tomaroberts / nii2dcm Goto Github PK

Currently manually push to PyPI. Implement GHA to push to PyPI on release:

• https://github.com/pypa/gh-action-pypi-publish

Related to #8 – need to improve class inheritance. Currently, the Dicom class is too MR biased.

TODO:

• shift the add_module() calls to DicomMRI subclass
• need to ensure init_study_tags() and init_series_tags() are called after all the other tags in DicomMRI subclass are initialised
• replicate this structure with DicomCT subclass that calls modules relevant to NEMA CT Image Module Table

It would be very useful to have an enhanced DICOM output option.

I get this exception when run nii2dcm under windows after pip install:

nTraceback (most recent call last):
  File "D:\tools\WPy64-39100\python-3.9.10.amd64\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "D:\tools\WPy64-39100\python-3.9.10.amd64\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "D:\tools\WPy64-39100\python-3.9.10.amd64\Scripts\nii2dcm.exe\__main__.py", line 4, in <module>
  File "D:\tools\WPy64-39100\python-3.9.10.amd64\lib\site-packages\nii2dcm\__main__.py", line 9, in <module>
    from nii2dcm._version import __version__
  File "D:\tools\WPy64-39100\python-3.9.10.amd64\lib\site-packages\nii2dcm\_version.py", line 2, in <module>
    __version__ = Version.from_git().serialize(metadata=False, style=Style.SemVer)
  File "D:\tools\WPy64-39100\python-3.9.10.amd64\lib\site-packages\dunamai\__init__.py", line 1058, in from_git
    _detect_vcs(vcs)
  File "D:\tools\WPy64-39100\python-3.9.10.amd64\lib\site-packages\dunamai\__init__.py", line 355, in _detect_vcs
    raise RuntimeError(
RuntimeError: This does not appear to be a Git project

seems the version is detect from current git directory and get a git exception?

Thanks @tomaroberts for your great package - using the cli if I add a reference image i get:

"/dcm_writer.py", line 89, in transfer_ref_dicom_series_tags for current_attribute in dcm.attributes_to_transfer:
AttributeError: 'Dicom' object has no attribute 'attributes_to_transfer'

I, i have to process a directory of nifti files for a conectome analisis and i succesfully converted the files into dicom, as the software only works on a directory of dicom files. Now the software doesnt process the input folder as the images are in ALS orientation. This can be fix on -dicom type modality or is an aditional step to implement?. ITK-SNAP recognize the imagen as dicom series but does not tell much about orientation.

First off - great tool!

I am having trouble with the tool, in ITK-snap and the imported DICOM the centres in the axial plane are way off (see below)

I am looking at the dataset:
https://openneuro.org/datasets/ds003949/versions/1.0.1

specifically in that example sub-336, I can't seem to find the error. I assume it's something to do with the way that the slice positions are calculated.

Any help would be great!

Hello!
when I run nii2dcm input.nii.gz output -d CT, I got :

dicom_type only for MR and SVR?

Currently output files do not have an extension, they are just output as:

IM_0001
IM_0002
...
IM_XXXX

AIDE requires files to have .dcm extension, so will implement this by default, e.g.:

IM_0001.dcm
IM_0002.dcm
...
IM_XXXX.dcm

Thanks for your work on nii2dcm! I'm considering integrating this as part of my QSM processing toolbox, QSMxT.

However, I'm having problems using it in my miniconda setup:

(qsmxt) ~/.../data/qsmtest/qsm: nii2dcm sub-1_ses-20231020_part-phase_T2Starw_romeo-unwrapped_normalized_pdf_rts_twopass_ref.nii dicom-output-directory/ --dicom-type MR
Traceback (most recent call last):
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/bin/nii2dcm", line 5, in <module>
    from nii2dcm.__main__ import cli
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/lib/python3.8/site-packages/nii2dcm/__main__.py", line 9, in <module>
    from nii2dcm._version import __version__
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/lib/python3.8/site-packages/nii2dcm/_version.py", line 2, in <module>
    __version__ = Version.from_git().serialize(metadata=False, style=Style.SemVer)
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/lib/python3.8/site-packages/dunamai/__init__.py", line 1058, in from_git
    _detect_vcs(vcs)
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/lib/python3.8/site-packages/dunamai/__init__.py", line 355, in _detect_vcs
    raise RuntimeError(
RuntimeError: This does not appear to be a Git project

It is related somehow to the dunamai package. Any idea what could be causing this?

I tried initialising a git repository in the local directory to see if that could be a workaround, but then I have a new problem:

(qsmxt) ~/.../data/qsmtest/qsm: nii2dcm -d MR sub-1_ses-20231020_part-phase_T2Starw_romeo-unwrapped_normalized_pdf_rts_twopass_ref.nii dicom-output-directory/
Traceback (most recent call last):
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/bin/nii2dcm", line 8, in <module>
    sys.exit(cli())
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/lib/python3.8/site-packages/nii2dcm/__main__.py", line 55, in cli
    run_nii2dcm(
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/lib/python3.8/site-packages/nii2dcm/run.py", line 38, in run_nii2dcm
    nii2dcm_parameters = nii2dcm.nii.Nifti.get_nii2dcm_parameters(nii)
  File "/home/ashley/neurodesktop-storage/miniconda3/envs/qsmxt/lib/python3.8/site-packages/nii2dcm/nii.py", line 38, in get_nii2dcm_parameters
    nInstances = nZ*nF
UnboundLocalError: local variable 'nZ' referenced before assignment

Looking at your code in nii.py, I can see that this is happening because of the dimensions of my file:

>>> nii.header['dim']
array([  3, 164, 205, 205,   0,   0,   0,   0], dtype=int16)

Which will not be handled correctly by the initialization code:

https://github.com/tomaroberts/nii2dcm/blob/09d20e02f61da2aa5e7a2e57bd420828021f0d92/nii2dcm/nii.py#L29C1-L35C58

My file is a 3D volume with 205 slices, each with dimensions 164x205. It is a quantitative susceptibility map with floating-point values in the range of about -4 to +3, with most values around zero.

• create build_and_test_cli.yml

• Build tests and upload test data for the following:

  • Dicom class
  • DicomMRI class
  • DicomMRISVR class

• Need to make DicomCT class, etc. and make tests. Can pull public MRI/CT data.

nii2dcm F:\Datasets\nii\AF_cta\Site2\CT\1052519\untitled_original.nii.gz F:\Code\DeepLearning\GAN\CTA-GAN\data\Site2\CT\1052519/
please help me !

Push to TestPyPI on pull-request?:

• https://github.com/pypa/gh-action-pypi-publish#advanced-release-management

• Create and shift to utils.py
• Or... create method within dcm.py Dicom class so that Date/Time can be called once during a DICOM creation run

Hello,

I am trying to convert .nii files into dicoms file and i ran the code using

nii2dcm {path_to_.nii} {output_dir} 

But the output files in the output_dir are not in .dcm format/with no .dcm extensions

eg.

Need to update nii2dcm with proper logging.

• Currently just some placeholder print() statements.
• Implement log levels

Realised that some DICOM Attributes are defined in more than one Module, e.g.:

• BitsAllocated is defined in both Image Pixel Module and MR Image Module

Current behaviour means that which ever Module is called second overrides. Not ideal.

TODO:

• when calling Module subclasses, check if Attributes already exist in the Dicom object and then perform relevant logic, e.g. overwrite and warn.

• create -r / --ref_dicom option which points at a DICOM file and transfers attributes to nii2dcm generated DICOM

Currently, when generating different types of DICOM (MRI, CT, different scanners, etc.) the intensity values/windowing in the output DICOM can be incorrect, e.g.:

Output DICOM contrast from input CT NIfTI dataset:

Some modalities are working, others are not.

TODO:

• improve the method of interpreting the NIfTI voxel values and correctly setting the contrast/windowing/slope tags in the DICOM files.

• Make build.yml