alexandreroutier
commented
4 years ago From Google Groups:
When using the convert
adni-to-bidscommand no matter which subset of data I use, I always receive this crash when its comes to the point of calculating paths of AV45 and Florbetaben PET images. I tried then with the flag for each modality and just as before only this one modality causes a crash. I am using clinica v0.3 and pandas is at v0.24.2 in my environment.PIB PET conversion done. Calculating paths of AV45 and Florbetaben PET images. Output will be stored in /home/grossi/Documents/ConversionTest/bids/conversion_info.
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*** Clinica crashed ***
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Exception type: IndexError
Exception value: single positional indexer is out-of-bounds Below are displayed information that were gathered when Clinica crashed.
This will help to understand what happened if you transfer those information to the Clinica development team.
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0 /home/grossi/miniconda3/envs/clinicaEnv/bin/clinica 10 sys.exit(execute()) 1 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/cmdline.py 521 execute args.func(args)
2 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids_cli.py 64 run_command args.modalities)
3 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids.py 145 convert_images adni_av45_fbb.convert_adni_av45_fbb_pet(source_dir, clinical_dir, dest_dir, subjs_list)
4 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/iotools/converters/adni_to_bids/adni_modalities/adni_av45_fbb_pet.py 41 convert_adni_av45_fbb_pet images = compute_av45_fbb_pet_paths(source_dir, csv_dir, dest_dir, subjs_list)
5 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/iotools/converters/adni_to_bids/adni_modalities/adni_av45_fbb_pet.py 106 compute_av45_fbb_pet_paths qc_visit = amyloid_qc_visit.iloc[0]
6 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/pandas/core/indexing.py 1500 __getitem__ return self._getitem_axis(maybe_callable, axis=axis)
7 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/pandas/core/indexing.py 2230 _getitem_axis self._validate_integer(key, axis) 8 /home/grossi/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/pandas/core/indexing.py 2139 _validate_integer raise IndexError("single positional indexer is out-of-bounds") ==================================================================================================================================================================================Alexandre
Hi!
With the help of @arnaudmarcoux, we identify some issues with the
adni-2-bidsconverter when used with thedevversion of Clinica:Possible regression issue: when converting a(n old) small ADNI sample, we noticed that T1w images were not more present in BIDS dataset.
Wrong BIDS FLAIR path: after convertsion, FLAIR images are stored under e.g.
sub-ADNI002S0295/ses-M60/FLAIR/sub-ADNI002S0295_ses-M60_FLAIR.{nii.gz|json}filename. Please read the BIDS specifications :FLAIRfolder does not exist, it should be inanatfolder.JSON files are missing for DWI files. When running manually
dcm2niix, JSON files are obtained from this ADNI sample. Ifdcm2niiis ran beforedcm2niix, I would advice to do the opposite. Indeed,dcm2niixalso compute needed field such asEffectiveEchoSpacingorTotalReadoutTime.Best, Alexandre