PET-tau does not found by adni-to-bids
Opened this issue · 2 comments
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_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
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 :
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/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
- OS: Ubuntu WSL runs on Windows 11
- Version 0.77
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.