Jana

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  • 2017-01-26 at 18:54 in reply to: Baseline Correction #1841
    Jana
    Moderator

    Dear Dounia
    There is no baseline correction available in the Preprocessing menu in jMRUI because the background may be estimated directly during quantitation.
    The Baseline correction2 in the « PreUtilis » to which you refer comes from the plug-in jmrui2xml, which is not included in the normal jmrui distribution. If you wish to use it and to learn more about the plug-in, please ask at for help.
    With kind regards
    Jana

    2017-01-17 at 13:21 in reply to: Phasing doesn't work anymore #1823
    Jana
    Moderator

    If your spectrum is black, it means that spectrum magnitude is displayed, so you will not see any change in the phase. To visualize the real component of a spectrum, choose Real in the View menu.

    • This reply was modified 7 years ago by Jana.
    • This reply was modified 7 years ago by Jana.
    2015-06-25 at 16:58 in reply to: Question regarding opening format types. #1393
    Jana
    Moderator

    Hm. I misunderstood the problem you have. For me the IMA file format was up to now known only as data format for images, not for CSI data.
    For Siemens CSI data we can currently only load .rda and dicom data formats and probably only some of them (unfortunately the DICOM format is not as standard as it should be).
    Your data are apparently wrongly interpreted by jMRUI (in CSI as 8x8x8 matrix, the same number of spectra as you got in 1d mode 8x8x8=512).
    I will try to implement this data format in jMRUI, but I cannot promise any deadline right now. Please would you provide me with information what sequence you used and about the data size (e.g. 2D/3D spatial encoding, parallel acquisition etc.)?

    Regards
    Jana

    2015-06-25 at 12:48 in reply to: Question regarding opening format types. #1391
    Jana
    Moderator

    In the MRSI mode, please make sure you check the boxes “Perform 2d FFT on raw data” and “Origin in the middle”. If this does not work, please upload you data on web and send me the link (jana at isibrno dot cz).

    Note: we are developing a new MRSI mode – all necessary information about data will be loaded from files and no user interaction (e.g. if k-space FFT should be performed) will be needed any more. The CSI position will be projected correctly into any image automatically.

    Regards
    Jana

    2015-06-25 at 10:04 in reply to: Question regarding opening format types. #1388
    Jana
    Moderator

    Try to open the MRSI file as Siemens DICOM Import. Please also post what scanner and acquisition software you use. Thanks.

    Regards
    Jana

    2015-06-24 at 17:46 in reply to: Problems opening 31P spectra acquired on Siemens Magnetom Prisma #1386
    Jana
    Moderator

    Try to select “Open” in the “File” menu and then choose your file. Please, post a message whether you succeeded. Thanks.

    With best regards
    Jana

    2015-06-24 at 17:15 in reply to: Question regarding opening format types. #1383
    Jana
    Moderator

    You do not have to select the data format (so it does not matter that there is no option to choose it). If the OpenAs list box is not used (the empty item is visible) jMRUI decides about the data format itself.
    In your case just ignore the OpenAs list box and
    – load MRSI data
    – then load an .IMA file (using the button beside the “Image:”)

    Best regards
    Jana

    • This reply was modified 8 years ago by Jana.
    2015-06-12 at 16:24 in reply to: Chemical notation peak name tags in 5.2 #1342
    Jana
    Moderator

    I will fix the bug as soon as possible. Thanks for reporting. Once I have it fixed I will post a message here with a link on the new patch.

    Jana

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