Problem converting GE P-file

[nickbolo]

Hello FSL-MRS developers, I've just installed (or so I think) FSL-MRS and spec2nii and look forward to using the tools. I got the following error messages when trying to convert a GE P-file (renamed):

% spec2nii ge P00102.7 Traceback (most recent call last): File "/Users/nick/opt/anaconda3/bin/spec2nii", line 10, in sys.exit(main()) File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/spec2nii.py", line 486, in main spec2nii(*args) File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/spec2nii.py", line 128, in init args.func(args) File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/spec2nii.py", line 353, in ge data,ref_data, orientation, dwelltime, meta = read_p_file(args.file) File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/GE.py", line 16, in read_p_file hdr = _read_hdr(filename) File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/GE.py", line 111, in _read_hdr byte_off,interp_off = _rev_info(rdb_rev) File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/GE.py", line 249, in _rev_info raise ValueError(f'Revision number {rev} not recognised.') ValueError: Revision number 26.00200080871582 not recognised.

I'm using Mac OS Catalina 10.15.7 Any idea what the problem is? Thanks, Nick

[wtclarke]

Hi @nickbolo

Thanks for the bug report and giving FSL-MRS a go. I'm currently working on spec2nii to update it to support the NIFTI-MRS standard (see https://github.com/wexeee/mrs_nifti_standard). As part of this I'm trying to provide much better support for GE and Philips file types. I'm working on the GE part currently and I hope to have a new release out in the next couple of days. I'll make sure that that newest p-file release number is handled.

Will

[nickbolo]

Hi Will,

Thanks for the quick reply! I look forward to the update.

If it is helpful, I also tried on another older P-file and got the following: ValueError: Revision number 15.00100040435791 not recognised.

Cheers, Nick

[wtclarke]

@nickbolo Hi Nick,

Sorry I forgot to update you about this. Spec2nii has had a few updates since your original message. Would you be up for trying again with the new version?

BW,

Will

[nickbolo]

?Hi Will,

Yes, I'll give it a whirl.

Thanks,

Best,

Nick

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From: Will Clarke @.***> Sent: Wednesday, March 31, 2021 3:53 AM To: wexeee/fsl_mrs Cc: Bolo,Nicolas R. (BIDMC - Psychiatry - Landmark); Mention Subject: [External] Re: [wexeee/fsl_mrs] Problem converting GE P-file (#5)

@nickbolohttps://urldefense.com/v3/__https://github.com/nickbolo__;!!CvMGjuU!vty7ydRwG4aIwutAe4oqRvazDIf9wP_RJVdPvfsGy0bbBe06uEcErdIlcl-PXHKpp05HCg$ Hi Nick,

Sorry I forgot to update you about this. Spec2nii has had a few updates since your original message. Would you be up for trying again with the new version?

BW,

Will

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[nickbolo]

Hi Will,

I got a bit further, but now the psd (or sequence) is not recognized. I am using GE's "presscsi".

Please see the error message below:

File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/GE/ge_pfile.py", line 99, in _process_svs_pfile

raise UnsupportedPulseSequenceError(f'Unrecognised sequence {psd}.')

spec2nii.GE.ge_pfile.UnsupportedPulseSequenceError: Unrecognised sequence presscsi.??

Cheers,

Nick

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This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

[wtclarke]

Hi Nick,

GE sequences require quite specific interpretation for each sequence type. I’m gradually adding them as I come across them. I hope though that this one will work with some existing code, and that I just need to add this sequence to the list. Would you be able to share a dataset?

Best wishes,

Will

From: nickbolo @.> Date: Friday, 14 May 2021 at 00:16 To: wexeee/fsl_mrs @.> Cc: William Clarke @.>, Comment @.> Subject: Re: [wexeee/fsl_mrs] Problem converting GE P-file (#5) Hi Will,

I got a bit further, but now the psd (or sequence) is not recognized. I am using GE's "presscsi".

Please see the error message below:

File "/Users/nick/opt/anaconda3/lib/python3.8/site-packages/spec2nii/GE/ge_pfile.py", line 99, in _process_svs_pfile

raise UnsupportedPulseSequenceError(f'Unrecognised sequence {psd}.')

spec2nii.GE.ge_pfile.UnsupportedPulseSequenceError: Unrecognised sequence presscsi.??

Cheers,

Nick

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This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/wexeee/fsl_mrs/issues/5#issuecomment-840888063, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFJJTTSSENE6XIIBF5LVTKDTNRMS3ANCNFSM4WSWWXGA.

[nickbolo]

Hi Will,

Yes, glad to share a dataset with you.

Best wishes, Nick

[wtclarke]

Just tidying up a little by closing old issues. If you did have a dataset to share, I'd be very happy to still look at this and include in spec2nii.