How to load CSI data?

[Mojdeh Dormishian]

Hello everyone,

I have a question regarding jMRUI v5.2 that I installed last week. I can not load the CSI data with jMRUI software. Do you think that I need a spcail plugin ? We have Siemens Scanner and our data is in DICOM. I explain you how I tried to laod the CSI files :

1. From
MRUI Wizard > MRSI > Open as :
but there is no CSI format. I tried with DICOM but I can not select anythig.

2. From
Custom > Clinical Examination > Siemens (test) > Mount DICOM directory > look in (where I load my folder)
I can see the csi-2D files but I can not load them. I have a message error : Error in Mrui Mode 1D(Data)

Thanks for your help.
Mojdeh Dormishian

[Ali Gordjinejad]

Hi Mojdeh,

We have a 3Tesla Trio Siemens Scanner and we have also trouble loading the CSI files with jMRUI. Did you save your files in the following way?:
In the Patient Brwoser go to -> “Applications”, -> “Dicom tools”, -> “Export Mr Spectroscopy”. The syngo software will save your data as dicom files on your (U) hard disk. Otherwise you will have trouble because the software will not be able to save the spectroscopy data.
You can go then afterwards within your Windows Explorer to: My computer, -> Med_System(U:). The files are available there and you can save it on your USB or….. On the jMRUI you can go to MRSI and try to open the file with the option: opens as-> Siemens DICOM Import. It should at least be able to read your file. But we have the problem that it is mixing the voxel order in a wrong way.

Ali Gordjinejad
Research Centre Juelich

[Mojdeh Dormishian]

Dear Ali,

Thanks for your answer. Finally I could load csi.files. I saved my csi files into .RDA format (they were in .dcm) and it works. I do not choose any option in “Open As” in “MRSI”. I just click on “Open” beside “MRSI” and I choose my csi.RDA and it loads the file.

Did you try to change the format of your files? Maybe it works by saving into .RDA

Mojdeh Dormishian
Hôpitaux Universitaires de Strasbourg

[Ali Gordjinejad]

Dear Mojdeh,

Great. Fortunately also my problem seems to be solved. I transfer the data again as dicom (but in the way I wrote last time) to jMRUI and tried to open it directly (as you did) with MRSI. And surprise,…. obviously it works now. Although I have to check whether the voxel are really on the right places, but ot looks very trustfull. Maybe it will also work with rda. as you did. I have to try it next time.

Best regards
Ali

• This reply was modified 8 years ago by Ali Gordjinejad.

Ali Gordjinejad
Research Centre Juelich

[Emily Belleau]

Hi Mojdeh,

How did you convert your dcms to rda? I am trying to make a mask of my MRS voxel and it would be super helpful to know how to convert the dcms to rda files.

Thanks,

Emily

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