Summary of what happened:
Hi,
I am new to fMRI processing and confused by my fMRIPrep results. I believe my fMRI data is multiband EPI since I used ABCD protocols, but I couldn’t find a corresponding DICOM tag in my raw data.
However, when checking the fMRIPrep results report, I noticed that the output appears to be single-band instead of multiband.
To convert my data into BIDS format, I used dcm2bids with the following config file:
{
"descriptions": [
{
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"SeriesDescription": "ABCD_T1w_MPR_vNav"
}
},
{
"datatype": "anat",
"suffix": "T2w",
"criteria": {
"SeriesDescription": "ABCD_T2w_MPR_vNav"
}
},
{
"descriptions": [
{
"datatype": "fmap",
"criteria": {
"SeriesDescription": "ABCD_fMRI_DistortionMap_PA"
},
"sidecar_changes": {
"IntendedFor": "task-memory",
"PhaseEncodingDirection": "j-"
},
"custom_entities": "distmap_PA"
}
]
},
{
"descriptions": [
{
"datatype": "fmap",
"criteria": {
"SeriesDescription": "ABCD_fMRI_DistortionMap_AP"
},
"sidecar_changes": {
"IntendedFor": "XXXX",
"PhaseEncodingDirection": "j"
},
"custom_entities": "distmap_AP"
}
]
},
{
"id": "XXXX",
"datatype": "func",
"suffix": "task-XXXX_run-01_bold",
"criteria": {
"SeriesDescription": "ABCD_fMRI"
},
"sidecar_changes": {
"TaskName": "task-XXXX_run-01_bold",
"PhaseEncodingDirection": "j"
}
},
{
"datatype": "func",
"suffix": "physio",
"criteria": {
"SeriesDescription": "ABCD_fMRI_PMU"
},
"filenameEntities": {
"task": "XXXX"
}
}
]
}
I would appreciate any insights into what might be causing this issue:
- Could my
dcm2bidsconfiguration be incorrect, leading to improper BIDS conversion? - Could my fMRIPrep command be missing parameters that ensure proper recognition of multiband data?
Any guidance on how to troubleshoot this would be greatly appreciated.
Thank you!
Command used (and if a helper script was used, a link to the helper script or the command generated):
After conversion, I ran fMRIPrep using Docker with the following command:
docker run --rm -e DOCKER_VERSION_8395080871=20.10.17 -it \
--platform linux/amd64 \
-v $FS_LICENSE:/opt/freesurfer/license.txt:ro \
-v $bids_root_dir:/data:ro \
-v $bids_root_dir/derivatives:/out \
-v $HOME:/scratch \
nipreps/fmriprep:24.1.1 /data /out participant \
--participant-label $subj \
--skip-bids-validation \
--nthreads $nthreads \
--stop-on-first-crash \
--mem_mb $mem_mb \
-w /scratch \
Version:
fmriprep 24.1.1
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data 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
