Bruker MRSI data

[Rui Simoes]

I have recently acquired MRSI data on a Bruker 7T with PV 6.0.1. No problem loading and processing these data with jMRUI 5.2 but have not yet succeed to load the respective reference image. The default format of the latter is “2dseq”. Do I need to convert to dicom before exporting from the console?

Thanks,
Rui

[Ludger Starke]

Dear Rui,

according to the help.htm manual/tutorial, which you will find in the jMRUI folder under /doc/help, only bitmap and (advanced) DICOM formats are supported for the reference image.

Which data ordering option did you chose? Using the default ordering I do not get the correct result. I am using PV 5.1 but probably there is no difference.

Cheers,

Ludger

[Rui Simoes]

Dear Ludger,

Thank you.

If you used acquisition-weighted, go with non-cartesian k-space filtering and just specify the total number of scans and repetitions.

Best,
Rui

[Ludger Starke]

Dear Rui,

I used the experiment mode standard. Thus the k-space should be sampled completely.

After trying more or less all available combinations of options, I have not yet had sensible data inside jMRUI while it looks fine in Paravision.

Could you, if just for the sake of documenting it somewhere on the internet, briefly summarize the steps you use to import the CSI data?

That would be so great. Thanks a lot!

Ludger

[Rui Simoes]

Hi Ludger,

Have you defined some degree of Fourier interpolation in the spatial dimension, prior to acquisition? If so, the problem we had was that jMRUI reads the matrix size from the acqp file (##$ACQ_size=( 3 ) -> displayed in the “Parameters” window of jMRUI), which is not the actual size of the fid. So we had to manually change the values (e.g. “4096 16 16” to “4096 32 32”). Then it worked fine.

Another problem was the filling order of the voxels. jMRUI plots from left-to-right (same as Bruker) but from bottom-to-top (Bruker = top-to-bottom). This should be corrected in the “Filling order” window, as detailed in the manual. We have not done it yet since we are testing another software.

Hope this helps. Good luck!

Rui

[Jens Rosenberg]

I am new to jMRUI. It seems like a useful tool but I have problems loading PV5.1 CSI data. I have tried DICOMs (created in PV5.1) but then I get an error about missing plugin? Using the “2dseq” file doesn’t work either. Which of the bruker format options should I use?

Thank you for your help
Jens

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