MEGA-PRESS analysis in Tarquin:

[Jamie Near, Dr.]

Dear Tarquin Community, 

One of my students is trying to analyze some 3T GABA-edited MEGA-PRESS data in Tarquin but is having some issues.  He ran the following command:

tarquin --input MegaPressTest.7_diff_lcm --input_w MegaPressTest.7_w_lcm --fs 5000 --ft 127e6 --format lcm --pul_seq mega_press --output_txt ./MPTest.txt --output_pdf ./MPTest.pdf --ext_pdf true --stack_pdf true --water_eddy true

However, in the resulting output, Tarquin appears to have ignored the “-pul_seq mega_press” argument, and seems to be fitting the spectrum as a conventional unedited experiment (See the attached output:  note the upright NAA peak and the large number of metabolite components in the output).  

The dataset that we gave as input “MegaPressTest.7_diff_lcm” was a difference spectrum, pre-processed and saved in the lcmodel raw format.  

I acknowledge that this dataset isn’t great, but I also think that Tarquin may not be behaving as expected.  Can anyone help spot what we’ve done wrong?

Thanks very much for your help!

Jamie

[Helge Zöllner]

Dear Jamie,

I guess you simply need to add the basis set which should be used in the analysis with --int_basis megapress_gaba. Addtionally, I would add --start_pnt 10, as it is recommended  for MEGA-PRESS in the documentation.

I hope this solves the issue.

Best,

Helge

[Jamie Near, Dr.]

Thanks Helge, 

We will give this a try.

Best wishes,

Jamie

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[Surya Gnyawali]

Hi Helge Zollner,

Do mind helping in changing the y-axis on the intensity vs chemical shift?

the screen shot is attached for your reference.

Thanks

Regrads,

Surya