Dear community,
currently, I’m trying to get the apptainer version for dcm2bids to work. For the anatomy it seems to be ok, but for the restings state scans I get alyways no pairing issues.
The field map are from Siemens using the sequence gre_field_mapping_2.5mm, because the SeriesDescription is the same for the two resting state runs (and also the gre_field images), I copied the dicom images in specific folders (rest_run1, rest_run2 and fmap_run1, fmap_run2)
Command used (and if a helper script was used, a link to the helper script or the command generated):
INFO | Running the following command: /venv/bin/dcm2bids -d /server/fo2-22/data/AcEx/BIDS/new_scaffold/sourcedata/sub-4499/ses-V3 -p 4499 -s V3 -c /server/fo2-22/data/AcEx/BIDS/dcm2bids_config_new1.json -o /server/fo2-22/data/AcEx/BIDS/new_scaffold/BIDS --clobber
INFO | OS version: Linux-5.14.0-503.35.1.el9_5.x86_64-x86_64-with-glibc2.36
INFO | Python version: 3.12.3 | packaged by conda-forge | (main, Apr 15 2024, 18:38:13) [GCC 12.3.0]
INFO | dcm2bids version: 3.2.0
INFO | dcm2niix version: v1.0.20240202
INFO | Checking for software update
WARNING | Checking latest version of UNFmontreal/Dcm2Bids was not possible, your machine is probably not connected to the Internet.
WARNING | Checking latest version of rordenlab/dcm2niix was not possible, your machine is probably not connected to the Internet.
INFO | participant: sub-4499
INFO | session: ses-V3
INFO | config: /server/fo2-22/data/AcEx/BIDS/dcm2bids_config_new1.json
INFO | BIDS directory: /server/fo2-22/data/AcEx/BIDS/new_scaffold/BIDS
INFO | Auto extract entities: False
INFO | Reorder entities: True
INFO | Validate BIDS: False
INFO | Running: dcm2niix -b y -ba y -z y -f %3s_%f_%p_%t -o /server/fo2-22/data/AcEx/BIDS/new_scaffold/BIDS/tmp_dcm2bids/sub-4499_ses-V3 /server/fo2-22/data/AcEx/BIDS/new_scaffold/sourcedata/sub-4499/ses-V3
INFO | Check log file for dcm2niix output
INFO | SIDECAR PAIRING
INFO | No Pairing <- 029_ses-V3_gre_field_mapping_2.5mm_20250123111111_e1
INFO | No Pairing <- 029_ses-V3_gre_field_mapping_2.5mm_20250123111111_e2
INFO | No Pairing <- 030_ses-V3_gre_field_mapping_2.5mm_20250123111111_e2_ph
INFO | No Pairing <- 031_ses-V3_Rest_ep2d_bold_s4_2p5mm_20250123111111
INFO | sub-4499_ses-V3_T1w <- 005_ses-V3_T1w_MPR_20250109124814
INFO | sub-4499_ses-V3_T2w <- 006_ses-V3_T2w_SPC_20250109124814
INFO | No Pairing <- 029_ses-V3_gre_field_mapping_2.5mm_20250109131757_e1
INFO | No Pairing <- 029_ses-V3_gre_field_mapping_2.5mm_20250109131757_e2
INFO | No Pairing <- 030_ses-V3_gre_field_mapping_2.5mm_20250109131757_e2_ph
INFO | No Pairing <- 031_ses-V3_Rest_ep2d_bold_s4_2p5mm_20250109131757
INFO | Moving acquisitions into BIDS folder "/server/fo2-22/data/AcEx/BIDS/new_scaffold/BIDS/sub-4499/ses-V3".
INFO | Logs saved in /server/fo2-22/data/AcEx/BIDS/new_scaffold/BIDS/tmp_dcm2bids/log/sub-4499_ses-V3_20250616-132644.log
INFO | --- dcm2bids end ---
PASTE CODE HERE
Version:
3.2.0Environment (Docker, Singularity / Apptainer, custom installation):
apptainer version 1.4.0-1.el9Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
PASTE LOG OUTPUT HERE
```{
"descriptions": [
{
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"SeriesDescription": "*T1w*"
},
"customLabels": "",
"sidecarChanges": {
"ProtocolName":"T1w_MPR"
}
},
{
"datatype": "anat",
"suffix": "T2w",
"criteria": {
"SeriesDescription": "*T2w*"
},
"customLabels": "",
"sidecarChanges": {
"ProtocolName":"T2w_SPC"
}
},
{
"id": "task-rest_run-01",
"datatype": "func",
"suffix": "bold",
"criteria": {
"Folder": "rest_run1"
},
"custom_entitites": "task-rest_run-01",
"sidecarChanges": {
"TaskName": "rest"
}
},
{
"id":"task-rest_run-02",
"datatype": "func",
"suffix": "bold",
"criteria": {
"Folder": "rest_run2"
},
"custom_entities": "task-rest_run-02",
"sidecarChanges": {
"TaskName": "rest"
}
},
{
"datatype": "fmap",
"suffix": "phasediff",
"criteria": {
"Folder": "fmap_run1"
},
"custom_entitites": "run-01",
"B0FieldIdentifier": "phasediff",
"sidecarChanges": {
"IntendedFor": [
"ses-<session>_task-rest_run-01_bold.nii.gz"
]
}
},
{
"datatype": "fmap",
"suffix": "magnitude1",
"criteria": {
"Folder": "fmap_run1"
},
"customentitiels": "run-01",
"sidecarChanges": {}
},
{
"dataType": "fmap",
"suffix": "phasediff",
"criteria": {
"Folder": "fmap_run2"
},
"customLabels": "run-02",
"B0FieldIdentifier": "phasediff",
"sidecarChanges": {
"IntendedFor": [
"ses-<session>_task-rest_run-02_bold.nii.gz"
]
}
},
{
"dataType": "fmap",
"suffix": "magnitude1",
"criteria": {
"Folder": "fmap_run2"
},
"customLabels": "run-02",
"sidecarChanges": {}
}
]
}
### Screenshots / relevant information:
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