bugs in lung1 dataset preprocess

[yanniangu]

I downloaded the lung1 dataset using the lung1.sh script and ran data/preprocessing/lung1/preprocess.ipynb to generate the annotations.csv file. However, when executing the following line in the notebook:

preprocessed_df = build_image_seed_dict(download_dir)

I encountered the following error:

_RemoteTraceback                          Traceback (most recent call last):
_RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/ailab/user/leiwenhui/.conda/envs/gyn/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/ailab/user/leiwenhui/.conda/envs/gyn/lib/python3.10/concurrent/futures/process.py", line 205, in _process_chunk
    return [fn(*args) for args in chunk]
  File "/ailab/user/leiwenhui/.conda/envs/gyn/lib/python3.10/concurrent/futures/process.py", line 205, in <listcomp>
    return [fn(*args) for args in chunk]
  File "/ailab/user/leiwenhui/.conda/envs/gyn/lib/python3.10/site-packages/fmcib/utils/idc_helper.py", line 225, in process_series_dir
    mask = sitk.ReadImage(str(list(series_dir.glob("*GTV-1*"))[0]))
IndexError: list index out of range
"""

The error above was caused by the following exception:

IndexError                                Traceback (most recent call last)
Cell In[6], [line 1](vscode-notebook-cell:?execution_count=6&line=1)
----> [1](vscode-notebook-cell:?execution_count=6&line=1) preprocessed_df = build_image_seed_dict(
      [2](vscode-notebook-cell:?execution_count=6&line=2)     download_dir
      [3](vscode-notebook-cell:?execution_count=6&line=3) )  # samples=5 is for testing purposes. Remove it to pre-process all images

File ~/.conda/envs/gyn/lib/python3.10/site-packages/fmcib/utils/idc_helper.py:273, in build_image_seed_dict(path, samples)
...
    [404](https://vscode-remote+ssh-002dremote-002bleiwenhui.vscode-resource.vscode-cdn.net/ailab/user/leiwenhui/gyn/foundation-cancer-image-biomarker/data/preprocessing/lung1/~/.conda/envs/gyn/lib/python3.10/concurrent/futures/_base.py:404)     finally:
    [405](https://vscode-remote+ssh-002dremote-002bleiwenhui.vscode-resource.vscode-cdn.net/ailab/user/leiwenhui/gyn/foundation-cancer-image-biomarker/data/preprocessing/lung1/~/.conda/envs/gyn/lib/python3.10/concurrent/futures/_base.py:405)         # Break a reference cycle with the exception in self._exception
    [406](https://vscode-remote+ssh-002dremote-002bleiwenhui.vscode-resource.vscode-cdn.net/ailab/user/leiwenhui/gyn/foundation-cancer-image-biomarker/data/preprocessing/lung1/~/.conda/envs/gyn/lib/python3.10/concurrent/futures/_base.py:406)         self = None

IndexError: list index out of range
``

This issue arises in the `process_series_dir` function in the `idc_helper.py` file when attempting to read the image using `sitk.ReadImage` from a directory containing `GTV-1` in its name. The error occurs because the list created by `series_dir.glob("*GTV-1*")` is empty, leading to an `IndexError` when attempting to access the first element.