preprocessing steps on the MRS data

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harshal patel

Mar 28, 2017, 12:53:52 PM3/28/17
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Dear TARQUIN Team,

Thank you first of all for developing TARQUIN and maintaining this software.

I do single voxel proton MRS on 3T Siemens scanner using MEGA-PRESS sequence and I use tarquin to analyze the data. 
I use following steps to run the  TARQUIN anaylsis.

1) I convert on and off spectra to dpt files,
2) use python script to create the substracted edited spectra
3) use tarquin command with megapress int_basis set, 1h_naa as the ref signal and unsuppressed water signal as input_w.

May i know the exact preprocessing steps performed on the edited spectra??

I mean does tarquin make DC offset correction, zero filling, frequency and phase corrections and so on......

I tried and had a look on the pubmed and on internet as well however i could not find the right information about preprocessing steps done on MEGA-PRESS data in TARQUIN. Could you also help me with the order in which the preprocessing is done on the MEGA-PRESS data in TARQUIN?

If you could help me any further i would really appreciate your efforts.

Thank you so much 

Best, Harshal

Martin Wilson

Mar 29, 2017, 5:11:33 AM3/29/17
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Hi Harshal,

From the options you specify (in order) -
- HSVD water removal is applied by default.
- frequency correction is applied (based on the 1h_naa signal).
- phase correction is automatically performed during fitting.
- zero-filling x2 is applied by default for display (this is a
cosmetic issue, fitting is performed only on the acquired data points
in the time-domain).


On 28 March 2017 at 17:53, 'harshal patel' via TARQUIN users' group
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harshal patel

Mar 29, 2017, 8:57:12 AM3/29/17
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Dear Martin,
Dear all,

Thank you so much for your quick reply. 
I have some follow up questions.

Does TARQUIN checks for the movements of the participant between two acquisitions? 
Does it make any movement related correction? 
Woud it be possible to get any movement parameters like in SPM?
Is there a measure in TARQUIN to look for between measurement movements?

On the command line after preprocessing it shows following information. Could you please explain what it means? 
FWHM right ppm ??
FWHM left ppm ??
Final Phi0 ??
Final Phi1 ??
Metabolite FWHM(ppm) = which metabolites?? could we also get it in Hertz?
BSL ??

Thank you so much for your precious time and efforts

Best, Harshal

Martin Wilson

Mar 30, 2017, 8:18:30 AM3/30/17
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It's not possible to know about movement just from MEGA-PRESS data.
You can examine changes in water frequencies over time that could be
explained by motion - but it's not like fMRI where you can get
translations, rotations etc.

FWHM right ppm - FWHM left ppm = Metabolite FWHM

Phi0 and Phi1 are phase correction parameters determined during fitting.

Metabolite FWHM is from the most intense singlet (tNAA, tCr, tCho) metabolite.

BSL - for my interest, but not useful in the general case.

Multiply PPM by 128 (or your exact field strength in MHz) to convert to Hz.


On 29 March 2017 at 13:57, 'harshal patel' via TARQUIN users' group
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