Metabolite Quantification using Siemens csi_30 and 135 without water unsupressed file

[Sai Manohar]

Dear Tarquin Community !

Greetings.

I am Sai Manohar, Phd student working on Huntington's disease from India. I am new to MR spectroscopy and also Tarquin. I require your valuable suggestions on multivoxel MR spectroscopy analysis

Objective:

1. To quantify NAA, Cho, Cr, Lactate, Lipids, m-Ins, Glu, Glc, Ala, Asp levels in the caudate, putamen and thalamus of  patients and control subjects and do relative statistics. 
2. To make a heat map of metabolite distribution across different regions of the brain.
   

Drawbacks:

1. Acquired using 1.5 T machine
   
2. I don't have the water unsuppressed file

Following are the parameters of the data:

Sequence: csi_se

Parameters:

1. 16 x 16 voxel grid
2. TE 30 and TE 135 (csi_30 and csi_135); TR: 1500 ms
3. 1 measurement with 4 averages.
4. Voxel size: 10x10x15mm

I have loaded the data using the default parameters, and did Fit,  I am getting lot of noise.

Support required:

1. What parameters should i use in the Data parameters, Preprocessing, Fitting, Postprocessing tabs.
   
2. How to check the quality of the peaks and reliability of  my results.
   

 

[Ben Rowland]

Hi Sai,

Welcome to the MRS community. The screenshot you have attached is for the first voxel in the acquisition, the corner of the data. It is important to understand that in most multi-voxel MRS acquisitions the excitation volume is a subset of the acquired volume, so the corner and edge voxels are expected to contain only noise. I suspect if you try looking at some of the other voxels in the centre of the grid then you will find more signal. You can do this by clicking on the arrows in the top row of the Tarquin window, you want to change the R and C values to something like 8,8 (or whichever voxel you want to look at).

Good luck.

Ben

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<csi_135_peak fitting_default parameters.JPG>

[Sai Manohar Thota]

Hi Ben and MRS community !

Most of my spectra are not passing the QC. I have attached the GNU plots for different voxels.

I have acquired Brain CSI at 135TE using 1.5T siemens scanner. Can you please advise.

Thank you,

Sai

Sai Manohar Thota,

PhD Student,

Sri Sathya Sai Institute of Higher Learning,

Puttaparthi, India.

To view this discussion on the web visit https://groups.google.com/d/msgid/tarquin_users_group/472D68DC-E36E-4056-A872-479371079ECC%40mac.com.

[Sai Manohar]

Hi Dr. Benjamin Rowland,

Thanks a lot for the suggestion. I got better signal from the central voxels. But still i was not clear regarding the parameters i need to use for the Pre-processing, Fitting .On what basis should I modify these parameters. I have attached screen shot with default parameters.

Can you kindly see and tell me , if that looks OK ?!

Thank you so much for your valuable suggestions and help,

Regards,

Sai