Help with import bids

amitkeinan · October 11, 2026, 9:32am

Hi,

I’m new in using the qunex hcppipelines. the data the I’m trying to preprocess is in bids format, I tried to use import_bids but something might be wrong with the syntax and I’m not sure what.

the command I ran:

qunex_container import_bids
–sessionsfolder=“${STUDY_FOLDER}/sessions”
–sessions=“${SESSIONS}”
–inbox=“${RAW_DATA}”
–bind=“/home/docker/volumes/hcppipelines/amitkeinan:/home/docker/volumes/hcppipelines/amitkeinan”
–archive=“leave”
–container=“${QUNEX_CONTAINER}”
–overwrite=yes

the error I got:

Running import_bids
==================
---> identifying files in /home/docker/volumes/hcppipelines/amitkeinan/rawdata
---> Inbox type: bids_study
---> Paths:
    bidsinfo    -> /home/docker/volumes/hcppipelines/amitkeinan/cd_study/info/bids
    bidsinbox   -> /home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/inbox/BIDS
    bidsarchive -> /home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/archive/BIDS
---> mapping files to QuNex bids folders
    ---> creating bids session S002759
    ---> creating bids session S002759_202508221215
    ---> creating bids session S125082
    ---> creating bids session S125082_202412111835
    ---> creating bids session S035513
    ---> creating bids session S035513_202411211521
    ---> creating bids session S036143
    ---> creating bids session S036143_202402201017
    ---> creating bids session S043941_202410201244
    ---> creating bids session S043941
    ---> creating bids session S140183_202210261924
    ---> creating bids session S140183
    ---> creating bids session S176993_202512051033
    ---> creating bids session S176993
    ---> creating bids session S199033
    ---> creating bids session S199033_202411191247
    ---> creating bids session S222954
    ---> creating bids session S222954_202410291354
    ---> creating bids session S288376_202409151819
    ---> creating bids session S288376
Running map_bids2nii for subject S002759
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S002759] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S002759, session 202508221215
==============================================================
---> linked 1.nii.gz <-- sub-S002759_ses-202508221215_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S002759_ses-202508221215_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S002759_ses-202508221215_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S002759_ses-202508221215_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S002759_ses-202508221215_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S002759_ses-202508221215_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S002759_ses-202508221215_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S002759_ses-202508221215_dir-AP_run-01_sbref.nii.gz
---> linked 9.nii.gz <-- sub-S002759_ses-202508221215_dir-PA_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S002759_ses-202508221215_task-emotionalnback_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S002759_ses-202508221215_task-emotionalnback_run-01_bold.nii.gz
---> linked 12.nii.gz <-- sub-S002759_ses-202508221215_task-rest_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S002759_ses-202508221215_task-rest_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S002759_ses-202508221215_dir-AP_run-01_dwi.nii.gz
---> linked 15.nii.gz <-- sub-S002759_ses-202508221215_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S125082
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S125082] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S125082, session 202412111835
==============================================================
---> linked 1.nii.gz <-- sub-S125082_ses-202412111835_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S125082_ses-202412111835_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S125082_ses-202412111835_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S125082_ses-202412111835_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S125082_ses-202412111835_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S125082_ses-202412111835_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S125082_ses-202412111835_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S125082_ses-202412111835_dir-AP_run-01_sbref.nii.gz
---> linked 9.nii.gz <-- sub-S125082_ses-202412111835_dir-PA_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S125082_ses-202412111835_task-emotionalnback_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S125082_ses-202412111835_task-emotionalnback_run-01_bold.nii.gz
---> linked 12.nii.gz <-- sub-S125082_ses-202412111835_task-rest_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S125082_ses-202412111835_task-rest_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S125082_ses-202412111835_dir-AP_run-01_dwi.nii.gz
---> linked 15.nii.gz <-- sub-S125082_ses-202412111835_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S035513
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S035513] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S035513, session 202411211521
==============================================================
---> linked 1.nii.gz <-- sub-S035513_ses-202411211521_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S035513_ses-202411211521_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S035513_ses-202411211521_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S035513_ses-202411211521_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S035513_ses-202411211521_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S035513_ses-202411211521_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S035513_ses-202411211521_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S035513_ses-202411211521_dir-AP_run-01_sbref.nii.gz
---> linked 9.nii.gz <-- sub-S035513_ses-202411211521_dir-PA_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S035513_ses-202411211521_task-emotionalnback_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S035513_ses-202411211521_task-emotionalnback_run-01_bold.nii.gz
---> linked 12.nii.gz <-- sub-S035513_ses-202411211521_task-rest_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S035513_ses-202411211521_task-rest_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S035513_ses-202411211521_dir-AP_run-01_dwi.nii.gz
---> linked 15.nii.gz <-- sub-S035513_ses-202411211521_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S036143
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S036143] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S036143, session 202402201017
==============================================================
---> linked 1.nii.gz <-- sub-S036143_ses-202402201017_acq-task_dir-AP_run-01_epi.nii.gz
---> linked 2.nii.gz <-- sub-S036143_ses-202402201017_acq-task_dir-PA_run-01_epi.nii.gz
---> linked 3.nii.gz <-- sub-S036143_ses-202402201017_task-movie1_run-01_sbref.nii.gz
---> linked 4.nii.gz <-- sub-S036143_ses-202402201017_task-movie1_run-01_bold.nii.gz
---> linked 5.nii.gz <-- sub-S036143_ses-202402201017_task-movie2_run-01_sbref.nii.gz
---> linked 6.nii.gz <-- sub-S036143_ses-202402201017_task-movie2_run-01_bold.nii.gz
---> linked 7.nii.gz <-- sub-S036143_ses-202402201017_task-movie3_run-01_sbref.nii.gz
---> linked 8.nii.gz <-- sub-S036143_ses-202402201017_task-movie3_run-01_bold.nii.gz
---> linked 9.nii.gz <-- sub-S036143_ses-202402201017_task-movie4_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S036143_ses-202402201017_task-movie4_run-01_bold.nii.gz
Running map_bids2nii for subject S043941, session 202410201244
==============================================================
---> linked 1.nii.gz <-- sub-S043941_ses-202410201244_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S043941_ses-202410201244_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S043941_ses-202410201244_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S043941_ses-202410201244_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S043941_ses-202410201244_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S043941_ses-202410201244_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S043941_ses-202410201244_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S043941_ses-202410201244_dir-AP_run-01_sbref.nii.gz
---> linked 9.nii.gz <-- sub-S043941_ses-202410201244_dir-PA_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S043941_ses-202410201244_task-emotionalnback_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S043941_ses-202410201244_task-emotionalnback_run-01_bold.nii.gz
---> linked 12.nii.gz <-- sub-S043941_ses-202410201244_task-rest_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S043941_ses-202410201244_task-rest_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S043941_ses-202410201244_dir-AP_run-01_dwi.nii.gz
---> linked 15.nii.gz <-- sub-S043941_ses-202410201244_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S043941
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S043941] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S140183, session 202210261924
==============================================================
---> linked 1.nii.gz <-- sub-S140183_ses-202210261924_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S140183_ses-202210261924_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S140183_ses-202210261924_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S140183_ses-202210261924_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S140183_ses-202210261924_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S140183_ses-202210261924_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S140183_ses-202210261924_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S140183_ses-202210261924_dir-AP_run-01_sbref.nii.gz
---> linked 9.nii.gz <-- sub-S140183_ses-202210261924_dir-PA_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S140183_ses-202210261924_task-rest_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S140183_ses-202210261924_task-rest_run-01_bold.nii.gz
---> linked 12.nii.gz <-- sub-S140183_ses-202210261924_dir-AP_run-01_dwi.nii.gz
---> linked 13.nii.gz <-- sub-S140183_ses-202210261924_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S140183
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S140183] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S176993, session 202512051033
==============================================================
---> linked 1.nii.gz <-- sub-S176993_ses-202512051033_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S176993_ses-202512051033_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S176993_ses-202512051033_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S176993_ses-202512051033_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S176993_ses-202512051033_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S176993_ses-202512051033_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S176993_ses-202512051033_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S176993_ses-202512051033_acq-task_dir-AP_run-01_epi.nii.gz
---> linked 9.nii.gz <-- sub-S176993_ses-202512051033_acq-task_dir-PA_run-01_epi.nii.gz
---> linked 10.nii.gz <-- sub-S176993_ses-202512051033_dir-AP_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S176993_ses-202512051033_dir-PA_run-01_sbref.nii.gz
---> linked 12.nii.gz <-- sub-S176993_ses-202512051033_task-emotionalnback_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S176993_ses-202512051033_task-emotionalnback_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S176993_ses-202512051033_task-musicmovement1_run-01_sbref.nii.gz
---> linked 15.nii.gz <-- sub-S176993_ses-202512051033_task-musicmovement1_run-01_bold.nii.gz
---> linked 16.nii.gz <-- sub-S176993_ses-202512051033_task-musicmovement2_run-01_sbref.nii.gz
---> linked 17.nii.gz <-- sub-S176993_ses-202512051033_task-musicmovement2_run-01_bold.nii.gz
---> linked 18.nii.gz <-- sub-S176993_ses-202512051033_task-rest_run-01_sbref.nii.gz
---> linked 19.nii.gz <-- sub-S176993_ses-202512051033_task-rest_run-01_bold.nii.gz
---> linked 20.nii.gz <-- sub-S176993_ses-202512051033_dir-AP_run-01_dwi.nii.gz
---> linked 21.nii.gz <-- sub-S176993_ses-202512051033_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S176993
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S176993] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S199033
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S199033] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S199033, session 202411191247
==============================================================
---> linked 1.nii.gz <-- sub-S199033_ses-202411191247_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S199033_ses-202411191247_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S199033_ses-202411191247_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S199033_ses-202411191247_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S199033_ses-202411191247_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S199033_ses-202411191247_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S199033_ses-202411191247_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S199033_ses-202411191247_dir-AP_run-01_sbref.nii.gz
---> linked 9.nii.gz <-- sub-S199033_ses-202411191247_dir-PA_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S199033_ses-202411191247_task-emotionalnback_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S199033_ses-202411191247_task-emotionalnback_run-01_bold.nii.gz
---> linked 12.nii.gz <-- sub-S199033_ses-202411191247_task-rest_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S199033_ses-202411191247_task-rest_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S199033_ses-202411191247_dir-AP_run-01_dwi.nii.gz
---> linked 15.nii.gz <-- sub-S199033_ses-202411191247_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S222954
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S222954] does not have a valid matching BIDS session!
     Please check your data!

Running map_bids2nii for subject S222954, session 202410291354
==============================================================
---> linked 1.nii.gz <-- sub-S222954_ses-202410291354_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S222954_ses-202410291354_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S222954_ses-202410291354_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S222954_ses-202410291354_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S222954_ses-202410291354_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S222954_ses-202410291354_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S222954_ses-202410291354_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S222954_ses-202410291354_dir-AP_run-01_sbref.nii.gz
---> linked 9.nii.gz <-- sub-S222954_ses-202410291354_dir-PA_run-01_sbref.nii.gz
---> linked 10.nii.gz <-- sub-S222954_ses-202410291354_task-emotionalnback_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S222954_ses-202410291354_task-emotionalnback_run-01_bold.nii.gz
---> linked 12.nii.gz <-- sub-S222954_ses-202410291354_task-rest_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S222954_ses-202410291354_task-rest_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S222954_ses-202410291354_dir-AP_run-01_dwi.nii.gz
---> linked 15.nii.gz <-- sub-S222954_ses-202410291354_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S288376, session 202409151819
==============================================================
---> linked 1.nii.gz <-- sub-S288376_ses-202409151819_acq-defaced_run-01_T1w.nii.gz
---> linked 2.nii.gz <-- sub-S288376_ses-202409151819_rec-norm_acq-defaced_run-01_T1w.nii.gz
---> linked 3.nii.gz <-- sub-S288376_ses-202409151819_acq-defaced_run-01_T2w.nii.gz
---> linked 4.nii.gz <-- sub-S288376_ses-202409151819_run-01_FLAIR.nii.gz
---> linked 5.nii.gz <-- sub-S288376_ses-202409151819_acq-dwi_dir-PA_run-01_epi.nii.gz
---> linked 6.nii.gz <-- sub-S288376_ses-202409151819_acq-rest_dir-AP_run-01_epi.nii.gz
---> linked 7.nii.gz <-- sub-S288376_ses-202409151819_acq-rest_dir-PA_run-01_epi.nii.gz
---> linked 8.nii.gz <-- sub-S288376_ses-202409151819_acq-task_dir-AP_run-01_epi.nii.gz
---> linked 9.nii.gz <-- sub-S288376_ses-202409151819_acq-task_dir-PA_run-01_epi.nii.gz
---> linked 10.nii.gz <-- sub-S288376_ses-202409151819_dir-AP_run-01_sbref.nii.gz
---> linked 11.nii.gz <-- sub-S288376_ses-202409151819_dir-PA_run-01_sbref.nii.gz
---> linked 12.nii.gz <-- sub-S288376_ses-202409151819_task-bjj2_run-01_sbref.nii.gz
---> linked 13.nii.gz <-- sub-S288376_ses-202409151819_task-bjj2_run-01_bold.nii.gz
---> linked 14.nii.gz <-- sub-S288376_ses-202409151819_task-climbing2_run-01_sbref.nii.gz
---> linked 15.nii.gz <-- sub-S288376_ses-202409151819_task-climbing2_run-01_bold.nii.gz
---> linked 16.nii.gz <-- sub-S288376_ses-202409151819_task-music2_run-01_sbref.nii.gz
---> linked 17.nii.gz <-- sub-S288376_ses-202409151819_task-music2_run-01_bold.nii.gz
---> linked 18.nii.gz <-- sub-S288376_ses-202409151819_task-rest_run-01_sbref.nii.gz
---> linked 19.nii.gz <-- sub-S288376_ses-202409151819_task-rest_run-01_bold.nii.gz
---> linked 20.nii.gz <-- sub-S288376_ses-202409151819_dir-AP_run-01_dwi.nii.gz
---> linked 21.nii.gz <-- sub-S288376_ses-202409151819_dir-PA_run-01_dwi.nii.gz
Running map_bids2nii for subject S288376
========================================
---> WARNING:
     Unrecognized session!
     This folder [/home/docker/volumes/hcppipelines/amitkeinan/cd_study/sessions/S288376] does not have a valid matching BIDS session!
     Please check your data!


Final report
============
subject S002759 image mapping failed
subject S002759, session 202508221215 image mapping completed
subject S125082 image mapping failed
subject S125082, session 202412111835 image mapping completed
subject S035513 image mapping failed
subject S035513, session 202411211521 image mapping completed
subject S036143 image mapping failed
subject S036143, session 202402201017 image mapping completed
subject S043941, session 202410201244 image mapping completed
subject S043941 image mapping failed
subject S140183, session 202210261924 image mapping completed
subject S140183 image mapping failed
subject S176993, session 202512051033 image mapping completed
subject S176993 image mapping failed
subject S199033 image mapping failed
subject S199033, session 202411191247 image mapping completed
subject S222954 image mapping failed
subject S222954, session 202410291354 image mapping completed
subject S288376, session 202409151819 image mapping completed
subject S288376 image mapping failed

---> ERROR in completing import_bids:
     Some actions failed
     Please check report!


-----------------------------------------
Finished at 2026-10-11 09:13:05

any help would be very appreciated!

thank you,

Amit

demsarjure · October 12, 2026, 3:25pm

Hi Amit,

It seems like the organization of folders is not completely BIDS compliant. Can you share one of the sessions with me so I can check this on my end, or is this some private data you cannot share?

Also when identifying sessions, you get a double hit for each one of them. For example:

    ---> creating bids session S140183_202210261924
    ---> creating bids session S140183

First one (S140183_202210261924) looks correct and fits the BIDS naming (SUBJECT_SESSION), I have no idea what the second folder is (S140183). Do you have a mix of BIDS and non-BIDS folders inside ${RAW_DATA}?

What you can also try is to onboard one session at a time. So you point --inbox directly to the BIDS folder of that session, and under --session set that session only.

Best, Jure