Closed shaharEd closed 2 weeks ago
I have found a similar error:
2024-05-06 10:15:36,235:INFO: Reading clinical data file: ADNIMERGE.csv
Traceback (most recent call last):
File "/miniconda3/lib/python3.11/site-packages/pandas/core/indexes/base.py", line 3802, in get_loc
return self._engine.get_loc(casted_key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 5745, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 5753, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'adas_Q1'
The issue occurs with the creation of a sessions.tsv file and is bypassed by commenting out lines 141-145 of adni_to_bids.py
# # -- Creation of sessions.tsv --
# cprint("Creating sessions files...")
# adni_utils.create_adni_sessions_dict(
# bids_ids, clinic_specs_path, clinical_data_dir, bids_subjs_paths
# )
Maybe this could be moved to an issue specifically related to handling sessions.tsv issues. I have not looked further to see what specifically is going on yet.
@shaharEd @tharpm95 did you download Original, Pre-processed, and Post-processed images ? (bullet point number 2 on the doc here).
If not, you get this behavior indeed. Otherwise, the converter should be able to find them. For example, this is what I got with a small subset of the original subjects:
Command used:
$ clinica convert adni-to-bids -m PET_TAU raw clinical bids
Output:
$ tree bids
bids
├── README
├── conversion_info
│ └── v0
│ └── 18FAV1451_pet_paths.tsv
├── dataset_description.json
├── participants.tsv
├── sub-ADNI011S6303
│ ├── ses-M000
│ │ ├── pet
│ │ │ └── sub-ADNI011S6303_ses-M000_trc-18FAV1451_pet.nii.gz
│ │ └── sub-ADNI011S6303_ses-M000_scans.tsv
│ ├── ses-M012
│ │ ├── pet
│ │ │ └── sub-ADNI011S6303_ses-M012_trc-18FAV1451_pet.nii.gz
│ │ └── sub-ADNI011S6303_ses-M012_scans.tsv
│ └── sub-ADNI011S6303_sessions.tsv
├── sub-ADNI016S6839
│ ├── ses-M000
│ │ ├── pet
│ │ │ └── sub-ADNI016S6839_ses-M000_trc-18FAV1451_pet.nii.gz
│ │ └── sub-ADNI016S6839_ses-M000_scans.tsv
│ ├── ses-M012
│ │ ├── pet
│ │ │ └── sub-ADNI016S6839_ses-M012_trc-18FAV1451_pet.nii.gz
│ │ └── sub-ADNI016S6839_ses-M012_scans.tsv
│ └── sub-ADNI016S6839_sessions.tsv
├── sub-ADNI022S6796
│ ├── ses-M000
│ │ ├── pet
│ │ │ └── sub-ADNI022S6796_ses-M000_trc-18FAV1451_pet.nii.gz
│ │ └── sub-ADNI022S6796_ses-M000_scans.tsv
│ ├── ses-M012
│ │ ├── pet
│ │ │ └── sub-ADNI022S6796_ses-M012_trc-18FAV1451_pet.nii.gz
│ │ └── sub-ADNI022S6796_ses-M012_scans.tsv
│ ├── ses-M024
│ │ ├── pet
│ │ │ └── sub-ADNI022S6796_ses-M024_trc-18FAV1451_pet.nii.gz
│ │ └── sub-ADNI022S6796_ses-M024_scans.tsv
│ └── sub-ADNI022S6796_sessions.tsv
└── sub-ADNI027S6648
├── ses-M000
│ ├── pet
│ │ └── sub-ADNI027S6648_ses-M000_trc-18FAV1451_pet.nii.gz
│ └── sub-ADNI027S6648_ses-M000_scans.tsv
└── sub-ADNI027S6648_sessions.tsv
Let me know if you're able to make it work or not.
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while running the adni-to-bids, the T1s are found by the command but the PET-TAU does not. This is the command I run:
clinica convert adni-to-bids -m T1 -m PET_TAU --subjects_list subjectsAD6575.txt ADNI ClinicalDatareduced/ BIDS3
This is the tree of the ADNI directory (contains only samples): . └── ADNI ├── 011_S_6303 │ ├── ADNI3_AV1451ACTau │ │ ├── 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_PETRaw_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_PETRaw_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_FLORTAUCIPIRAC_ │ │ └── 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-2AC_ │ │ └── 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_6x5Tau │ ├── 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_PETRaw_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
This is the output: `2024-02-13 18:42:31,724:INFO:Loading a subjects lists provided by the user... 2024-02-13 18:42:31,753:INFO:Calculating paths of T1 images. Output will be stored in /mnt/d/ADNI_ShaharAndMeitar/BIDS3/conversion_info/v1. 2024-02-13 18:42:34,569:INFO:No T1 image path found for subject 168_S_6843 in visit bl with image ID 1275415 2024-02-13 18:42:35,160:INFO:No T1 image path found for subject 305_S_6810 in visit m24 with image ID 1523609 2024-02-13 18:42:35,380:INFO:No T1 image path found for subject 941_S_6962 in visit m12 with image ID 1597858 2024-02-13 18:42:36,906:INFO:No T1 image path found for subject 127_S_6549 in visit bl with image ID 1073644 2024-02-13 18:42:37,826:INFO:Paths of T1 images found. Exporting images into BIDS ... 2024-02-13 18:42:37,855:INFO:[T1] Processing subject 022_S_6796in session m12 2024-02-13 18:42:37,855:INFO:[T1] Processing subject 011_S_6303in session bl 2024-02-13 18:42:37,855:INFO:[T1] Processing subject 011_S_6303in session m12 2024-02-13 18:42:37,855:INFO:[T1] Processing subject 022_S_6796in session bl 2024-02-13 18:42:37,858:INFO:[T1] Processing subject 022_S_6796in session m24 2024-02-13 18:42:37,862:INFO:[T1] Processing subject 036_S_6231in session bl 2024-02-13 18:42:37,862:INFO:[T1] Processing subject 100_S_6713in session bl 2024-02-13 18:42:37,862:INFO:[T1] Processing subject 032_S_6600in session m12 2024-02-13 18:42:37,862:INFO:[T1] Processing subject 100_S_6713in session m42 2024-02-13 18:42:37,862:INFO:[T1] Processing subject 116_S_6543in session bl 2024-02-13 18:42:37,862:INFO:[T1] Processing subject 032_S_6600in session bl 2024-02-13 18:42:37,863:INFO:[T1] Processing subject 116_S_6543in session m12 2024-02-13 18:42:37,863:INFO:[T1] Processing subject 135_S_6389in session m12 2024-02-13 18:42:37,864:INFO:[T1] Processing subject 100_S_6713in session m30 2024-02-13 18:42:37,864:INFO:[T1] Processing subject 135_S_6389in session m24 2024-02-13 18:42:37,864:INFO:[T1] No path specified for 168_S_6843 in session bl 2024-02-13 18:42:37,864:INFO:[T1] Processing subject 305_S_6810in session bl 2024-02-13 18:42:37,865:INFO:[T1] No path specified for 305_S_6810 in session m24 2024-02-13 18:42:37,865:INFO:[T1] Processing subject 135_S_6389in session bl 2024-02-13 18:42:37,865:INFO:[T1] Processing subject 941_S_6962in session bl 2024-02-13 18:42:37,865:INFO:[T1] Processing subject 305_S_6810in session m12 2024-02-13 18:42:37,948:INFO:Attempting to convert sub-ADNI100S6713_ses-M042_T1w. 2024-02-13 18:42:37,951:INFO:Attempting to convert sub-ADNI100S6713_ses-M000_T1w. 2024-02-13 18:42:37,959:INFO:Attempting to convert sub-ADNI116S6543_ses-M000_T1w. 2024-02-13 18:42:37,960:INFO:Attempting to convert sub-ADNI116S6543_ses-M012_T1w. 2024-02-13 18:42:37,966:INFO:Attempting to convert sub-ADNI135S6389_ses-M024_T1w. 2024-02-13 18:42:37,968:INFO:Attempting to convert sub-ADNI100S6713_ses-M030_T1w. 2024-02-13 18:42:37,981:INFO:Attempting to convert sub-ADNI032S6600_ses-M000_T1w. 2024-02-13 18:42:37,981:INFO:Attempting to convert sub-ADNI011S6303_ses-M000_T1w. 2024-02-13 18:42:37,981:INFO:Attempting to convert sub-ADNI022S6796_ses-M000_T1w. 2024-02-13 18:42:37,983:INFO:Attempting to convert sub-ADNI305S6810_ses-M012_T1w. 2024-02-13 18:42:37,984:INFO:Attempting to convert sub-ADNI011S6303_ses-M012_T1w. 2024-02-13 18:42:37,984:INFO:Attempting to convert sub-ADNI032S6600_ses-M012_T1w. 2024-02-13 18:42:37,986:INFO:Attempting to convert sub-ADNI305S6810_ses-M000_T1w. 2024-02-13 18:42:37,987:INFO:Attempting to convert sub-ADNI135S6389_ses-M000_T1w. 2024-02-13 18:42:37,988:INFO:Attempting to convert sub-ADNI135S6389_ses-M012_T1w. 2024-02-13 18:42:37,991:INFO:Attempting to convert sub-ADNI022S6796_ses-M024_T1w. 2024-02-13 18:42:37,991:INFO:Attempting to convert sub-ADNI022S6796_ses-M012_T1w. 2024-02-13 18:42:37,994:INFO:Attempting to convert sub-ADNI036S6231_ses-M000_T1w. 2024-02-13 18:42:38,007:INFO:Attempting to convert sub-ADNI941S6962_ses-M000_T1w. 2024-02-13 18:42:44,161:INFO:[T1] No path specified for 941_S_6962 in session m12 2024-02-13 18:42:44,161:INFO:[T1] Processing subject 016_S_6839in session bl 2024-02-13 18:42:44,272:INFO:Attempting to convert sub-ADNI016S6839_ses-M000_T1w. 2024-02-13 18:42:45,810:INFO:[T1] Processing subject 016_S_6839in session m12 2024-02-13 18:42:45,830:INFO:Attempting to convert sub-ADNI016S6839_ses-M012_T1w. 2024-02-13 18:42:46,141:INFO:[T1] Processing subject 016_S_6839in session m24 2024-02-13 18:42:46,183:INFO:Attempting to convert sub-ADNI016S6839_ses-M024_T1w. 2024-02-13 18:42:46,532:INFO:[T1] Processing subject 027_S_6648in session bl 2024-02-13 18:42:46,549:INFO:[T1] Processing subject 035_S_7001in session bl 2024-02-13 18:42:46,556:INFO:Attempting to convert sub-ADNI027S6648_ses-M000_T1w. 2024-02-13 18:42:46,570:INFO:Attempting to convert sub-ADNI035S7001_ses-M000_T1w. 2024-02-13 18:43:27,688:INFO:[T1] Processing subject 098_S_6601in session bl 2024-02-13 18:43:27,753:INFO:[T1] Processing subject 116_S_6100in session bl 2024-02-13 18:43:27,799:INFO:Attempting to convert sub-ADNI098S6601_ses-M000_T1w. 2024-02-13 18:43:27,864:INFO:Attempting to convert sub-ADNI116S6100_ses-M000_T1w. 2024-02-13 18:43:28,242:INFO:[T1] Processing subject 116_S_6100in session m12 2024-02-13 18:43:28,325:INFO:Attempting to convert sub-ADNI116S6100_ses-M012_T1w. 2024-02-13 18:43:29,318:INFO:[T1] Processing subject 116_S_6100in session m24 2024-02-13 18:43:29,374:INFO:Attempting to convert sub-ADNI116S6100_ses-M024_T1w. 2024-02-13 18:43:29,775:INFO:[T1] No path specified for 127_S_6549 in session bl 2024-02-13 18:43:29,776:INFO:[T1] Processing subject 127_S_6549in session m12 2024-02-13 18:43:29,828:INFO:Attempting to convert sub-ADNI127S6549_ses-M012_T1w. 2024-02-13 18:43:31,217:INFO:[T1] Processing subject 127_S_6549in session m24 2024-02-13 18:43:31,245:INFO:Attempting to convert sub-ADNI127S6549_ses-M024_T1w. 2024-02-13 18:43:32,126:INFO:[T1] Processing subject 135_S_6840in session bl 2024-02-13 18:43:32,158:INFO:Attempting to convert sub-ADNI135S6840_ses-M000_T1w. 2024-02-13 18:43:32,219:INFO:[T1] Processing subject 301_S_6592in session bl 2024-02-13 18:43:32,249:INFO:Attempting to convert sub-ADNI301S6592_ses-M000_T1w. 2024-02-13 18:43:32,413:INFO:[T1] Processing subject 301_S_6592in session m12 2024-02-13 18:43:32,413:INFO:[T1] Processing subject 341_S_6820in session bl 2024-02-13 18:43:32,444:INFO:Attempting to convert sub-ADNI301S6592_ses-M012_T1w. 2024-02-13 18:43:32,448:INFO:Attempting to convert sub-ADNI341S6820_ses-M000_T1w. 2024-02-13 18:44:01,649:INFO:Calculating paths of TAU PET images. Output will be stored in /mnt/d/ADNI_ShaharAndMeitar/BIDS3/conversion_info/v1. 2024-02-13 18:44:02,228:INFO:No TAU image path found for subject 011_S_6303 in visit bl with image ID 995807 2024-02-13 18:44:02,402:INFO:No TAU image path found for subject 011_S_6303 in visit m12 with image ID 1174084 2024-02-13 18:44:02,861:INFO:No TAU image path found for subject 022_S_6796 in visit bl with image ID 1236620 2024-02-13 18:44:03,158:INFO:No TAU image path found for subject 022_S_6796 in visit m12 with image ID 1343474 2024-02-13 18:44:03,358:INFO:No TAU image path found for subject 022_S_6796 in visit m24 with image ID 1487881 2024-02-13 18:44:03,531:INFO:No TAU image path found for subject 032_S_6600 in visit bl with image ID 1074907 2024-02-13 18:44:03,684:INFO:No TAU image path found for subject 032_S_6600 in visit m12 with image ID 1259805 2024-02-13 18:44:03,871:INFO:No TAU image path found for subject 036_S_6231 in visit bl with image ID 999915 2024-02-13 18:44:04,077:INFO:No TAU image path found for subject 100_S_6713 in visit bl with image ID 1170558 2024-02-13 18:44:04,330:INFO:No TAU image path found for subject 100_S_6713 in visit m30 with image ID 1544842 2024-02-13 18:44:04,967:INFO:No TAU image path found for subject 116_S_6543 in visit bl with image ID 1051991 2024-02-13 18:44:05,205:INFO:No TAU image path found for subject 116_S_6543 in visit m12 with image ID 1215182 2024-02-13 18:44:05,646:INFO:No TAU image path found for subject 135_S_6389 in visit bl with image ID 1020506 2024-02-13 18:44:05,905:INFO:No TAU image path found for subject 135_S_6389 in visit m12 with image ID 1187730 2024-02-13 18:44:06,121:INFO:No TAU image path found for subject 135_S_6389 in visit m24 with image ID 1327965 2024-02-13 18:44:06,178:INFO:No TAU image path found for subject 168_S_6843 in visit bl with image ID 1304853 2024-02-13 18:44:06,336:INFO:No TAU image path found for subject 305_S_6810 in visit m12 with image ID 1405852 2024-02-13 18:44:06,517:INFO:No TAU image path found for subject 305_S_6810 in visit m24 with image ID 1524971 2024-02-13 18:44:06,613:INFO:No TAU image path found for subject 941_S_6962 in visit bl with image ID 1482712 2024-02-13 18:44:06,729:INFO:No TAU image path found for subject 941_S_6962 in visit m12 with image ID 1606692 2024-02-13 18:44:07,071:INFO:No TAU image path found for subject 016_S_6839 in visit bl with image ID 1296385 2024-02-13 18:44:07,357:INFO:No TAU image path found for subject 016_S_6839 in visit m12 with image ID 1439331 2024-02-13 18:44:07,557:INFO:No TAU image path found for subject 027_S_6648 in visit bl with image ID 1134392 2024-02-13 18:44:07,741:INFO:No TAU image path found for subject 035_S_7001 in visit bl with image ID 1546611 2024-02-13 18:44:07,872:INFO:No TAU image path found for subject 098_S_6601 in visit bl with image ID 1092129 2024-02-13 18:44:08,621:INFO:No TAU image path found for subject 116_S_6100 in visit bl with image ID 977849 2024-02-13 18:44:08,967:INFO:No TAU image path found for subject 116_S_6100 in visit m12 with image ID 1119630 2024-02-13 18:44:09,308:INFO:No TAU image path found for subject 116_S_6100 in visit m24 with image ID 1282760 2024-02-13 18:44:09,468:INFO:No TAU image path found for subject 127_S_6549 in visit bl with image ID 1071354 2024-02-13 18:44:09,633:INFO:No TAU image path found for subject 127_S_6549 in visit m12 with image ID 1245605 2024-02-13 18:44:09,812:INFO:No TAU image path found for subject 127_S_6549 in visit m24 with image ID 1359916 2024-02-13 18:44:09,963:INFO:No TAU image path found for subject 135_S_6840 in visit bl with image ID 1270381 2024-02-13 18:44:10,149:INFO:No TAU image path found for subject 301_S_6592 in visit bl with image ID 1074132 2024-02-13 18:44:10,341:INFO:No TAU image path found for subject 301_S_6592 in visit m12 with image ID 1261267 2024-02-13 18:44:10,522:INFO:No TAU image path found for subject 341_S_6820 in visit bl with image ID 1261271 2024-02-13 18:44:10,541:INFO:Paths of TAU PET images found. Exporting images into BIDS ... 2024-02-13 18:44:10,575:INFO:[TAU] No path specified for 011_S_6303 in session bl 2024-02-13 18:44:10,575:INFO:[TAU] No path specified for 022_S_6796 in session m24 2024-02-13 18:44:10,575:INFO:[TAU] No path specified for 011_S_6303 in session m12 2024-02-13 18:44:10,575:INFO:[TAU] No path specified for 100_S_6713 in session bl 2024-02-13 18:44:10,576:INFO:[TAU] No path specified for 022_S_6796 in session m12 2024-02-13 18:44:10,576:INFO:[TAU] No path specified for 032_S_6600 in session bl 2024-02-13 18:44:10,576:INFO:[TAU] No path specified for 116_S_6543 in session m12 2024-02-13 18:44:10,577:INFO:[TAU] No path specified for 035_S_7001 in session bl 2024-02-13 18:44:10,577:INFO:[TAU] No path specified for 016_S_6839 in session bl 2024-02-13 18:44:10,577:INFO:[TAU] No path specified for 036_S_6231 in session bl 2024-02-13 18:44:10,577:INFO:[TAU] No path specified for 100_S_6713 in session m30 2024-02-13 18:44:10,577:INFO:[TAU] No path specified for 016_S_6839 in session m12 2024-02-13 18:44:10,577:INFO:[TAU] No path specified for 098_S_6601 in session bl 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 116_S_6100 in session m12 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 116_S_6100 in session bl 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 116_S_6100 in session m24 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 305_S_6810 in session m12 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 127_S_6549 in session m12 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 135_S_6389 in session m12 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 127_S_6549 in session m24 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 341_S_6820 in session bl 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 127_S_6549 in session bl 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 135_S_6389 in session m24 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 301_S_6592 in session m12 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 135_S_6389 in session bl 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 027_S_6648 in session bl 2024-02-13 18:44:10,579:INFO:[TAU] No path specified for 301_S_6592 in session bl 2024-02-13 18:44:10,579:INFO:[TAU] No path specified for 135_S_6840 in session bl 2024-02-13 18:44:10,578:INFO:[TAU] No path specified for 022_S_6796 in session bl 2024-02-13 18:44:10,579:INFO:[TAU] No path specified for 116_S_6543 in session bl 2024-02-13 18:44:10,579:INFO:[TAU] No path specified for 168_S_6843 in session bl 2024-02-13 18:44:10,579:INFO:[TAU] No path specified for 305_S_6810 in session m24 2024-02-13 18:44:10,579:INFO:[TAU] No path specified for 941_S_6962 in session m12 2024-02-13 18:44:10,579:INFO:[TAU] No path specified for 941_S_6962 in session bl 2024-02-13 18:44:10,580:INFO:[TAU] No path specified for 032_S_6600 in session m12 2024-02-13 18:44:10,704:INFO:Creating modality agnostic files... 2024-02-13 18:44:10,746:INFO:Creating participants.tsv... 2024-02-13 18:44:13,092:INFO:The following subjects of dataset directory were not found in your BIDS folder : 011S0002, 011S0003, 022S0004, 011S0005, 100S0006, 022S0007, 011S0010, 022S0014, 100S0015, 011S0016, 011S0021, 011S0023, 082S5282, 100S5280, 067S0029, 035S0033, 100S0035, 067S0038, 099S0040, 007S0041, 023S0042, 082S5279, 018S0043, 022S0044, 067S0045, 100S0047, 123S0050, 099S0051, 011S0053, 099S0054, 018S0055, 067S0056, 082S5278, 018S0057, 023S0058, 067S0059, 099S0060, 023S0061, 027S5277, 022S0066, 010S0067, 007S0068, 100S0069, 007S0070, 123S0072, 135S5275, 027S0074, 067S0076, 067S0077, 023S0078, 018S0080, 023S0081, 023S0083, 023S0084, 136S0086, 018S0087, 123S0088, 073S0089, 135S5273, 099S0090, 123S0091, 023S0093, 123S0094, 022S0096, 020S0097, 067S0098, 007S0101, 130S0102, 018S0103, 123S0106, 136S0107, 123S0108, 068S0109, 067S0110, 099S0111, 127S0112, 123S0113, 027S0116, 027S0118, 027S0120, 131S0123, 041S0125, 023S0126, 007S0128, 022S0129, 022S0130, 128S0138, 023S0139, 021S0141, 018S0142, 032S0147, 037S0150, 018S0155, 035S0156, 021S0159, 098S0160, 135S5269, 010S0161, 123S0162, 114S0166, 011S0168, 014S0169, 098S0171, 114S0173, 067S0176, 067S0177, 021S0178, 027S0179, 037S0182, 011S0183, 136S0184, 136S0186, 153S5267, 032S0187, 128S0188, 100S0190, 136S0194, 136S0195, 136S0196, 128S0200, 035S0204, 128S0205, 068S0210, 020S0213, 032S0214, 128S0216, 023S0217, 022S0219, 005S0221, 005S0222, 005S0223, 128S0225, 128S0227, 114S0228, 128S0229, 128S0230, 021S0231, 130S0232, 013S0240, 011S0241, 067S0243, 128S0245, 007S0249, 027S0256, 067S0257, 128S0258, 127S0259, 127S0260, 041S0262, 128S0266, 098S0269, 128S0272, 021S0273, 021S0276, 041S0282, 137S0283, 067S0284, 130S0285, 018S0286, 130S0289, 067S0290, 099S0291, 007S5265, 035S0292, 007S0293, 002S0295, 032S5263, 100S0296, 123S0298, 136S0299, 136S0300, 137S0301, 018S5262, 037S0303, 082S0304, 027S0307, 128S0310, 073S0311, 073S0312, 041S0314, 072S0315, 153S5261, 007S0316, 131S0319, 031S0321, 005S0324, 013S0325, 037S0327, 014S0328, 023S0331, 021S0332, 018S0335, 067S0336, 021S0337, 035S0341, 021S0343, 007S0344, 031S0351, 099S0352, 016S0354, 016S0359, 033S5259, 116S0360, 116S0361, 011S0362, 082S0363, 137S0366, 018S0369, 116S0370, 114S0374, 023S0376, 037S0377, 114S0378, 116S0382, 130S5258, 131S0384, 073S0386, 023S0388, 053S0389, 123S0390, 116S0392, 127S0393, 127S0394, 127S0397, 032S0400, 068S0401, 027S0403, 126S0405, 018S0406, 041S0407, 027S0408, 114S0410, 002S0413, 002S5256, 007S0414, 114S0416, 027S0417, 010S0419, 010S0420, 130S0423, 021S0424, 018S0425, 136S0426, 136S0429, 127S0431, 133S0433, 094S0434, 131S0436, 137S0438, 131S0441, 068S0442, 073S0445, 005S0448, 130S0449, 018S0450, 131S0457, 114S0458, 027S0461, 057S0464, 037S0467, 082S0469, 099S0470, 010S0472, 068S0473, 057S0474, 068S0476, 068S0478, 032S0479, 137S0481, 006S0484, 027S0485, 116S0487, 133S0488, 094S0489, 099S0492, 133S0493, 131S0497, 128S0500, 037S0501, 013S0502, 130S0505, 126S0506, 053S0507, 033S0511, 033S0513, 033S0514, 009S5252, 128S0517, 073S0518, 014S0519, 014S0520, 128S0522, 133S0525, 094S0526, 128S0528, 099S0533, 099S0534, 062S0535, 016S0538, 037S0539, 022S0543, 022S0544, 128S0545, 005S0546, 016S5251, 014S0548, 018S5250, 041S0549, 099S0551, 037S0552, 036S5248, 005S0553, 031S0554, 035S0555, 014S0557, 014S0558, 002S0559, 014S0563, 073S0565, 037S0566, 033S0567, 031S0568, 013S0575, 036S0576, 036S0577, 062S0578, 136S0579, 037S0588, 013S0592, 041S0598, 114S0601, 005S0602, 041S5244, 023S0604, 126S0605, 126S0606, 067S0607, 128S0608, 126S5243, 128S0611, 023S0613, 031S0618, 002S0619, 053S0621, 127S0622, 023S0625, 021S0626, 037S0627, 133S0629, 137S0631, 018S0633, 133S0638, 082S0640, 082S0641, 021S0642, 057S0643, 027S0644, 021S0647, 116S0648, 116S0649, 006S0653, 036S0656, 116S0657, 014S0658, 098S0667, 019S5242, 137S0668, 137S0669, 052S0671, 036S0672, 036S0673, 006S0675, 032S0677, 041S0679, 023S5241, 018S5240, 021S5237, 006S0681, 018S0682, 127S0684, 137S0686, 012S0689, 062S0690, 136S0695, 141S0696, 007S0698, 016S0702, 126S0708, 126S0709, 094S0711, 012S0712, 128S0715, 141S0717, 032S0718, 012S0720, 041S0721, 133S0792, 021S5236, 033S0723, 033S0724, 033S0725, 141S0726, 133S0727, 002S0729, 062S0730, 006S0731, 033S0733, 033S0734, 033S0739, 128S0740, 033S0741, 033S5235, 100S0747, 036S0748, 022S0750, 009S0751, 021S0753, 127S0754, 036S0759, 036S0760, 082S0761, 141S0767, 114S5234, 062S0768, 016S0769, 128S0770, 133S0771, 109S0777, 129S0778, 057S0779, 002S0782, 130S0783, 010S0786, 141S0790, 062S0793, 137S0796, 137S0800, 130S5231, 068S0802, 012S0803, 141S0810, 067S0812, 036S0813, 005S0814, 002S0816, 031S0821, 029S0824, 137S0825, 067S0828, 010S0829, 082S0832, 116S0834, 027S0835, 029S0836, 057S0839, 137S0841, 009S0842, 029S0843, 029S0845, 027S0850, 141S0851, 141S0852, 141S0853, 011S0856, 013S0860, 009S0862, 128S0863, 002S5230, 126S0865, 029S0866, 031S0867, 036S0869, 029S0871, 068S0872, 136S0873, 136S0874, 029S0878, 099S0880, 020S0883, 023S0887, 033S0889, 116S0890, 126S0891, 100S0892, 098S0896, 041S0898, 020S0899, 010S0904, 033S0906, 003S0908, 073S0909, 133S0913, 029S0914, 141S0915, 023S0916, 012S0917, 053S0919, 033S0920, 033S0922, 033S0923, 022S0924, 127S0925, 023S0926, 082S0928, 005S0929, 100S0930, 003S0931, 012S0932, 057S0934, 073S5227, 002S0938, 057S0941, 128S0947, 109S0950, 052S0951, 052S0952, 002S0954, 002S0955, 130S0956, 099S0958, 022S0961, 023S0963, 109S0967, 130S0969, 137S0972, 137S0973, 036S0976, 032S0978, 114S0979, 003S0981, 141S0982, 024S0985, 132S0987, 052S0989, 016S0991, 137S0994, 009S5224, 100S0995, 013S0996, 036S1001, 041S1002, 141S1004, 057S1007, 012S1009, 041S1010, 109S1013, 109S1014, 094S1015, 033S1016, 002S1018, 036S1023, 141S1024, 094S1027, 016S1028, 009S1030, 133S1031, 127S1032, 012S1033, 099S1034, 029S5219, 013S1035, 032S1037, 029S1038, 051S1040, 137S1041, 128S1043, 053S1044, 023S1046, 141S1051, 052S1054, 133S1055, 029S1056, 003S1057, 003S1059, 100S1062, 024S1063, 031S1066, 002S1070, 051S1072, 029S1073, 003S1074, 068S1075, 126S1077, 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941S7074, 027S7071, 035S7050, 067S7061, 035S7073, 126S7083, 033S7079, 073S7052, 941S7085, 073S6952, 014S7080, 021S7092, 033S7088, 037S7035, 014S7072, 067S7068, 070S7078, 073S7082, 033S7100, 016S6892, 035S7076, 011S7089, 035S7105, 033S7114, 053S7086, 035S7049, 082S7117, 035S7121, 123S7125 /home/shaharedelman/AMN/lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py:641: PerformanceWarning: indexing past lexsort depth may impact performance. dxsum_df.loc[(alternative_id, "sc"), "DIAGNOSIS"].values[0] 2024-02-13 18:44:13,198:INFO:Creating sessions files... Traceback (most recent call last): File "/home/shaharedelman/AMN/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3802, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 165, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 5745, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 5753, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'adas_Q1'
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/shaharedelman/AMN/bin/clinica", line 8, in
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'`
As one can see, there's another error while excecuting the clinical extraction. I wonder if there's a link between the two. I attach the Clinical csvs that I provided the command:
├── ADAS_ADNI1_13Feb2024.csv ├── ADAS_ADNIGO23_13Feb2024.csv ├── ADNIMERGE_13Feb2024.csv ├── AMYQC_13Feb2024.csv ├── APOERES_13Feb2024.csv ├── AV45META_13Feb2024.csv ├── AV45QC_13Feb2024.csv ├── BLCHANGE_13Feb2024.csv ├── CDR_13Feb2024.csv ├── DATADIC_13Feb2024.csv ├── DXSUM_PDXCONV_ADNIALL_13Feb2024.csv ├── ECOGPT_13Feb2024.csv ├── MAYOADIRL_MRI_IMAGEQC_12_08_15_13Feb2024.csv ├── MAYOADIRL_MRI_QUALITY_ADNI3_13Feb2024.csv ├── MMSE_13Feb2024.csv ├── MOCA_13Feb2024.csv ├── MPRAGEMETA_13Feb2024.csv ├── MRI3META_13Feb2024.csv ├── MRILIST_13Feb2024.csv ├── MRIMETA_13Feb2024.csv ├── MRIQUALITY_13Feb2024.csv ├── NPIQ_13Feb2024.csv ├── PETC3_13Feb2024.csv ├── PETQC_13Feb2024.csv ├── PET_META_LIST_13Feb2024.csv ├── PIBQC_13Feb2024.csv ├── TAUMETA3_13Feb2024.csv ├── TAUMETA_13Feb2024.csv ├── TAUQC3_13Feb2024.csv └── TAUQC_13Feb2024.csv