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Shaunak Mukherjee,

Centre for Advanced Imaging,

University of Queensland.

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2-D COMPUTATIONAL SPECTROSCOPY OF BRAIN METABOLITESA COMPUTER SCIENCE STUDENT’S HUMBLE SOJOURN INTO UNCHARTERED WATERS

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The (initial) objectivesUsing non-uniform sampling (NUS) to obtain high-resolution spectra from relatively sparse data records, from compounds such as gamma-aminobutyric acid (GABA)

Using the Maximum entropy (MaxEnt) reconstruction principle, (a non-FT method of spectrum analysis) to effectively analyze the high-resolution spectra thus obtained from the NUS data set

Changing the parameters governing them and observing the effect on the aforementioned spectra

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So how did we start? Well, the first step was to obtain the data sets of those spectra, more specifically, the “cosynus” and the “nusidx” files.

We then tweaked the two parameters :

A) the line-width of the spectra (“LW”)

B) the J-coupling constant between the various protons in the GABA molecule

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And how did we do that?

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The picture represents the compilation of the data file (containing the changed parameters) through the /proc2.com command in the ASAP workstation.

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The result of the compilation is obviously, a Maximum Entropy Reconstructed file (me_recon_ser.ft2).

BUT WHAT CAN WE POSSIBLY DO WITH THAT?

As we know, the .ft2 file will not really come of use to us in order to analyze the spectra on-screen.

WE CONVERT IT TO A .UCSF FILE.As Sparky itself puts it, -

“A UCSF NMR data file is a binary file with a 180 byte header, followed by 128 byte headers for each axis of the spectrum, followed by the spectrum data. All integer and float values in the file have big endian byte order independent of the native byte order for the machine that wrote the file”.

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So how do we do that? By adding the “pipe2ucsf” command.

pipe2ucsf me_recon_ser.ft2 lw<#>J<#>.ucsf

Where, ‘#’ denotes the value of the line-width and the J-coupling.

Now that it has finally been converted to the .UCSF, we go to Sparky, and run it, where we get the following spectra.

NOTE : Only the cross and diagonal peaks pertaining to the observed molecules have been displayed.

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The spectra obtained in the Sparky interface.

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Yes, yes. The pattern looks beautiful. What do we do with it, then?

We now use the various functions in Sparky, and integrate the area under the various peaks, and build a specific data set with the line-widths, the J-coupling, and the areas –incrementing the “lw” and “J” by 2 units each time, finally obtaining a grand total of 363 data entries.

Sample data-set : LW18.0

j0

1.869 2.976 lw 26.632 28.704 vol 2.481e+05 rms 16.2%

1.870 2.258 lw 22.200 25.311 vol 2.061e+05 rms 21.5%

1.869 1.869 lw 33.795 41.196 vol 5.540e+05 rms 25.9%

j2

1.870 2.976 lw 26.515 28.600 vol 2.470e+05 rms 14.7%

1.870 2.259 lw 22.637 25.191 vol 2.073e+05 rms 18.0%

1.869 1.869 lw 33.918 41.057 vol 5.566e+05 rms 21.9%

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And now.. We plot the graphs – between the “lw”, the “j-coupling” and the areas of the peaks.

0 5 1 0 1 5 2 0 2 50

100

200

300

400

500

600

700

800

lw v/s (area of) P1

0 5 1 0 1 5 2 0 2 50

50000

100000

150000

200000

250000

300000

350000

400000

450000

LW v/s (area of) p2

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On to the next phase. We now delve into the actual structure of the GABA and the Creatine molecules, and try to analyze them using certain other paramaters.

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Further analysis?We use TOPSPIN, another software by Bruker, to analyze the data further, specifically using the NMR simulation tool.

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The hamiltonian i.e. The spin system, configured with GABA, creatine, NAA, etc.

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The original pulse program -

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It needs modifying, doesn’t it?

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So what did we do there? Modified the pulses –

> added certain new waveforms – “Gauss1.1000”, “sinc1.1000”, “uqcai.rf”

>added some new delays

>modified the phases of the pulses

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Important parameters P4 : 42.8 Hz

P1, P2 : 831.7 Hz

SPNAM :

i) sinc1.1000

Ii) Gauss1.1000

Iii) uqcai.rf

DELAYS : d1 = 1s, d2 = d3 = d4 = d5 = D

4D + P1 + 2P2 + 2P4 = (23 + 4*26.5) ms = 129 ms. ( 1 / J ) -> echo time

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Question is, WHY? > Modifying the echo time ( to be 1/ J where the coupling constant is J ) , relaxation time, acquisition time, etc.

WHY?

>Let’s delve into the magnetic side of things.

>The next slide will make it clearer.

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Courtesy : Wikipedia

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The given Bloch module – (The pulse is originally applied as Mz)

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We tweak the power of the pulses given in increments of 2 Hz, and plot the differences in the integrated areas of the peaks obtained in the GABA and Creatine molecules. Enclosed, is the plot.

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SO WHAT DID WE LEARN? A whole lot.

Forayed into NMR, MRI and all other difficult abbreviations, and kind of enjoyed it.

FUTURE WORK?

If I have the pleasure of coming back here again, will try to continue the data processing and obtain even better spectra, and analyze them.

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Acknowledgments. Thank YOU, Dr. Tesiram. Wouldn’t have been possible without you.

Thank you to, well, so many people – Aish, Theo, Hari, Gagan, Rajiv, Sami, Venkat – basicallt everyone at CAI. This project would have drowned in the beach without you guys.

Thank you for making this the best summer ever. :’)

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THAT’S ALL, FOLKS. :D