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aramis-lab / clinicadl

Framework for the reproducible processing of neuroimaging data with deep learning methods
https://clinicadl.readthedocs.io/
MIT License
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Seems A bug? cannot import name 'T1LinearCLI' from 'clinica.pipelines.t1_linear.t1_linear_cli #235

Closed fpeng2003 closed 3 years ago

fpeng2003 commented 3 years ago

I run my code and tutorial example, run into same error: cannot import name 'T1LinearCLI' from 'clinica.pipelines.t1_linear.t1_linear_cli

!clinicadl preprocessing quality-check t1-linear OasisCaps QC_result.tsv !clinicadl classify ./OasisCaps ./OasisCaps/participants.tsv ./model_exp3_splits_1 'test-Oasis'

Traceback (most recent call last): File "/usr/local/bin/clinicadl", line 8, in sys.exit(main()) File "/usr/local/lib/python3.7/dist-packages/clinicadl/main.py", line 9, in main parser = cli.parse_command_line() File "/usr/local/lib/python3.7/dist-packages/clinicadl/cli.py", line 378, in parse_command_line from clinica.pipelines.t1_linear.t1_linear_cli import T1LinearCLI ImportError: cannot import name 'T1LinearCLI' from 'clinica.pipelines.t1_linear.t1_linear_cli' (/usr/local/lib/python3.7/dist-packages/clinica/pipelines/t1_linear/t1_linear_cli.py)

Please help!

14thibea commented 3 years ago

Hello !

Current version of ClinicaDL does not support anymore t1-linear preprocessing, as it is now done by Clinica. To use it please use the command clinica run t1-linear and it should work!

fpeng2003 commented 3 years ago

Thank you very much for your quick response, it means a lot to me. I struggled a whole day on this issue. I followed the tutorial: https://aramislab.paris.inria.fr/clinicadl/tuto/Notebooks-AD-DL/preprocessing.html#tensor-extraction-with-the-deeplearning-prepare-data-pipeline. I did run the folllowing command without problem. !clinica run t1-linear ./OasisBids_example ./OasisCaps_example --n_procs 2

The problem commands are: !clinicadl preprocessing quality-check t1-linear OasisCaps QC_result.tsv !clinicadl classify ./OasisCaps ./OasisCaps/participants.tsv ./model_exp3_splits_1 'test-Oasis' it seems that everytime run clinicadl, same error appear. I even try to install clinicadl 1.0.3, even worse.

Would you please let me know the how to run:? what commands to use? !clinicadl preprocessing quality-check t1-linear OasisCaps QC_result.tsv !clinicadl classify ./OasisCaps ./OasisCaps/participants.tsv ./model_exp3_splits_1 'test-Oasis'

Where to find correct tutorial?

Thanks a lot

14thibea commented 3 years ago

Hello,

The tutorials were not updated with the latest versions (sorry for that, it will be done soon) You will find the correct commands in the documentation which is up-to-date

The correct commands would be: clinicadl quality-check t1-linear CAPS_DIRECTORY OUTPUT_TSV clinicadl predict INPUT_MAPS_DIRECTORY DATA_GROUP

fpeng2003 commented 3 years ago

Thank you very much for your response. I really like your tutorial, clear and practical. Do you know any tool to process OASIS-3 Dataset, or any example program? Thanks

14thibea commented 3 years ago

Hello,

The BIDS converter of OASIS-3 was recently added to Clinica (https://aramislab.paris.inria.fr/clinica/docs/public/latest/Converters/OASIS3TOBIDS/) It works on the same way than the OASIS-1 converter, once converted you can use the other tools of Clinica / ClinicaDL on it! If you have any issue using this converter please open an issue on Clinica repo https://github.com/aramis-lab/clinica

SonaLily commented 3 years ago

Hello, I am fpeng2003, but with another account. I did test and got errors. I post my questions here: https://github.com/aramis-lab/clinica/issues/458 Issue: error !clinica convert oasis3-to-bids Oasis3test Oasis3test/ClinicalData Oasis3BidsRun #458

================== I got error when I do: !clinica convert oasis3-to-bids Oasis3test Oasis3test/ClinicalData Oasis3BidsRun

File "/usr/local/lib/python3.7/dist-packages/clinica/iotools/converters/oasis3_to_bids/oasis3_utils.py", line 47, in find_clinical_data raise FileNotFoundError("Clinical data not found or incomplete") FileNotFoundError: Clinical data not found or incomplete

I do have this file in Oasis3test/ClinicalData: ADRCclinicalData.csv which I downloaded from xnat. My question is: Is any special requirement on this file? is it possible you can provide an file with correct format?

I also tried to dowdload Bids directly from xnat and tried to process those data by:

!clinica run t1-linear Oasis3BIDStest Oasis3Cap --n_procs 2 I got following message: 2021-10-10 12:13:47,002:WARNING:Could not determine if /content/gdrive/MyDrive/AIOasis3Azheimer/Oasis3Cap is a CAPS or BIDS directory. Clinica will assume this is a CAPS directory. 2021-10-10 12:13:50,102:ERROR:Clinica faced error(s) while trying to read files in your BIDS directory. Clinica encountered 4 problem(s) while getting T1w MRI:

My question is: is it possible to process bids files downloaded directly from Oasis3 by clinica? if yes, how to do?

Thanks a lot!

ghisvail commented 3 years ago

@SonaLily please avoid double posting to facilitate support. Thanks.

14thibea commented 3 years ago

I am closing this issue as it was answered on Clinica repo https://github.com/aramis-lab/clinica/issues/458.