Tarquin for 13C MR Spectroscopy

[Saurabh Shaw]

Hi Everyone,

First of all I would like to thank the developers for creating this spectacular software.

I have been working with 13C Spectroscopy and have tried using this software for fitting the spectrum with the basis sets and possibly quantifying metabolites.

I have simulated the metabolites used in the basis set using Vespa and have used LCModel to create the .basis file which I feed to Tarquin.

Some of the challenges with 13C is that there is no water peak. Also, we do not have a metabolite for zero referencing of the signal.

I have been unable to acquire very reasonable fits yet. I wanted to ask if anyone has any suggestions for me.

The details of the data files and the parameters I have used are given below:
Input file type: GE P file
Echo time: 0 (As the sequence was a Pulse Acquire)
Data points: 4096
Sampling Frequency: 10000
Transmitter Frequency: 32131330 Hz (Center frequency used for 13C)
Preprocessing parameters:

1. Water Cutoff - 0 Hz
2. Convolution width - 0
3. Reference offset - 0

Fitting parameters:

1. Start point - 1
2. End point - 4096
3. Lambda - 0.2
4. Initial mu - 0.001
5. Maximum iterations - 75
6. Initial beta - 0
7. Water Concentration - 35880
8. Water attenuation - 0.7
9. Max metabolite shift (ppm) - 0.03
10. Max broad shift (ppm) - 0.1

Post processing:

1. Zero filling factor - 2
2. Right PPM limit - 50
3. Left PPM limit - 200
4. Baseline smoothing points - 25
5. Line-broadening (Hz) - 10
   

External basis: The .basis file from LCModel.

I manually phase the spectrum before running the fit. I am attaching the processed signal and the fit.

Thanks in advance.

Saurabh Shaw

[Martin Wilson]

Hi Saurabh,

The usual problem with fitting non-1H MRS is calibrating the ppm axis.
Is there a known signal at a known frequency in all your data? I
suggest you manually calibrate the ppm axis for now unless you have
hundreds of spectra. Your parameters fitting look ok, I would use a
start point of 5 or more as the first data points are usually a bit
distorted.

Martin

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[Pom Sailasuta]

Hi martin,

I am running TARQUIN version 4.2.7 for linux, I am missing 'post processing' button in advanced fit. Do I need to get latest version?

thanks

Pom

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Pom

[Pom Sailasuta]

Never mind, I downloaded version 4.3.2 and I got the missing option.

Pom

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Pom