Problem with Siemens Dicom (.IMA)

Home > Forums > jMRUI Software > General support > Problem with Siemens Dicom (.IMA)

Viewing 8 posts - 1 through 8 (of 8 total)
  • Author
    Posts
  • #1542
    Samira Raminfard
    Participant

    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

    #1543
    Mai
    Participant

    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.

    #1547
    Samira Raminfard
    Participant

    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:
    result

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

    Thanks in advanced
    Samira

    #1549
    Ali Gordjinejad
    Participant

    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

    #1590
    Chao Suo
    Participant

    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

    #1619
    Samira Raminfard
    Participant

    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

    #1625
    Tamara Simpson
    Participant

    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

    #2171
    Samuel Holly
    Participant

    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

Viewing 8 posts - 1 through 8 (of 8 total)
  • You must be logged in to reply to this topic.