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How to run Tthe Run Preprocessing Pipeline successfully? #4

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HanBBBB opened this issue Oct 14, 2024 · 0 comments
Open

How to run Tthe Run Preprocessing Pipeline successfully? #4

HanBBBB opened this issue Oct 14, 2024 · 0 comments

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@HanBBBB
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HanBBBB commented Oct 14, 2024

When I ran this code
clinica convert adni-to-bids -m T1 E:\pycharm\AXIAL-main\dataset\ADNI1_Complete\ADNI E:\pycharm\AXIAL-main\CSV E:\pycharm\AXIAL-main\bids
at the very end of the execution, the following result was outputted.

2024-10-14 01:28:57,742:INFO:Paths of T1 images found. Exporting images into BIDS ...
2024-10-14 01:33:39,386:INFO:Creating modality agnostic files...
2024-10-14 01:33:39,415:INFO:Creating participants.tsv...
Traceback (most recent call last):
File "E:\Anaconda\envs\clinicaEnv\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "E:\Anaconda\envs\clinicaEnv\lib\runpy.py", line 86, in run_code
exec(code, run_globals)
File "E:\Anaconda\envs\clinicaEnv\Scripts\clinica.exe_main
.py", line 7, in
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\clinica\cmdline.py", line 92, in main
cli()
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\click\core.py", line 1157, in call
return self.main(*args, **kwargs)
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\click\core.py", line 1078, in main
rv = self.invoke(ctx)
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\click\core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\click\core.py", line 1688, in invoke
return process_result(sub_ctx.command.invoke(sub_ctx))
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\click\core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\click\core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\clinica\iotools\converters\adni_to_bids\adni_to_bids_cli.py", line 79, in cli
adni_to_bids.convert_clinical_data(
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\clinica\iotools\converters\adni_to_bids\adni_to_bids.py", line 123, in convert_clinical_data
participants_df = bids.create_participants_df(
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\clinica\iotools\bids_utils.py", line 115, in create_participants_df
file_to_read = load_clinical_csv(
File "E:\Anaconda\envs\clinicaEnv\lib\site-packages\clinica\iotools\converters\adni_to_bids\adni_utils.py", line 1650, in load_clinical_csv
raise IOError(
OSError: Expecting to find exactly one file in folder E:\pycharm\AXIAL-main\CSV matching pattern APOERES(
\d{1,2}[A-Za-z]{3}\d{4})?.csv. 0 files were found instead :
[- ]

Does this result have any impact on my subsequent operations?
Based on this, when I run this code,I encountered such an error. How can I resolve it?

python data_preprocessing.py --bids_path E:\pycharm\AXIAL-main\bids --n_proc 10 --checkpoint checkpoint.txt

1728889143409

I would greatly appreciate any guidance or suggestions you can provide, as it will help me with my next steps in research.

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