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Software tools for the NIfTI-MRS data format

License: BSD 3-Clause "New" or "Revised" License

Python 99.26% Makefile 0.33% Batchfile 0.41%
mrs mrsi nifti-format

nifti_mrs_tools's People

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dc-3t avatar dimitripapadopoulos avatar musicinmybrain avatar wtclarke avatar

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dimitripapadopoulos markmikkelsen musicinmybrain dc-3t

nifti_mrs_tools's Issues

FSL MRS issue traced back to ValueError in nifti_mrs

I am trying to use FSL MRS interactively and I've run into the following error:

Cell In[29], line 2
      1 # %%
----> 2 data = mrs_io.read_FID(path)
      3 mrs = data.mrs(basis_file=fsl_basis_file_path)                     
      4             #    ref_data=final_wref)

File ~/Documents/Repositories/fsl_mrs/fsl_mrs/utils/mrs_io/main.py:91, in read_FID(filename)
     88     filename = Path(filename).resolve()
     90 try:
---> 91     return fsl_nmrs.NIFTI_MRS(filename)
     92 except (NotNIFTI_MRS, fslpath.PathError):
     93     data_type, id_ext = _check_datatype(Path(filename))

File ~/Documents/Repositories/fsl_mrs/fsl_mrs/core/nifti_mrs.py:100, in NIFTI_MRS.__init__(self, *args, **kwargs)
     54 def __init__(self, *args, **kwargs):
     55     """Create a NIFTI_MRS object with the given image data or file name.
     56 
     57     This is a wrapper around the nifti_mrs.nifti_mrs.NIFTI_MRS class to
   (...)
     98     (if it is called).
     99     """
--> 100     super().__init__(*args, **kwargs)
...
    105         else:
--> 106             raise ValueError(f'User-defined key {key} must contain a "Description" field"')
    108 return obj

ValueError: User-defined key conversion_time must contain a "Description" field"

This happens with every input file, but we used FSL MRS to fit all of this data this summer, so I know it worked a few months ago.

I went through the data file using the following code:

img = nib.load(path)
data = img.get_fdata(dtype=np.complex64)
header = img.header
hdr_ext_codes = img.header.extensions.get_codes()
mrs_hdr_ext = json.loads(img.header.extensions[hdr_ext_codes.index(44)].get_content())
print(mrs_hdr_ext)

And got the following output showing that 'conversion_time' does in fact have a filled in value pair.

{'SpectrometerFrequency': [123.2],
 'ResonantNucleus': ['1H'],
 'EchoTime': 0.144,
 'RepetitionTime': 2.0,
 'DeviceSerialNumber': 'NA',
 'Manufacturer': 'simulated',
 'ManufacturersModelName': 'NA',
 'SoftwareVersions': 'NA',
 'PatientDoB': 'NA',
 'PatientName': 'NA',
 'PatientPosition': 'HFS',
 'PatientSex': 'NA',
 'PatientWeight': 0,
 'ConversionMethod': 'Manual',
 'ConversionTime': '2023-04-22T15:58:10.128',
 'OriginalFile': ['denoiser_physics_model_512_dataset.mat'],
 'conversion_time': '2023-06-02T09:04:55.836'}

Do you have any suggestions for what could be causing this and how to fix it or work around it?

Best,
John

Unnecessary file nifti_mrs/standard/explanatory_doc/conf.py

An unnecessary file nifti_mrs/standard/explanatory_doc/conf.py, the Doxygen configuration for the standard specification https://github.com/wtclarke/mrs_nifti_standard/, is included in both the sdists and wheels, when only nifti_mrs/standard/definitions.json is really needed or wanted. This isn’t particularly harmful, but it isn’t really right either.

$ python3.12 -m venv _e
$ . _e/bin/activate
(_e) $ pip install nifti-mrs
(_e) $ find _e/lib/python3.12/site-packages/nifti_mrs/standard/
_e/lib/python3.12/site-packages/nifti_mrs/standard/
_e/lib/python3.12/site-packages/nifti_mrs/standard/definitions.json
_e/lib/python3.12/site-packages/nifti_mrs/standard/explanatory_doc
_e/lib/python3.12/site-packages/nifti_mrs/standard/explanatory_doc/conf.py
_e/lib/python3.12/site-packages/nifti_mrs/standard/explanatory_doc/__pycache__
_e/lib/python3.12/site-packages/nifti_mrs/standard/explanatory_doc/__pycache__/conf.cpython-312.pyc

$ gh repo clone wtclarke/nifti_mrs_tools
$ cd nifti_mrs_tools
$ python3 -m build
$ tar -tzf dist/nifti_mrs-1.2.0.tar.gz | grep standard
nifti_mrs-1.2.0/src/nifti_mrs/standard/
nifti_mrs-1.2.0/src/nifti_mrs/standard/definitions.json
nifti_mrs-1.2.0/src/nifti_mrs/standard/explanatory_doc/
nifti_mrs-1.2.0/src/nifti_mrs/standard/explanatory_doc/conf.py

Expected:

$ python3.12 -m venv _e
$ . _e/bin/activate
(_e) $ pip install nifti-mrs
(_e) $ find _e/lib/python3.12/site-packages/nifti_mrs/standard/
_e/lib/python3.12/site-packages/nifti_mrs/standard/
_e/lib/python3.12/site-packages/nifti_mrs/standard/definitions.json

$ tar -tzf dist/nifti_mrs-1.2.0.tar.gz | grep standard
nifti_mrs-1.2.0/src/nifti_mrs/standard/
nifti_mrs-1.2.0/src/nifti_mrs/standard/definitions.json

Tests fail when file endianness does not match host endianness

While packaging this for Fedora Linux, for which the big-endian s390x is a primary architecture, I found that the routines assume the file endianness and host endianness match. This results in six test failures:

=========================== short test summary info ============================
FAILED tests/test_nifti_mrs.py::test_nifti_mrs_save - nifti_mrs.validator.nif...
FAILED tests/test_script_mrs_tools.py::test_merge - subprocess.CalledProcessE...
FAILED tests/test_script_mrs_tools.py::test_split - subprocess.CalledProcessE...
FAILED tests/test_script_mrs_tools.py::test_reorder - subprocess.CalledProces...
FAILED tests/test_script_mrs_tools.py::test_reshape - subprocess.CalledProces...
FAILED tests/test_script_mrs_tools.py::test_conjugate - subprocess.CalledProc...
=================== 6 failed, 44 passed, 1 skipped in 1.96s ====================

I have attached the full build log.

This StackOverflow question suggests one way of detecting endianness in a NIfTI file.

I would understand if you chose not to support NIfTI files that don’t match the host endianness, but I thought I should at least report the issue.

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