CatPhan604 Error

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1

Hello,

I have been using TIGRE as an external CT reconstruction tool, and appending a DICOM header to it for analysis by pylinac. I have run the pylinac demo as well as a sample from a clinically reconstructed ct which both work. My own files give this error though.

Traceback (most recent call last):
File “C:\Users\drman\PycharmProjects\pythonProject\main.py”, line 9, in
mycbct.analyze()
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\pylinac\ct.py”, line 1992, in analyze
self.localize()
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\pylinac\ct.py”, line 1699, in localize
self._phantom_center_func = self.find_phantom_axis()
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\pylinac\ct.py”, line 1727, in find_phantom_axis
p30, p70 = np.percentile(center_x, [30, 70])
File “<array_function internals>”, line 200, in percentile
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\numpy\lib\function_base.py”, line 4205, in percentile
return _quantile_unchecked(
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\numpy\lib\function_base.py”, line 4473, in _quantile_unchecked
return _ureduce(a,
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\numpy\lib\function_base.py”, line 3752, in _ureduce
r = func(a, **kwargs)
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\numpy\lib\function_base.py”, line 4639, in _quantile_ureduce_func
result = _quantile(arr,
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\numpy\lib\function_base.py”, line 4745, in _quantile
take(arr, indices=-1, axis=DATA_AXIS)
File “<array_function internals>”, line 200, in take
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\numpy\core\fromnumeric.py”, line 190, in take
return _wrapfunc(a, ‘take’, indices, axis=axis, out=out, mode=mode)
File “C:\Users\drman\PycharmProjects\pythonProject\venv\lib\site-packages\numpy\core\fromnumeric.py”, line 57, in _wrapfunc
return bound(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.

attached is one slice of the image I’m trying to analyze.

Thank you so much for your help!!

testfile92.dcm (514 KB)

2

One slice isn’t going to help me help you. You can send the whole dataset via the google form here: https://forms.gle/er2Gaoz7UfwjNJY19

3

Hey I shared those files with you on google forms, did you get a chance to look at them?

Thanks again

4

Something is fishy with the FOV. The image size is 512x512 and the pixel spacing is 0.65mm/pixel. This gives an FOV of 333mm, but the ReconstructionDiameter says 250, which is ~33% discrepancy. Pylinac is expecting a catphan of a certain size. If I change the catphan expected size to 133 (default is 101) the phantom is now detected. Unfortunately, this causes a lot of problems elsewhere because the physical values are expected to be accurate. The HU values are also off by ~1000, but that won’t stop the analysis. The slice thickness also seems iffy. It’s reported as 2.5mm but the distance in slices between the high contrast and HU modules was ~20 slices. The physical distance is 40mm for the 504, so i’m tempted to think the real slice thickness is 2. The ImagePatientPosition tag also did not vary which it should.

Unfortunately, I spent my available time just getting this far. The TL;DR is that you should check the DICOM tags to ensure they are accurate.

You can get somewhere by overriding the mm_per_pixel propery like so: catphan mm override (github.com)

5

I have made significant progress, although I am getting a new error. I found that originally my scans were backwards and flipped horizontally, which was part o the problem. Their pixel values were also off due to my poor HU mapping. I now have some data that works and some that doesn’t with the error text as follows

Traceback (most recent call last):
File “C:\Users\Physics 3\PycharmProjects\pythonProject\main.py”, line 9, in
print(mycbct.results())
^^^^^^^^^^^^^^^^
File “C:\Users\Physics 3\PycharmProjects\pythonProject\venv\Lib\site-packages\pylinac\ct.py”, line 2111, in results
f"MTF 80% (lp/mm): {self.ctp528.mtf.relative_resolution(80):2.2f}",
^^^^^^^^^^^^^^^
File “C:\Users\Physics 3\PycharmProjects\pythonProject\venv\Lib\site-packages\cached_property.py”, line 36, in get
value = obj.dict[self.func.name] = self.func(obj)
^^^^^^^^^^^^^^
File “C:\Users\Physics 3\PycharmProjects\pythonProject\venv\Lib\site-packages\pylinac\ct.py”, line 1126, in mtf
raise ValueError(
ValueError: Did not find any spatial resolution pairs to analyze. File an issue on github (https://github.com/jrkerns/pylinac/issues) if this is a valid dataset.

Process finished with exit code 1

I would greatly appreciate the assistance, I’ll also provide you with the data I’m using via the google form.