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My question concerns opening the files:
In the MRSI part it is written, that the jMRUI supports also .IMA files format. But when I want to open the file, there is no option for .IMA ? Can you help me?Best regards
Ali GordjinejadAli Gordjinejad
Research Centre JuelichYou 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
JanaThank you very much Jana,
It works. But the same problem occurs like when I am opening the file as Dicom:
It mixes all signals in the wrong voxel order.I am wondering since “Tarquin” is reading the files in the right order. Do you know maybe why this happens?best regards
AliAli Gordjinejad
Research Centre JuelichTry to open the MRSI file as Siemens DICOM Import. Please also post what scanner and acquisition software you use. Thanks.
Regards
JanaThank you Jana for your help;
Actually, I have also tried as you suggested. But it doesn’t work also. I measured 31P spectroscopy (CSI) at a 3 T Trio scanner from Siemens. I also tried everykind of saving the files like: -> export spectroscopy, offline,….when I opened the file (8×8 matrix) I just got noise. Interesting is that: when I open the file not in MRSI but in “1D/Time Series” I get the signals (it contain also the desired 31P pics (64 pics)…). But instead of 64 I get 511 signals.The rest is just noise.
best regards
AliAli Gordjinejad
Research Centre JuelichIn 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
JanaDear Jana,
I did what you told and it still doesn’t work. I have send the files to your e-mail adress since I didn’t where I have to upload the file on the jmrui web. If that is fine can you maybe just confirm me quickly if you got the mail? Thanks.
best regards
AliAli Gordjinejad
Research Centre JuelichHm. 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
JanaDear Jana,
Thank you for your efforts. In my case I choose just one slice that means it is a 2D measurement. The CSI sequense is the standard Siemens one. To my knowledge there also not the option like parallel aquisition and (maybe there are and I am not aware about it)….you can just choose an 8x8x8 Matrix oder 16x16x16…and you can only choose further Parameter like TR,TE, average….not more. For me, just in the case to know how jmrui can read the file (or which Format, doesn’t matter which one) in a proper way it will be helpful. According to you it is right now just rda. and dcm. but unfortunatly also dcm. makes trouble. Maybe it helps if I would know how to read .rda file
best regards
AliAli Gordjinejad
Research Centre Juelich
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