Unable to pair Topup scan to BOLD fmri

Hi all,

I am using Fmriprep v21 for a dataset with multiple sessions. Right now my folder structure is:

/dbstore/Rijnstate/SYNAPSE/BIDS3/sub-009
├── ses-01
│ ├── anat
│ │ ├── sub-009_ses-01_T1w.json
│ │ └── sub-009_ses-01_T1w.nii.gz
│ ├── dwi
│ │ ├── sub-009_ses-01_run-01_dwi.json
│ │ ├── sub-009_ses-01_run-01_dwi.nii.gz
│ │ ├── sub-009_ses-01_run-02_dwi.bval
│ │ ├── sub-009_ses-01_run-02_dwi.bvec
│ │ ├── sub-009_ses-01_run-02_dwi.json
│ │ └── sub-009_ses-01_run-02_dwi.nii.gz
│ ├── fmap
│ │ ├── sub-009_ses-01_dir-AP_epi.json
│ │ └── sub-009_ses-01_dir-AP_epi.nii.gz
│ └── func
│ ├── sub-009_ses-01_task-rest_bold.json
│ └── sub-009_ses-01_task-rest_bold.nii.gz
├── ses-02
│ ├── anat
│ │ ├── sub-009_ses-02_T1w.json
│ │ └── sub-009_ses-02_T1w.nii.gz
│ ├── dwi
│ │ ├── sub-009_ses-02_run-01_dwi.json
│ │ ├── sub-009_ses-02_run-01_dwi.nii.gz
│ │ ├── sub-009_ses-02_run-02_dwi.bval
│ │ ├── sub-009_ses-02_run-02_dwi.bvec
│ │ ├── sub-009_ses-02_run-02_dwi.json
│ │ └── sub-009_ses-02_run-02_dwi.nii.gz
│ ├── fmap
│ │ ├── sub-009_ses-02_dir-AP_epi.json
│ │ └── sub-009_ses-02_dir-AP_epi.nii.gz
│ └── func
│ ├── sub-009_ses-02_task-rest_bold.json
│ └── sub-009_ses-02_task-rest_bold.nii.gz
├── ses-03
│ ├── anat
│ │ ├── sub-009_ses-03_T1w.json
│ │ └── sub-009_ses-03_T1w.nii.gz
│ ├── dwi
│ │ ├── sub-009_ses-03_run-01_dwi.json
│ │ ├── sub-009_ses-03_run-01_dwi.nii.gz
│ │ ├── sub-009_ses-03_run-02_dwi.bval
│ │ ├── sub-009_ses-03_run-02_dwi.bvec
│ │ ├── sub-009_ses-03_run-02_dwi.json
│ │ └── sub-009_ses-03_run-02_dwi.nii.gz
│ ├── fmap
│ │ ├── sub-009_ses-03_dir-AP_epi.json
│ │ └── sub-009_ses-03_dir-AP_epi.nii.gz
│ └── func
│ ├── sub-009_ses-03_task-rest_bold.json
│ └── sub-009_ses-03_task-rest_bold.nii.gz
├── ses-04
│ ├── anat
│ │ ├── sub-009_ses-04_T1w.json
│ │ └── sub-009_ses-04_T1w.nii.gz
│ ├── dwi
│ │ ├── sub-009_ses-04_run-01_dwi.json
│ │ ├── sub-009_ses-04_run-01_dwi.nii.gz
│ │ ├── sub-009_ses-04_run-02_dwi.bval
│ │ ├── sub-009_ses-04_run-02_dwi.bvec
│ │ ├── sub-009_ses-04_run-02_dwi.json
│ │ └── sub-009_ses-04_run-02_dwi.nii.gz
│ ├── fmap
│ │ ├── sub-009_ses-04_dir-AP_epi.json
│ │ └── sub-009_ses-04_dir-AP_epi.nii.gz
│ └── func
│ ├── sub-009_ses-04_task-rest_bold.json
│ └── sub-009_ses-04_task-rest_bold.nii.gz
├── ses-05
│ ├── anat
│ │ ├── sub-009_ses-05_T1w.json
│ │ └── sub-009_ses-05_T1w.nii.gz
│ ├── dwi
│ │ ├── sub-009_ses-05_dwi.bval
│ │ ├── sub-009_ses-05_dwi.bvec
│ │ ├── sub-009_ses-05_dwi.json
│ │ └── sub-009_ses-05_dwi.nii.gz
│ ├── fmap
│ │ ├── sub-009_ses-05_dir-AP_epi.json
│ │ └── sub-009_ses-05_dir-AP_epi.nii.gz
│ └── func
│ ├── sub-009_ses-05_task-rest_bold.json
│ └── sub-009_ses-05_task-rest_bold.nii.gz
└── ses-06
├── anat
│ ├── sub-009_ses-06_T1w.json
│ └── sub-009_ses-06_T1w.nii.gz
├── dwi
│ ├── sub-009_ses-06_dwi.bval
│ ├── sub-009_ses-06_dwi.bvec
│ ├── sub-009_ses-06_dwi.json
│ └── sub-009_ses-06_dwi.nii.gz
├── fmap
│ ├── sub-009_ses-06_dir-AP_epi.json
│ └── sub-009_ses-06_dir-AP_epi.nii.gz
└── func
├── sub-009_ses-06_task-rest_bold.json
└── sub-009_ses-06_task-rest_bold.nii.gz

I am trying to pair a topup scan per session to it’s respective bold fmri scan. Unfortunately, fmriprep does not work and BIDS validator gives the following error:

sub-009_ses-01_dir-AP_epi.nii.gz 610.716 KB | application/gzip

Location:

BIDS3/sub-009/ses-01/fmap/sub-009_ses-01_dir-AP_epi.nii.gz

Reason:

‘IntendedFor’ property of this fieldmap (’/sub-009/ses-01/fmap/sub-009_ses-01_dir-AP_epi.nii.gz’) does not point to an existing file(’/ses-01/func/sub-009_ses-01_task-rest_bold.nii.gz’). Please mind that this value should not include subject level directory (’/sub-009/’).

Evidence:

/ses-01/func/sub-009_ses-01_task-rest_bold.nii.gz

I tried multiple variations of the pathname in ‘Intendedfor’, but none seem to work (fe removing /, including the full path, etc).

Does anyone have an idea what the problem is?

Thank you in advance!
Kind regards, Joey Verdijk

The session issue could be a bug. But you’re going to have an additional issue: https://github.com/nipreps/fmriprep/issues/2667

We’re working to restore support for BOLD series that only have reverse-phase-encoded fieldmaps.

Please follow-up on GitHub.

Okay, thank you for your quick answer. I will continue without phase encoding correction and will await a new version of fmriprep.

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