FSL-MRS spec2nii Siemens dicom conversion issue

MRS Software Other
1

Hi,

I’m new to fsl-mrs and am trying to load DICOM images from an MRSI sequence acquired on a Siemens Prisma 3T system using spec2nii. The MRSI sequence I ran is described here: https://doi.org/10.1016/j.neuroimage.2014.09.032

When I run spec2nii dicom ~/pathtodicomfolder I get the following error message:

'/Users/simin/fsl/lib/python3.11/site-packages/spec2nii/Siemens/dicomfunctions.py:10: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment',
 'Please use with caution.  We would be grateful for your help in improving them',
 '  import nibabel.nicom.dicomwrappers',
 'Found 3 files.',
 'Traceback (most recent call last):',
 '  File "/Users/simin/fsl/bin/spec2nii", line 10, in <module>',
 '    sys.exit(main())',
 '             ^^^^^^',
 '  File "/Users/simin/fsl/lib/python3.11/site-packages/spec2nii/spec2nii.py", line 666, in main',
 '    spec2nii(*args)',
 '  File "/Users/simin/fsl/lib/python3.11/site-packages/spec2nii/spec2nii.py", line 283, in __init__',
 '    args.func(args)',
 '  File "/Users/simin/fsl/lib/python3.11/site-packages/spec2nii/spec2nii.py", line 512, in dicom',
 '    self.imageOut, self.fileoutNames = multi_file_dicom(files_in, args.fileout, args.tag, args.verbose)',
 '                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^',
 '  File "/Users/simin/fsl/lib/python3.11/site-packages/spec2nii/Siemens/dicomfunctions.py", line 118, in multi_file_dicom',
 '    specDataCmplx, orientation, dwelltime, meta_obj = process_siemens_csi(img, verbose=verbose)',
 '                                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^',
 '  File "/Users/simin/fsl/lib/python3.11/site-packages/spec2nii/Siemens/dicomfunctions.py", line 308, in process_siemens_csi',
 '    return process_siemens_csi_xa(img, verbose)',
 '           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^',
 '  File "/Users/simin/fsl/lib/python3.11/site-packages/spec2nii/Siemens/dicomfunctions.py", line 314, in process_siemens_csi_xa',
 "    raise NotImplementedError('Method process_siemens_csi_xa not implemented, example data needed!')",
 'NotImplementedError: Method process_siemens_csi_xa not implemented, example data needed!'

The software version on the scanner is VE11C. Is this version supported?

Thanks for any suggestions / ideas,

Simon

2

Hi @simin ,

Ah this must be an enhanced DICOM coming from a VE11c scanner then, I have heard of this but hadn’t yet encountered it (at first enhanced DICOM were only seemingly coming from the XA line scanners, hence the error).

I haven’t yet included MRSI/CSI handling in this pathway (SVS is), because I haven’t got any example data. If you had some, that I can host as part of the public dataset, I’d be very happy to add it. This just needs to be a small (low resolution) scan on a phantom.

BW

Will

3

Hi @wclarke,

thank you very much for the quick reply. I could record some phantom data with the sequence next week. Alternatively, I could get permission to upload the in-vivo data from one of the control subjects and remove personal data from the dicom header. Where can I upload the data?

Best wishes,

Simon

4

Hi @simin ,

There are so many issues with hosting human data that I would greatly prefer phantom. It should be pretty small int erms of data size, so you could just send it to the email listed here: William Clarke — Wellcome Centre for Integrative Neuroimaging

Will

5

Hi @wclarke,

Thanks a lot. I will record some low resolution data next week and will email it to you.

Best wishes,

Simon

6

Hi @wclarke,

I’ve just sent you an email with some phantom data at a reduced resolution. Hope the attachment size was okay and it reached your inbox.

All the best,

Simon

1 Like
7

Thanks for providing the data @simin , Roland was also in touch about this with more data. As such it’s now in the codebase and will be in version 0.7.1 (out in the next few days). If you want it now you can clone from github and do a local installation (pip install .).

Will

1 Like
8

Hi @wclarke,

That’s great. Thanks for the quick implementation! I’ll try to run spec2nii with the GitHub version tomorrow.

Best wishes,

Simon