adni-to-bids conversion error in PET data #868

takaakiyoshim · 2023-01-18T07:53:07Z

takaakiyoshim
Jan 18, 2023

Hi.
I tried to convert ADNI data including T1w, fmri and PET by using adni-to-bids function, but PET could not be converted.
I tried to do again by using "-m PET AMYLOID" option, but it failed.
Additionnally, I ran t1-freesurfer pipeline successfully in my environment.

Input is like this

clinica -v convert adni-to-bids /mnt/nasNew10_Yoshimoto/ADNI/Subjects_ADNI3_InitialVisitCont_CN_MCI_3Modalities/RawData/ADNI /mnt/nasNew10_Yoshimoto/ADNI/csv_ADNI /mnt/nasNew10_Yoshimoto/ADNI/Subjects_ADNI3_InitialVisitCont_CN_MCI_3Modalities/BIDS_output -m PET_AMYLOID

Output looked like this

Traceback (most recent call last):
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/bin/clinica", line 8, in <module>
    sys.exit(main())
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/cmdline.py", line 92, in main
    cli()
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids_cli.py", line 74, in cli
    adni_to_bids.convert_clinical_data(
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids.py", line 154, in convert_clinical_data
    adni_utils.create_adni_scans_files(conversion_path, bids_subjs_paths)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py", line 881, in create_adni_scans_files
    conversion_df = converted_dict[converted_mod]
KeyError: 't1'

My environment is
Ubuntsu 20.04.3 LTS
Clinica environment is
conda 22.11.1
python3.10.8

I think that it is simlar issue as below.
#394

Do you have any solution about it?

Answered by ghisvail

Jan 18, 2023

@takaakiyoshim Thanks for providing detailed information about your issue.

I tried to convert ADNI data including T1w, fmri and PET by using adni-to-bids function, but PET could not be converted.

Could you please give us a minimal example which we can use to reproduce the issue? A list of subjects for the collection you downloaded from ADNI would be a good starting point.

Best regards,
Ghis

View full answer

ghisvail · 2023-01-18T09:32:10Z

ghisvail
Jan 18, 2023

@takaakiyoshim Thanks for providing detailed information about your issue.

I tried to convert ADNI data including T1w, fmri and PET by using adni-to-bids function, but PET could not be converted.

Could you please give us a minimal example which we can use to reproduce the issue? A list of subjects for the collection you downloaded from ADNI would be a good starting point.

Best regards,
Ghis

2 replies

takaakiyoshim Jan 18, 2023
Author

Thank you for your kind reply.

Attached file is list of subjects in downloaded data.
idaSearch_1_03_2023.csv

For example, I made subject list which contained only "002_s_0413", and tried to run as bellow.

clinica -v convert adni-to-bids --subjects_list=sublist.txt /mnt/nasNew10_Yoshimoto/ADNI/Subjects_ADNI3_InitialVisitCont_CN_MCI_3Modalities/RawData/ADNI /mnt/nasNew10_Yoshimoto/ADNI/csv_ADNI /mnt/nasNew10_Yoshimoto/ADNI/Subjects_ADNI3_InitialVisitCont_CN_MCI_3Modalities/BIDS_output02

Tree of input directory as bellow.

.
├── Accelerated_Sagittal_MPRAGE
├── ADNI_Brain_PET__Raw_AV45
├── ADNI_Brain_PET__Raw_Tau
├── Axial_3D_PASL__Eyes_Open_
├── Axial_rsfMRI__Eyes_Open_
├── Axial_T2_STAR
├── Field_Mapping
├── HighResHippocampus
├── Perfusion_Weighted
└── Sagittal_3D_FLAIR

Tree of output directory as bellow. It did not contain nifity PET data.

├── ses-M132
│   ├── anat
│   ├── func
│   └── sub-ADNI002S0413_ses-M132_scans.tsv
└── sub-ADNI002S0413_sessions.tsv

Best regards,
Takaaki

ghisvail Jan 18, 2023

Sounds to me that you downloaded the raw PET data without preprocessing, am I correct?

Clinica looks for preprocessed PET data tagged Co-registered, Averaged. Make sure you enabled Pre-processed in the IMAGE TYPES section of the search options of the ADNI advanced search form. The search results should look like the following screenshot below.

takaakiyoshim · 2023-01-18T15:31:53Z

takaakiyoshim
Jan 18, 2023
Author

It's very thankful advice !
I have downloaded preprocessed PET data as bellow.

├── AV1451_Coreg,_Avg,_Standardized_Image_and_Voxel_Size
├── AV1451_Coreg,_Avg,_Std_Img_and_Vox_Siz,_Uniform_6mm_Res
├── AV1451_Coreg,_Avg,_Std_Img_and_Vox_Siz,_Uniform_Resolution
├── AV1451_Co-registered,_Averaged
├── AV1451_Co-registered_Dynamic
├── AV45_Coreg,_Avg,_Standardized_Image_and_Voxel_Size
├── AV45_Coreg,_Avg,_Std_Img_and_Vox_Siz,_Uniform_6mm_Res
├── AV45_Coreg,_Avg,_Std_Img_and_Vox_Siz,_Uniform_Resolution
├── AV45_Co-registered,_Averaged
└── AV45_Co-registered_Dynamic

I ran adni-to-bids again , but same error such as my first post was reproduced.

clinica -v convert adni-to-bids /mnt/nasNew10_Yoshimoto/ADNI/Subjects_ADNI3_InitialVisitCont_CN_MCI_3Modalities/RawData_PET/ADNI /mnt/nasNew10_Yoshimoto/ADNI/csv_ADNI /mnt/nasNew10_Yoshimoto/ADNI/Subjects_ADNI3_InitialVisitCont_CN_MCI_3Modalities/BIDS_output -m PET_AMYLOID

Traceback (most recent call last):
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/bin/clinica", line 8, in <module>
    sys.exit(main())
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/cmdline.py", line 92, in main
    cli()
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids_cli.py", line 74, in cli
    adni_to_bids.convert_clinical_data(
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids.py", line 154, in convert_clinical_data
    adni_utils.create_adni_scans_files(conversion_path, bids_subjs_paths)
  File "/home/yoshimoto/miniconda3/envs/clinicaEnv/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py", line 881, in create_adni_scans_files
    conversion_df = converted_dict[converted_mod]
KeyError: 't1'

1 reply

takaakiyoshim Jan 20, 2023
Author

In the previous post, I specified different input directories between fmri and T1w data and PET data, and same bids output directroy.
Now, I have specified output directory for PET data and run again, it works well.

Thank you for your kind instruction!

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