adni-to-bids fails to find pet tau paths AND no key adas_q1

[shaharEd]

I run adni-to-bids from clinica, on modalities T1 and pet_tau. while the command creates successfully the bids directories of the T1s, it fails to find the PET-tau directories - meaning, in 18FAV1451_pet_paths the path column contains only empty cells - therefore fails to export them to the BIDS directory.
In addition, during the excecution, I get this error:
Traceback (most recent call last): File "/home/shaharedelman/AMN/bin/clinica", line 8, in <module> sys.exit(main()) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/clinica/cmdline.py", line 92, in main cli() File "/home/shaharedelman/AMN/lib/python3.10/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids_cli.py", line 79, in cli adni_to_bids.convert_clinical_data( File "/home/shaharedelman/AMN/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids.py", line 145, in convert_clinical_data adni_utils.create_adni_sessions_dict( File "/home/shaharedelman/AMN/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py", line 978, in create_adni_sessions_dict write_adni_sessions_tsv(df_subj_session, bids_subjs_paths) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py", line 707, in write_adni_sessions_tsv df_subj_sessions["adas_Q1"] File "/home/shaharedelman/AMN/lib/python3.10/site-packages/pandas/core/frame.py", line 3807, in __getitem__ indexer = self.columns.get_loc(key) File "/home/shaharedelman/AMN/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3804, in get_loc raise KeyError(key) from err KeyError: 'adas_Q1'

Information

The command I ran:
clinica convert adni-to-bids --subjects_list subjects.txt ADNI/ ClinicalDatareduced/ BIDS3

The output:
2024-02-13 18:38:19,131:INFO:Loading a subjects lists provided by the user... 2024-02-13 18:38:19,158:INFO:Calculating paths of TAU PET images. Output will be stored in /mnt/d/ADNI_ShaharAndMeitar/BIDS3/conversion_info/v0. 2024-02-13 18:38:19,943:INFO:No TAU image path found for subject 011_S_6303 in visit bl with image ID 995807 2024-02-13 18:38:20,108:INFO:No TAU image path found for subject 011_S_6303 in visit m12 with image ID 1174084 2024-02-13 18:38:20,752:INFO:No TAU image path found for subject 022_S_6796 in visit bl with image ID 1236620 2024-02-13 18:38:21,020:INFO:No TAU image path found for subject 022_S_6796 in visit m12 with image ID 1343474 2024-02-13 18:38:21,325:INFO:No TAU image path found for subject 022_S_6796 in visit m24 with image ID 1487881 2024-02-13 18:38:21,640:INFO:No TAU image path found for subject 032_S_6600 in visit bl with image ID 1074907 2024-02-13 18:38:21,815:INFO:No TAU image path found for subject 032_S_6600 in visit m12 with image ID 1259805 2024-02-13 18:38:22,056:INFO:No TAU image path found for subject 036_S_6231 in visit bl with image ID 999915 2024-02-13 18:38:22,476:INFO:No TAU image path found for subject 100_S_6713 in visit bl with image ID 1170558 2024-02-13 18:38:22,711:INFO:No TAU image path found for subject 100_S_6713 in visit m30 with image ID 1544842 2024-02-13 18:38:23,387:INFO:No TAU image path found for subject 116_S_6543 in visit bl with image ID 1051991 2024-02-13 18:38:23,628:INFO:No TAU image path found for subject 116_S_6543 in visit m12 with image ID 1215182 2024-02-13 18:38:24,347:INFO:No TAU image path found for subject 135_S_6389 in visit bl with image ID 1020506 2024-02-13 18:38:24,545:INFO:No TAU image path found for subject 135_S_6389 in visit m12 with image ID 1187730 2024-02-13 18:38:24,803:INFO:No TAU image path found for subject 135_S_6389 in visit m24 with image ID 1327965 2024-02-13 18:38:24,923:INFO:No TAU image path found for subject 168_S_6843 in visit bl with image ID 1304853 2024-02-13 18:38:25,114:INFO:No TAU image path found for subject 305_S_6810 in visit m12 with image ID 1405852 2024-02-13 18:38:25,284:INFO:No TAU image path found for subject 305_S_6810 in visit m24 with image ID 1524971 2024-02-13 18:38:25,569:INFO:No TAU image path found for subject 941_S_6962 in visit bl with image ID 1482712 2024-02-13 18:38:25,680:INFO:No TAU image path found for subject 941_S_6962 in visit m12 with image ID 1606692 2024-02-13 18:38:26,428:INFO:No TAU image path found for subject 016_S_6839 in visit bl with image ID 1296385 2024-02-13 18:38:26,654:INFO:No TAU image path found for subject 016_S_6839 in visit m12 with image ID 1439331 2024-02-13 18:38:26,902:INFO:No TAU image path found for subject 027_S_6648 in visit bl with image ID 1134392 2024-02-13 18:38:27,170:INFO:No TAU image path found for subject 035_S_7001 in visit bl with image ID 1546611 2024-02-13 18:38:27,417:INFO:No TAU image path found for subject 098_S_6601 in visit bl with image ID 1092129 2024-02-13 18:38:28,370:INFO:No TAU image path found for subject 116_S_6100 in visit bl with image ID 977849 2024-02-13 18:38:28,667:INFO:No TAU image path found for subject 116_S_6100 in visit m12 with image ID 1119630 2024-02-13 18:38:29,044:INFO:No TAU image path found for subject 116_S_6100 in visit m24 with image ID 1282760 2024-02-13 18:38:29,619:INFO:No TAU image path found for subject 127_S_6549 in visit bl with image ID 1071354 2024-02-13 18:38:29,806:INFO:No TAU image path found for subject 127_S_6549 in visit m12 with image ID 1245605 2024-02-13 18:38:29,998:INFO:No TAU image path found for subject 127_S_6549 in visit m24 with image ID 1359916 2024-02-13 18:38:30,288:INFO:No TAU image path found for subject 135_S_6840 in visit bl with image ID 1270381 2024-02-13 18:38:30,632:INFO:No TAU image path found for subject 301_S_6592 in visit bl with image ID 1074132 2024-02-13 18:38:30,814:INFO:No TAU image path found for subject 301_S_6592 in visit m12 with image ID 1261267 2024-02-13 18:38:30,954:INFO:No TAU image path found for subject 341_S_6820 in visit bl with image ID 1261271 2024-02-13 18:38:30,964:INFO:Paths of TAU PET images found. Exporting images into BIDS ... 2024-02-13 18:38:30,998:INFO:[TAU] No path specified for 011_S_6303 in session bl 2024-02-13 18:38:30,999:INFO:[TAU] No path specified for 032_S_6600 in session m12 2024-02-13 18:38:30,999:INFO:[TAU] No path specified for 022_S_6796 in session bl 2024-02-13 18:38:30,999:INFO:[TAU] No path specified for 032_S_6600 in session bl 2024-02-13 18:38:30,999:INFO:[TAU] No path specified for 011_S_6303 in session m12 2024-02-13 18:38:31,000:INFO:[TAU] No path specified for 016_S_6839 in session bl 2024-02-13 18:38:31,000:INFO:[TAU] No path specified for 941_S_6962 in session m12 2024-02-13 18:38:31,000:INFO:[TAU] No path specified for 016_S_6839 in session m12 2024-02-13 18:38:31,000:INFO:[TAU] No path specified for 027_S_6648 in session bl 2024-02-13 18:38:30,999:INFO:[TAU] No path specified for 022_S_6796 in session m12 2024-02-13 18:38:31,000:INFO:[TAU] No path specified for 036_S_6231 in session bl 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 116_S_6100 in session bl 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 022_S_6796 in session m24 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 035_S_7001 in session bl 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 116_S_6100 in session m12 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 127_S_6549 in session bl 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 100_S_6713 in session bl 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 116_S_6100 in session m24 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 135_S_6840 in session bl 2024-02-13 18:38:31,001:INFO:[TAU] No path specified for 301_S_6592 in session m12 2024-02-13 18:38:31,002:INFO:[TAU] No path specified for 127_S_6549 in session m12 2024-02-13 18:38:31,002:INFO:[TAU] No path specified for 301_S_6592 in session bl 2024-02-13 18:38:31,002:INFO:[TAU] No path specified for 098_S_6601 in session bl 2024-02-13 18:38:31,002:INFO:[TAU] No path specified for 341_S_6820 in session bl 2024-02-13 18:38:31,002:INFO:[TAU] No path specified for 127_S_6549 in session m24 2024-02-13 18:38:31,002:INFO:[TAU] No path specified for 116_S_6543 in session bl 2024-02-13 18:38:31,003:INFO:[TAU] No path specified for 135_S_6389 in session bl 2024-02-13 18:38:31,003:INFO:[TAU] No path specified for 135_S_6389 in session m12 2024-02-13 18:38:31,003:INFO:[TAU] No path specified for 116_S_6543 in session m12 2024-02-13 18:38:31,003:INFO:[TAU] No path specified for 100_S_6713 in session m30 2024-02-13 18:38:31,003:INFO:[TAU] No path specified for 135_S_6389 in session m24 2024-02-13 18:38:31,003:INFO:[TAU] No path specified for 305_S_6810 in session m24 2024-02-13 18:38:31,003:INFO:[TAU] No path specified for 305_S_6810 in session m12 2024-02-13 18:38:31,005:INFO:[TAU] No path specified for 941_S_6962 in session bl 2024-02-13 18:38:31,005:INFO:[TAU] No path specified for 168_S_6843 in session bl 2024-02-13 18:38:31,034:INFO:Creating modality agnostic files... 2024-02-13 18:38:31,068:INFO:Creating participants.tsv...

The directory of the ADNI contains only samples and look like this:
`.
└── ADNI
├── 011_S_6303
│   ├── ADNI3_AV1451__AC__Tau
│   │   ├── 2018-05-07_14_01_16.0
│   │   │   └── I994488
│   │   └── 2019-05-28_13_32_37.0
│   │   └── I1169561
│   └── Accelerated_Sagittal_MPRAGE
│   ├── 2018-04-12_13_06_54.0
│   │   └── I985197
│   └── 2019-04-30_09_41_30.0
│   └── I1160021
├── 016_S_6839
│   ├── ADNI_Brain_AC_3D_Tau
│   │   ├── 2020-02-05_16_47_59.0
│   │   │   └── I1288854
│   │   └── 2021-03-31_16_53_00.0
│   │   └── I1430126
│   ├── Accelerated_Sagittal_MPRAGE
│   │   ├── 2019-12-03_14_08_15.0
│   │   │   └── I1263249
│   │   ├── 2021-03-25_15_29_33.0
│   │   │   └── I1426627
│   │   └── 2022-05-25_08_01_32.0
│   │   └── I1584529
│   └── Accelerated_Sagittal_MPRAGE_REPEAT
│   └── 2022-05-25_08_01_32.0
│   └── I1584509
├── 022_S_6796
│   ├── ADNI_Brain_PET__Raw_Tau
│   │   ├── 2019-09-26_15_04_49.0
│   │   │   └── I1234740
│   │   ├── 2020-09-23_15_23_37.0
│   │   │   └── I1343146
│   │   └── 2021-08-31_16_43_43.0
│   │   └── I1487007
│   └── Accelerated_Sagittal_MPRAGE
│   ├── 2019-09-03_15_16_30.0
│   │   └── I1223029
│   ├── 2020-09-09_09_04_03.0
│   │   └── I1342083
│   └── 2021-08-24_12_59_15.0
│   └── I1484349
├── 027_S_6648
│   ├── ADNI_Brain_PET__Raw_Tau
│   │   └── 2019-02-19_15_56_49.0
│   │   └── I1132743
│   └── Accelerated_Sagittal_IR-FSPGR
│   └── 2019-01-02_13_58_31.0
│   └── I1108061
├── 032_S_6600
│   ├── ADNI_Brain_PET__Raw_Tau
│   │   ├── 2018-11-15_14_22_03.0
│   │   │   └── I1073404
│   │   └── 2019-11-19_15_20_05.0
│   │   └── I1258425
│   └── Accelerated_Sagittal_MPRAGE
│   ├── 2018-10-19_07_41_54.0
│   │   └── I1061844
│   └── 2019-11-21_13_55_35.0
│   └── I1259263
├── 035_S_7001
│   ├── ADNI_3_FLORTAUCIPIR__AC_
│   │   └── 2022-02-15_14_35_01.0
│   │   └── I1545727
│   └── Accelerated_Sagittal_MPRAGE_Phase_A-P
│   └── 2021-10-21_13_59_50.0
│   └── I1509946
├── 036_S_6231
│   ├── ADNI3-TAU-2__AC_
│   │   └── 2018-04-05_16_12_13.0
│   │   └── I999010
│   └── Accelerated_Sagittal_MPRAGE
│   └── 2018-03-05_12_34_45.0
│   └── I973656
├── 098_S_6601
│   ├── ANONYMIZED_Tau
│   │   └── 2018-12-07_15_38_01.0
│   │   └── I1083868
│   └── Sag_Accel_IR-FSPGR
│   └── 2018-10-16_11_35_56.0
│   └── I1061746
├── 100_S_6713
│   ├── DYNAMIC_Brain_AC
│   │   └── 2022-02-09_16_39_01.0
│   │   └── I1543478
│   ├── DYNAMIC_Brain_AC_Tau
│   │   └── 2019-05-28_17_31_49.0
│   │   └── I1169287
│   └── Sagittal_3D_Accelerated_MPRAGE
│   ├── 2019-04-18_15_00_39.0
│   │   └── I1156438
│   ├── 2021-09-01_14_12_11.0
│   │   └── I1487245
│   └── 2022-08-30_14_06_17.0
│   └── I1617908
├── 116_S_6100
│   ├── Accelerated_Sagittal_MPRAGE
│   │   ├── 2017-10-31_11_07_13.0
│   │   │   └── I1092329
│   │   ├── 2019-01-25_11_42_31.0
│   │   │   └── I1120772
│   │   └── 2020-01-29_08_23_13.0
│   │   └── I1281547
│   ├── Accelerated_Sagittal_MPRAGE_ND
│   │   ├── 2017-10-31_11_07_13.0
│   │   │   └── I1092326
│   │   ├── 2019-01-25_11_42_31.0
│   │   │   └── I1120771
│   │   └── 2020-01-29_08_23_13.0
│   │   └── I1281545
│   └── PET_AV-1451_6x5__Tau
│   ├── 2018-03-09_15_57_45.0
│   │   └── I971992
│   ├── 2019-01-18_15_42_18.0
│   │   └── I1118166
│   └── 2020-01-29_13_08_02.0
│   └── I1282058
├── 116_S_6543
│   ├── Accelerated_Sagittal_MPRAGE
│   │   ├── 2018-08-21_09_14_55.0
│   │   │   └── I1038941
│   │   └── 2019-12-02_11_38_53.0
│   │   └── I1261558
│   ├── Accelerated_Sagittal_MPRAGE_ND
│   │   ├── 2018-08-21_09_14_55.0
│   │   │   └── I1038940
│   │   └── 2019-12-02_11_38_53.0
│   │   └── I1261559
│   └── PET_AV-1451_6x5__Tau
│   ├── 2018-09-24_14_35_38.0
│   │   └── I1051418
│   └── 2019-08-16_15_16_13.0
│   └── I1212547
├── 127_S_6549
│   ├── AV_1451_30_MIN_DYN_Tau
│   │   ├── 2019-10-18_15_40_04.0
│   │   │   └── I1243166
│   │   └── 2020-10-29_15_40_01.0
│   │   └── I1358596
│   └── Accelerated_Sagittal_IR-FSPGR
│   ├── 2019-10-18_13_10_17.0
│   │   └── I1243100
│   └── 2020-10-29_13_08_02.0
│   ├── I1358465
│   └── I1358466
├── 135_S_6389
│   ├── Accelerated_Sag_IR-FSPGR
│   │   ├── 2018-05-29_14_10_21.0
│   │   │   └── I1003730
│   │   ├── 2019-07-09_10_47_37.0
│   │   │   └── I1185266
│   │   └── 2020-07-29_09_52_25.0
│   │   └── I1325980
│   └── Dyn_Brain_VPHD_6i16s_AC_Tau
│   ├── 2018-07-03_15_52_04.0
│   │   └── I1017333
│   ├── 2019-07-09_15_57_10.0
│   │   └── I1185100
│   └── 2020-07-28_14_53_32.0
│   └── I1325727
├── 135_S_6840
│   ├── Accelerated_Sag_IR-FSPGR
│   │   └── 2019-12-05_15_20_25.0
│   │   └── I1263423
│   └── Dyn_Brain_VPHD_6i16s_AC_Tau
│   └── 2019-12-16_16_14_27.0
│   └── I1267327
├── 168_S_6843
│   └── ADNI_AC_Tau
│   └── 2020-03-17_14_34_01.0
│   └── I1304642
├── 301_S_6592
│   ├── ADNI3_3D_AC_Tau
│   │   └── 2018-11-13_14_15_02.0
│   │   └── I1073650
│   ├── ANONYMIZED_Tau
│   │   └── 2019-11-21_13_29_15.0
│   │   └── I1259707
│   └── Sagittal_3D_Accelerated_MPRAGE
│   ├── 2018-10-23_11_52_57.0
│   │   └── I1063917
│   └── 2019-11-19_12_33_02.0
│   └── I1258251
├── 305_S_6810
│   ├── ADNI_Brain_PET__Raw_Tau
│   │   └── 2021-01-05_16_06_09.0
│   │   └── I1405489
│   └── Sagittal_3D_Accelerated_MPRAGE
│   ├── 2019-11-02_10_38_41.0
│   │   └── I1252573
│   └── 2020-12-07_14_11_10.0
│   └── I1384753
├── 341_S_6820
│   ├── Accelerated_Sagittal_MPRAGE
│   │   └── 2019-09-25_11_22_22.0
│   │   └── I1231978
│   └── PET_AC_TAU
│   └── 2019-11-21_14_20_02.0
│   └── I1259828
└── 941_S_6962
├── Accelerated_Sagittal_MPRAGE
│   └── 2021-07-13_11_46_55.0
│   └── I1467526
└── PET_Brain_DYNAMIC_6x5MIN_Tau
└── 2021-08-17_14_40_03.0
└── I1481815

207 directories
`

I think the problem might be the variance in the PET directories for each subject. Or, maybe the two errors (the ADAS_q1 not found and the not-finding of the tau images) are connected?

Thanks for help
Shahar