Summary of what happened:
Hi, experts,
- I’m curious about why the following warning is generated. Additionally, is the warning critical? I work with batch scripts in a Windows environment.
- WARNING | {‘task’} have not been found for datatype ‘func’ and suffix ‘bold’.
- I’m curious if I should use the following code
- –bids_validate --force_dcm2bids --clobber
Command used (and if a helper script was used, a link to the helper script or the command generated):
@echo off
setlocal enabledelayedexpansion
set "source_folder=D:\ys\sourcedata"
set "dcm2bids_command=dcm2bids -c code\dcm2bids_config.json -s 1 --auto_extract_entities"
for /d %%i in ("%source_folder%\*") do (
set "folder_name=%%~nxi"
set "participant_id=!folder_name:~0,3!"
start cmd /k "%dcm2bids_command% -d "%%i" -p "!participant_id!""
)
Version:
v. 3.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
→ anaconda
Python version: 3.12.3 | packaged by conda-forge
Data formatted according to a validatable standard? Please provide the output of the validator:
sub-056/ses-1
├── anat
│ ├── sub-056_ses-1_T1w.json
│ ├── sub-056_ses-1_T1w.nii
│ ├── sub-056_ses-1_T2w.json
│ └── sub-056_ses-1_T2w.nii
├── fmap
│ ├── sub-056_ses-1_magnitude1.json
│ ├── sub-056_ses-1_magnitude1.nii
│ ├── sub-056_ses-1_magnitude2.json
│ ├── sub-056_ses-1_magnitude2.nii
│ ├── sub-056_ses-1_phasediff.json
│ └── sub-056_ses-1_phasediff.nii
└── func
├── sub-056_ses-1_task-rest_run-01_bold.json
├── sub-056_ses-1_task-rest_run-01_bold.nii
├── sub-056_ses-1_task-rest_run-02_bold.json
└── sub-056_ses-1_task-rest_run-02_bold.nii
Relevant log outputs (up to 20 lines):
2024-05-13 03:20:39.857 - INFO - dcm2niix_gen.execute | Check log file for dcm2niix output
2024-05-13 03:20:39.860 - INFO - sidecar.build_acquisitions | SIDECAR PAIRING
2024-05-13 03:20:39.860 - WARNING - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-05-13 03:20:39.860 - INFO - sidecar.build_acquisitions | sub-056_ses-1_task-rest_bold <- 056_AAA_ep2d_FOV240_3x3x3_30sl_TR2000_TE30_bw1096Hz_whole_brain_20151104110000_17
2024-05-13 03:20:39.860 - WARNING - sidecar.searchDcmTagEntity | {'task'} have not been found for datatype 'func' and suffix 'bold'.
2024-05-13 03:20:39.860 - INFO - sidecar.build_acquisitions | sub-056_ses-1_task-rest_bold <- 056_AAA_ep2d_FOV240_3x3x3_30sl_TR2000_TE30_bw1096Hz_whole_brain_20151104110000_22
2024-05-13 03:20:39.860 - INFO - sidecar.build_acquisitions | sub-056_ses-1_magnitude1 <- 056_AAA_field_map_20151104110000_27_e1
2024-05-13 03:20:39.860 - INFO - sidecar.build_acquisitions | sub-056_ses-1_magnitude2 <- 056_AAA_field_map_20151104110000_27_e2
2024-05-13 03:20:39.860 - INFO - sidecar.build_acquisitions | sub-056_ses-1_phasediff <- 056_AAA_field_map_20151104110000_28_e2_ph
2024-05-13 03:20:39.861 - INFO - sidecar.build_acquisitions | sub-056_ses-1_T1w <- 056_AAA_t1_mpr_sag_p2_1mm_WholeBrain_20151104110000_29
2024-05-13 03:20:39.861 - INFO - sidecar.build_acquisitions | sub-056_ses-1_T2w <- 056_AAA_t2_tirm_tra_dark-fluid_20151104110000_30
2024-05-13 03:20:39.861 - INFO - sidecar.find_runs | sub-056\ses-1\func\sub-056_ses-1_task-rest_bold has 2 runs
2024-05-13 03:20:39.861 - INFO - sidecar.find_runs | Adding run information to the acquisition
2024-05-13 03:20:39.861 - INFO - dcm2bids_gen.run | Moving acquisitions into BIDS folder "d:\ys\sub-056\ses-1".
Screenshots / relevant information:
<config file>
{
"dcm2niixOptions": "-ba n",
"descriptions": [
{
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"SeriesDescription": "t1*",
"EchoTime": 0.00236,
"RepetitionTime": 2.3
},
"sidecar_changes": {
"ProtocolName": "T1"
}
},
{
"datatype": "anat",
"suffix": "T2w",
"criteria": {
"SeriesDescription": "t2*",
"EchoTime": 0.093,
"RepetitionTime": 9
},
"sidecar_changes": {
"ProtocolName": "T2"
}
},
{
"id": "task_rest",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest",
"criteria": {
"EchoTime": 0.03,
"RepetitionTime": 2
}
},
{
"datatype": "fmap",
"suffix": "magnitude1",
"criteria": {
"ProtocolName": "field_map",
"EchoTime": 0.00492
},
"sidecar_changes": {
"IntendedFor": "task_rest"
}
},
{
"datatype": "fmap",
"suffix": "magnitude2",
"criteria": {
"ProtocolName": "field_map",
"EchoTime": 0.00738,
"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"]
},
"sidecar_changes": {
"IntendedFor": "task_rest"
}
},
{
"datatype": "fmap",
"suffix": "phasediff",
"criteria": {
"ProtocolName": "field_map",
"EchoTime": 0.00738,
"ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"]
},
"sidecar_changes": {
"IntendedFor": "task_rest"
}
}
]
}