series_name doesn't work as expected

[markus-hinsche]

I have a directory full of DICOM files of different series:

• series "38" has 96 slices,
• series "34" has 96 slices,
• series "46" has 88 slices,
• series "42" has 88 slices,

I use the following code to read

tfm = monai.transforms.LoadImage(series_name='42', series_meta=True)
pixel_arr, meta = tfm("path/to/dir/with/dicoms")

Since I am dealing with DICOM files(don't have .dcm ending though), I would expect ITKReader to be the reader that will be used.

However I get the following output: https://gist.github.com/markus-hinsche/c78278f462b10d72b4ccdd9cd14be712

I think the reason is that name = names_generator.GetFileNames(series_identifier) in

MONAI/monai/data/image_reader.py

Line 265 in b030839

name = names_generator.GetFileNames(series_identifier)

sets name = ()(empty tuple) because GetFileNames doesn't work as expected.

In contrast when running

tfm = monai.transforms.LoadImage()
pixel_arr, meta = tfm("path/to/dir/with/dicoms")

I get 96 slices (because pixel_arr shape is (320, 260, 96)), so it reads the first series.

Any idea how I can get a specific series name?

[kbressem]

ITKReader accepts the argument series_name.

You can initialize the reader and pass it to LoadImage.

https://docs.monai.io/en/stable/data.html#itkreader

series_name (str) – the name of the DICOM series if there are multiple ones. used when loading DICOM series.