Negative GABA values

MRS Software Gannet
#1

I’m getting negative GABA values…
This was during a visual task in the visual cortex:

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Has anyone else seen something like this?

#2

I think this is likely an error with the water being positive

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In commonest errors Examples — Gannet
It shows a similar example
And seems to suggest I can change the MRS_struct to include:
ONOFFfirst = ‘offfirst’ or ‘onfirst’
or
Waterpositive = ‘positive’ or ‘negative’

But changing MRS_struct.p.ON_OFF_first to ‘offfirst’ or ‘onfirst’ doesn’t seem to change anything

and I can’t find any ‘waterpositive’ field

#3

Hi @weberam2,

In the latest version of Gannet, the phase of the data is determined automatically. The examples you linked to are for prior versions of Gannet.

In this case, the automatic phasing has failed. You will need to invert the spectra manually. The simplest way to do this is to add this line of code right after line 400 in GannetLoad.m:

MRS_struct.fids.data = -MRS_struct.fids.data;

Remember to comment this line out for all other datasets.

Mark

#4

This worked! Thank YOU!

#5

hi all,

I am getting a similar issue with negative GABA values.

I’m using Gannet 3.3.1, and so added in the code to invert the spectra manually, but now my Cr Frequency chart looks messed up. Did I do the right thing?

Original.pdf (526.5 KB)
SpectraFlipped.pdf (531.7 KB)

(It might be that this data is poor quality, and unusable, but I’m just trying to figure out the flips!)

thanks!

#6

Hi @mollysimmonite,

Where in the code did you add the flip?

Mark

#7

Hey @mmikkel

Thanks for a speedy response!

I threw it into GannetLoad.m right about line 400 - between 'Global zero-order phase correction" and “Line-broadening, zero-filling and FFT”.

Molly

#8

Hmm, are you able to share your data so I can debug? mam4041@med.cornell.edu

#9

of course! will send this afternoon - much appreciated!

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