Problems loading Siemens PRESS DICOM data

Hello all,

Thank you for the developers of this software. As a fairly new PhD student that is working on analysing some PRESS data, I’m quite impressed and thankful for its user-friendly design and comprehensive pipeline.

Currently, I’m having a bit of trouble with loading DICOM data exported from a Siemens Skyra machine - software version was syngo MR D11. I have attached the job file and error message received.

Thanks,
Mike

jobDCM.txt (8.4 KB)

Error message.txt (1020 Bytes)

Hi Mike,

Thanks for getting in touch. I can load some Siemens DICOM test data on my own machine without any problems. The error message

Error in read_dcm_header (line 29)
tline = fgets(fid); % get first line

Error in io_loadspec_dicom (line 32)
DicomHeader = read_dcm_header(filesInFolder{1});

suggests that Osprey can’t find a file in one of the folders that you specified in the job file

files       = {'H:\PhD\Test\sub-03\ses-01\mrs_GM\sub-03_press_ref'};
files_ref   = {'H:\PhD\Test\sub-03\ses-01\mrs_GM\sub-03_press_wref'};

Can you confirm that these are the two folders where your data is supposed to be found (I’m a bit suspicious that both of them carry the bit ref in them), and that the folders contain nothing but .dcm or .ima files?

If you have made sure that’s the case, please try and share the (de-identified) dataset with us through your institutional file storage or via e-mail (see the Osprey GitHub README file).

Thanks,
Georg

Thank you Georg,

Can confirm that both folders are where I exported the single dicom files for each acquisition. I have sent you the de-identified files via email to check over.

Kind regards,
Mike

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Mike and Georg,

Were you able to resolve this? I too am getting an error when trying to load Siemens dicom (IMA) files from an SV-Press acquisition (no editing). I have been able to successfully load other Siemens data (RDA), so this problem seems to be limited to the dicom data. (Note: Helge/Georg, this is separate from my other issue loading the Philips enhanced dicom data).

Here is the error log. I get the same error regardless of whether I use my jobIMA.m file or try straight from the create job GUI.

Loading raw data from dataset 1 out of 1 total datasets…
Error using fgets
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in read_dcm_header (line 29)
tline = fgets(fid); % get first line

Error in io_loadspec_dicom (line 32)
DicomHeader = read_dcm_header(filesInFolder{1});

Error in osp_LoadDICOM (line 65)
raw = io_loadspec_dicom(MRSCont.files{kk});

Error in OspreyLoad (line 64)
[MRSCont] = osp_LoadDICOM(MRSCont);

Error in osp_onLoad (line 33)
MRSCont = OspreyLoad(MRSCont);

Error while evaluating UIControl Callback.

Thanks again for all that you all do!

Jessica

Hi Jessica,

can you share your jobFile and DICOM data with me?

Helge

Just wanted to let the developers here that I am also getting the exact same error:

For DICOM data, metabolite and water reference data need to be in separate folders. These folders may only contain MRS data, no imaging or anything else. The files and files_ref entries in the job file need to point to the folders (see the Siemens IMA example).

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Hi Everyone

I figured out the fix to this.
The issue was the path to the data in the job file.
In the job file, I had provided the path to the folder where all the averages are stored like this
files (counter) = {‘…\MetaboliteData_64Avg'};
but for the water ref data I had provided the path to the file (not folder). Like this
files_ref(counter) = {’…\WaterRef\SVS_FMRI_05.MR.SHAH_SHIMTEST.0010.0001.2023.10.19.15.35.08.876655.726430189.IMA’};

This was an inconsistency that was creating the problem. After changing the path to the folder for the waterRef data as well, the issue was resolved.

Best
Shah

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Thanks Georg.
That was indeed the problem.

Best
Shah

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Can we restore your deleted post? I think it’ll be useful for other users.

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