Hi,
I am using bidscoiner to transform my data to BIDS format, which works pretty well. it finds and renames all of my scans so that my directory (took as example ses02 because it-s most complete) looks like this
sub-003
│ ├── ses-02
│ │ ├── anat
│ │ │ ├── sub-003_ses-mri02_acq-MPRAGE_run-1_T1w.json
│ │ │ ├── sub-003_ses-mri02_acq-MPRAGE_run-1_T1w.nii.gz
│ │ │ ├── sub-003_ses-mri02_acq-SPC_run-1_T2w.json
│ │ │ └── sub-003_ses-mri02_acq-SPC_run-1_T2w.nii.gz
│ │ ├── fmap
│ │ │ ├── sub-003_ses-mri02_acq-MB_dir-COL_run-1_epi.json
│ │ │ └── sub-003_ses-mri02_acq-MB_dir-COL_run-1_epi.gz
│ │ ├── func
│ │ │ ├── sub-003_ses-mri02_task-1back_run-1_echo-1_bold.json
│ │ │ ├── sub-003_ses-mri02_task-1back_run-1_echo-1_bold.nii.gz
│ │ │ ├── sub-003_ses-mri02_task-1back_run-1_echo-1_sbref.json
│ │ │ └── sub-003_ses-mri02_task-1back_run-1_echo-1_sbref.nii.gz
Unfortunately if I look in my output file from fmriprep
191015-08:56:30,989 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.4.1:
* BIDS dataset path: /project/xxxx/analysis/BIDS.
* Participant list: ['003'].
* Run identifier: 20191015-085619_1d98ff63-0f80-4427-8246-047980302c41.
191015-08:56:45,604 nipype.workflow IMPORTANT:
Creating bold processing workflow for “/project/xxx/analysis/BIDS/sub-003/ses-mri02/func/sub-003_ses-mri02_task-1back_run-1_echo-1_bold.nii.gz” (0.62 GB / 724 TRs). Memory resampled/largemem=2.47/6.94 GB.
191015-08:56:45,690 nipype.workflow IMPORTANT:
No single-band-reference found for sub-003_ses-mri02_task-1back_run-1_echo-1_bold.nii.gz
191015-08:56:47,514 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
191015-08:56:47,730 nipype.workflow IMPORTANT:
SDC: fieldmap estimation of type “epi” intended for /project/xxx/analysis/BIDS/sub-003/ses-mri02/func/sub-003_ses-mri02_task-1back_run-1_echo-1_bold.nii.gz found.
191015-08:56:48,615 nipype.workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
How does fmriprep search for single-band reference images? How can I fix it?
Thanks a lot!