ClinicaDL tsvtools "get-labels": Failed!

Shahzad ALi

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Apr 29, 2025, 5:00:05 PMApr 29

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Dear Camille,

Thank you for your support. I’m using the following command in clinicadl to get labels for ADNI data:

clinicadl tsvtools get-labels BIDS_Dir output_dir --missing_mods Summary/missing_mods/ --merged_tsv Summary/merged.tsv --modality t1w -d CN -d AD -d MCI --keep_smc

And it giving the error:

13:36:05 - output of clinica iotools check-missing-modalities: BIDS_Dir/Summary/missing_mods
INFO:clinicadl.tsvtools:output of clinica iotools check-missing-modalities: BIDS_Dir/Summary/missing_mods
13:36:06 - Dropped subjects (bad session name, example ses-Nv): 0
INFO:clinicadl.tsvtools:Dropped subjects (bad session name, example ses-Nv): 0
13:36:06 - Missing diagnoses: 6342
INFO:clinicadl:Missing diagnoses: 6342
13:36:06 - Missing diagnoses not found: 6342
INFO:clinicadl:Missing diagnoses not found: 6342
Traceback (most recent call last):
File "/Users/user/miniconda3/envs/clinicadlEnv/bin/clinicadl", line 8, in <module>
sys.exit(cli())
   ^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/click/core.py", line 1161, in __call__
return self.main(*args, **kwargs)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/click/core.py", line 1082, in main
rv = self.invoke(ctx)
   ^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/click/core.py", line 1697, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/click/core.py", line 1443, in invoke
return ctx.invoke(self.callback, **ctx.params)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/click/core.py", line 788, in invoke
return __callback(*args, **kwargs)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/clinicadl/tsvtools/get_labels/get_labels_cli.py", line 78, in cli
get_labels(
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/clinicadl/tsvtools/get_labels/get_labels.py", line 379, in get_labels
missing_mods_df = pd.read_csv(file, sep="\t")
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/pandas/util/_decorators.py", line 211, in wrapper
return func(*args, **kwargs)
   ^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/pandas/util/_decorators.py", line 331, in wrapper
return func(*args, **kwargs)
   ^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
return _read(filepath_or_buffer, kwds)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 605, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1442, in __init__
self._engine = self._make_engine(f, self.engine)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1753, in _make_engine
return mapping[engine](f, **self.options)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/user/miniconda3/envs/clinicadlEnv/lib/python3.11/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 79, in __init__
self._reader = parsers.TextReader(src, **kwds)
   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pandas/_libs/parsers.pyx", line 547, in pandas._libs.parsers.TextReader.__cinit__
File "pandas/_libs/parsers.pyx", line 636, in pandas._libs.parsers.TextReader._get_header
File "pandas/_libs/parsers.pyx", line 852, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1965, in pandas._libs.parsers.raise_parser_error
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb0 in position 37: invalid start byte

Could you guide me on how to proceed? I have attached the contents of missing_mods directory (attached screenshot).

Thanks in advance!

Best,

Shahzad

-----------------------------------------------------------------------

missing_mods_dir.png

Shahzad ALi

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May 2, 2025, 7:38:49 AMMay 2

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Hi Dear Camille,

Can you help me in resolving this issue?

Best,

Shahzad

-----------------------------------------------------------------------

camille brianceau

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May 5, 2025, 3:12:09 AMMay 5

to Clinica

Hi Shahzad,

It seems like your issue isn’t related to ClinicaDL, but rather to your TSV file, which is likely corrupted or improperly formatted. I recommend checking the structure—make sure it's tab-separated, includes the correct headers, and doesn’t contain any unexpected characters.

If everything looks normal on your side, feel free to come back to me, and we can look into it further.