Problem with Siemens Dicom (.IMA)

[Samira Raminfard]

Dear jMRUI team,

There is a problem by .IMA file. When I load the Siemens dicom file the spectra appear in reverse form than the same .rda file.
How can I fix this problem?
I have taken screen shot from the spectra but I do not know how to upload it here.

Thanks
Samira

[Mai]

Hi

I have been working with some images from a siemens sytem, and before upload the spectra in jMRUI, I have to process the dicom image, I used this code in matlab:
http://www.mathworks.com/matlabcentral/fileexchange/9768-dicom-utilities

With this code you will have files with format .txt and them you can open in jMRUI and make the analysis.

Regards.

[Samira Raminfard]

Hi,
Thanks a lot for the code.
Unfortunately, I didn’t get the text I needed,
There weren’t any errors to debug.
Here is a screenshot after running the code:

I would really appreciate it if you could help me out.

Thanks in advanced
Samira

[Ali Gordjinejad]

Hi jMRUI team,

I have the following Problem by loading 31P (Siemens magnetom) regarding MRSI: Whatever I choose by “filling order” (whether “default” or “custom” with “load from files”) jMRUI doesn’t care about the voxel order and put the highest signal in the middel. What should I do? Is it only possible to solve the problem with the matlab code? The problem is I don’t have matlab license for downloading the code.
best regards
Ali Gordjinejad

Ali Gordjinejad
Research Centre Juelich

[Chao Suo]

Hi Samira,

I found a temporary solution following Maikol’s suggestion. After reading out the complex number of spectrum using the dicom toolbox, I overwrote these values in a text file which created by “save as text file” in jMRUI. Importantly, if I reverse the imaginary part, i.e., “+” => “-” and “-” => “+”, then loaded in jMRUI. The spectrum is now in the same direction as rda file.

I’m not 100% sure that is the correct way to do so, and looking forward to other solutions.

BTW, I used jMRUI v5,2.
Regards,
Chao

Chao Suo
Monash University

[Samira Raminfard]

Hi Chao,
Thank you very much for you answer.
I’m so sorry for delay.
Finally, I could open the file.It seems correct!

Regards
Samira

[Tamara Simpson]

Hi there

I’m just wondering if anyone else can confirm what Chao has suggested as being a good method for reversing the Siemens spectra? I will have about 200+ files to change by the time I finish collecting data which will be quite labour intensive doing it this way. Are there any other suggestions?

Regards
Tamara

[Samuel Holly]

Hello,

@Tamara: indeed what Chao suggested is the correct approach – it is known as complex conjugation. You can conjugate your spectra in jMRUI (for sure from v5.2 onward) by selecting 1D/Time series > select your file > go to Preprocessing > Mathematics > Conjugate signal/Reverse spectrum

Best regards

[Author]

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