LalithShiyam
commented
1 year ago Hi @JasonMTIC, thank for you highlighting the bug, I think, the bug is due to the silly flip along the fourth dimension when you give the siemens (sms) tag. Because right now the program assumes its natively 4d when we pass a 'sms' tag. I will make a quick fix in a bit.
see below
Microsoft Windows [Version 10.0.19044.3324] (c) Microsoft Corporation. All rights reserved.
C:\Users\MTIC>cd C:\QIMP_Data
C:\QIMP_Data>nifti2dicom\Scripts\activate.bat
(nifti2dicom) C:\QIMP_Data>nifti2dicom -d C:\QIMP_Data\MOOSE\2023-08Studies\WEE^JOSEPHINE^^MRS_121.892_CT_2023-08-08_100303_PET^MTIC.FDG.RTP.Partial.Body.(Adult)_MTIC.CT.5.0.iMAR_n354__00000 -n C:\QIMP_Data\MOOSE\2023-08Studies\CT_2_mtic_ct_50_imar.nii -o C:\QIMP_Data\MOOSE\2023-08__Studies\dicom_output -desc "Test N2D" -t img -v sms
←[38;5;141m _ __ _ (_) / /() \ _/ ()__ __ / \/ / // / // // / / / \/ ` \ / / / / / / // // // /_/ / / // // / / / / / / // //// _/_//__/_,/_/_/__// // /_/←[0m ←[38;5;141mA package to convert NIfTI images to DICOM format using a reference DICOM series. Nifti2dicom is a part of the ENHANCE.PET (https://enhance.pet/) framework←[0m
←[38;5;141m 🔍 IDENTIFIED DATASETS:←[0m
←[38;5;208m Image dimensions: 3←[0m ←[38;5;40m Loading NIfTI image: C:\QIMP_Data\MOOSE\2023-08Studies\CT_2_mtic_ct_50_imar.nii←[0m Traceback (most recent call last): File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "C:\QIMP_Data\nifti2dicom\Scripts\nifti2dicom.exe\ main__.py", line 7, in
File "C:\QIMP_Data\nifti2dicom\Lib\site-packages\nifti2dicom\converter.py", line 280, in main
save_dicom_from_nifti_image(args.dicom_dir, args.nifti_path, args.output_dir, args.series_description, args.vendor)
File "C:\QIMP_Data\nifti2dicom\Lib\site-packages\nifti2dicom\converter.py", line 132, in save_dicom_from_nifti_image
image_data = np.flip(image_data, (1, 3))
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\QIMP_Data\nifti2dicom\Lib\site-packages\numpy\lib\function_base.py", line 340, in flip
axis = _nx.normalize_axis_tuple(axis, m.ndim)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\QIMP_Data\nifti2dicom\Lib\site-packages\numpy\core\numeric.py", line 1380, in normalize_axis_tuple
axis = tuple([normalize_axis_index(ax, ndim, argname) for ax in axis])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\QIMP_Data\nifti2dicom\Lib\site-packages\numpy\core\numeric.py", line 1380, in
axis = tuple([normalize_axis_index(ax, ndim, argname) for ax in axis])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
numpy.exceptions.AxisError: axis 3 is out of bounds for array of dimension 3
(nifti2dicom) C:\QIMP_Data>