Error: Too many NIFTI images with the name
Closed this issue · 1 comments
i think something went wrong with the dcm2niix conversion. For some reason the individual volumes of the fMRI series were not merged together into a single 4D file
`INFO | --- dcm2bids start ---
INFO | Running the following command: /home/junhong.yu/dcm2bids/bin/dcm2bids -d /home/junhong.yu/PGMH/sourcedata/GEMH_0004/ -o /home/junhong.yu/PGMH/not_defaced/ -p 0004 -c /home/junhong.yu/PGMH/code/dcm2bids_config.json --auto_extract_entities --force_dcm2bids
INFO | OS version: Linux-3.10.0-693.el7.x86_64-x86_64-with-centos-7.5.1804-Core
INFO | Python version: 3.7.10 (default, Jun 4 2021, 06:52:02) [GCC 9.3.0]
INFO | dcm2bids version: 3.1.1
INFO | dcm2niix version: v1.0.20230411
INFO | Checking for software update
INFO | Currently using the latest version of dcm2bids.
INFO | Currently using the latest version of dcm2niix.
INFO | participant: sub-0004
INFO | config: /home/junhong.yu/PGMH/code/dcm2bids_config.json
INFO | BIDS directory: /home/junhong.yu/PGMH/not_defaced
INFO | Auto extract entities: True
INFO | Validate BIDS: False
INFO | Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004 /home/junhong.yu/PGMH/sourcedata/GEMH_0004
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131925
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131925
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131926
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131926
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131925
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131926
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131926
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/016_GEMH_0004_DeIdentified_20220520131925
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131936
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131937
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131934
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131934
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131937
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131937
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131934
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131936
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131938
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131936
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131934
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131935
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131934
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131935
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131936
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131935
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131936
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131939
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131938
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131938
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131937
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/018_GEMH_0004_DeIdentified_20220520131938
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/009_GEMH_0004_DeIdentified_20220520131819_e2_ph
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/009_GEMH_0004_DeIdentified_20220520131819_e2_ph
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/009_GEMH_0004_DeIdentified_20220520131819_e2_ph
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/009_GEMH_0004_DeIdentified_20220520131819_e2_ph
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131602
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131602
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131602
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131602
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131558
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131558
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131559
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131559
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131558
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131601
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131558
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131601
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131601
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131601
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/006_GEMH_0004_DeIdentified_20220520131557
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131547
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131548
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131548
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131547
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131548
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131547
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131549
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131548
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131549
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131548
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131549
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131547
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131547
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131549
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/001_GEMH_0004_DeIdentified_20220520131549
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131932
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131932
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131932
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131929
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131931
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131929
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131929
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131931
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131931
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131932
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131928
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131928
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131928
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131927
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131928
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131930
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131930
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131930
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131929
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131931
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/017_GEMH_0004_DeIdentified_20220520131930
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131552
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131552
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131552
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131553
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131554
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131553
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131554
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131552
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131552
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131553
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131551
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131556
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131555
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131556
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131556
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131554
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131553
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131551
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131554
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131553
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131556
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131555
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131555
Error: Too many NIFTI images with the name /home/junhong.yu/PGMH/not_defaced/tmp_dcm2bids/sub-0004/005_GEMH_0004_DeIdentified_20220520131555
Error: Converted 2330 of 2440 files
`
Dear @CogBrainHealthLab ,
I suggest you to submit this question on neurostars with the tags dcm2niix and dcm2bids.
Since it's a dcm2niix issue and it could be useful for other users, it will make more sense to raise this issue on neurostars
Best,
Arnaud