ERROR: screenshots/fornix module failed for subject ...
RDoerfel opened this issue · comments
Description
When running
python qatools.py --subjects_dir /indirect/tmp_brainage/data/derivatives/freesurfer --output_dir /indirect/tmp_brainage/data/derivatives/freesurfer_qc --screenshots --fornix --outlier --screenshots-html --fornix-html --subjects sub-ADNI002S0413_ses-M000
I'm getting two errors:
ERROR: screenshots module failed for subject ... ``ERROR: fornix module failed for subject ...
I get the summary measures in the end, but no screenshots, etc. are appearing.
Also, I had problems during the installation process. I used the following steps:
conda create -n qatools python==3.8
conda activate qatools
pip3 install --user git+https://github.com/Deep-MI/BrainPrint-python.git
pip3 install --user git+https://github.com/Deep-MI/LaPy.git
pip3 install --user -r requirements.txt
When running, it is missing skimage, so I had to install it by hand.
When digging into it:
It fails in:
With:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/users/rubendorfel/.conda/envs/qatools/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/users/rubendorfel/.conda/envs/qatools/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 586, in read_csv
return _read(filepath_or_buffer, kwds)
File "/users/rubendorfel/.conda/envs/qatools/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 488, in _read
return parser.read(nrows)
File "/users/rubendorfel/.conda/envs/qatools/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1047, in read
index, columns, col_dict = self._engine.read(nrows)
File "/users/rubendorfel/.conda/envs/qatools/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 223, in read
chunks = self._reader.read_low_memory(nrows)
File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory
File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1925, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 6 fields in line 82, saw 7
Regarding to this it can be solved using:
on_bad_lines='skip' instead of error_bad_lines=False in pd.read_csv(...)
Hello, thanks for reporting this issue and also for looking into it. We are currently working on a major revision of the toolbox that addresses e.g. dependency issues, and issues with the screenshots module. Maybe one option for you is to try the 'freesurfer-module-dev' branch, which has some more recent updates than the default branch.
Great, I'll do that!
If you need any help in development/testing, let me know @kdiers. Think it is quite a helpful tool for qc-ing big datasets
Thank you very much. We are working on releasing the new version of the toolbox until end of this month, so around that time some tests and feedback would be very useful - if it fits, of course.
We have now released version 2.0, and the reported issues should be solved, therefore closing this issue now. Feel free to go ahead with some testing if you like, and to reopen this issue if anything persists. Thanks!
great work @kdiers and right in time! I'll give it a shoot next week.