Misidentification of edit On and Off scans - Siemens MEGA-PRESS for GABA

MRS Software Osprey
1

I have 3T Siemens MEGA-PRESS data, exported in individual single-average .dcm files. When I load these files into Osprey, it seems that it misidentifies a few “ON” scans as “OFF”, and vice versa - note the mixture of both peaks and flat lines around 2ppm:

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It seems this may be causing an issue with the alignment, as well (although any other thoughts on this are much appreciated).

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I am curious how Osprey determines which scans are “ON” and “OFF”, and if there is a different way I should be importing my data to make it more clear which are “ON” and which are “OFF”.

Thank you!
Kevin

2

Hi Kevin,
I think the problem is how the data will be read in (with the script io_loadspec_dicom). The order depends on the order of the data in the folder and not based on the instance number. Maybe a replacement of “fids(:,kk) = dicom_get_spectrum_siemens(fd);” with something like “fids(:,infoDicom.InstanceNumber) = dicom_get_spectrum_siemens(fd);” in your script io_loadspec_dicom.m can solve the problem.

Heiner

3

Thanks so much, Heiner. That worked perfectly.

4

I’m glad to hear that it’s helping! @admin, would that be a general way to make the read-in process more robust or might this create other problems elsewhere?

Heiner