (red/yellow) background, then the spectra are phased negatively. This happens when the residual water signal is negative with respect to the rest of the spectrum (common using Philips-MOIST). The simple solution is to change the MRS_struct.p.WaterPositive parameter in GannetPreInitialise.m.
If you successfully do that and rerun the data, then they should look more like this:
Solution 2: ON and OFF are incorrectly identified.
If the creatine stripe is correct (red on blue; spectra phased positively) and the difference spectra are still negative, then the issue is the ordering of ON and OFF spectra. The simple solution is to change the MRS_struct.p.onofforder parameter in GannetPreInitialise.m. It is either 'onfirst' or 'offfirst' depending on the acquisition order.
So here's the summary:
"Gannet makes my GABA difference spectra negative".
"Are your creatine signals phased positively?".
If yes, change MRS_struct.p.onofforder; if no, change MRS_struct.p.WaterPositive.
There is a third scenario, which is probably not that bad, but is worth fixing anyway - that is, when both these parameters are set wrong. In that case, the GABA spectrum will be positive, but the Creatine stripes will appear negative. So flip 'onfirst'/'offfirst' and the WaterPositive setting.
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