Fieldmaps not used for SDC in fmriprep

AJK · September 26, 2023, 6:05pm

Summary of what happened:

My fieldmaps are not being used to perform SDC. I believe the sidecar files (IntendedFor field) is correctly specified, and they are correctly detected by fmriprep because it does "Preprocessed B0 mapping acquisition) for my fmaps, which are one true fieldmap with a magnitude image. They just aren’t used for susceptibility distortion correction of the subsequent functional runs.

Command used (and if a helper script was used, a link to the helper script or the command generated):

singularity run --cleanenv -B LUNA:/data -B LUNA/derivatives/fmriprep-22.1.1:/out -B /lscratch/adamkra:/work singularity_images/fmriprep-22.1.1.simg LUNA LUNA/derivatives/fmriprep-22.1.1 participant --participant-label LUNA017 -w /lscratch/adamkra -vv --omp-nthreads 24 --nthreads 24 --mem 100000 --use-syn-sdc --cifti-output --output-spaces MNI152NLin2009cAsym:res-2 anat fsnative fsaverage5 --use-aroma --skip_bids_validation --dummy-scans 3 --fd-spike-threshold 0.5 --dvars-spike-threshold 1.5

And here is the IntendedFor field from one of the fieldmaps (/fmap/sub-LUNA017_ses-ETX_run-01_fieldmap.nii.gz; and its associated magnitude image: /fmap/sub-LUNA017_ses-ETX_run-01_magnitude.nii.gz).

"IntendedFor": ["bids::ses-ETX/func/sub-LUNA017_ses-ETX_task-noncon2_bold.nii.gz","bids::ses-ETX/func/sub-LUNA017_ses-ETX_task-con2_bold.nii.gz",
    "bids::ses-ETX/func/sub-LUNA017_ses-ETX_task-emoreg_bold.nii.gz"]

Version:

     fMRIPrep 22.1.1

Environment (Docker, Singularity, custom installation):

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

BIDS-formatted and fully validated

Relevant log outputs (up to 20 lines):

In the log, it says …

"Found usable B0-map (fieldmap) estimator(s) <b0_fmap01> to correct <LUNA/sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-con2_bold.nii.gz> for susceptibility-derived distortions."

…but in the html report, it still says “Susceptibility distortion correction: None” for that functional run.

Perhaps I’m missing something very obvious, but would appreciate any help in figuring this one out! Thank you

Steven · September 26, 2023, 6:25pm

Hi @AJK and welcome to neurostars!

Can you return the output of tree on a subject directory (the raw data, as well as an fmriprep output)? Also, can you show the full log of BIDS validation please?

Thanks,
Steven

AJK · September 26, 2023, 7:05pm

Thanks so much for the quick reply!

Here is the tree output for the subject directory (just for context, these participants have two sessions, but for this participant, no fmaps were collected in one session for some reason, so I’m only including info from the ETX session which did have fmaps and will have SDC) :

sub-LUNA017
├── ses-ETX
    ├── anat
    │   ├── sub-LUNA017_ses-ETX_T1w.json
    │   ├── sub-LUNA017_ses-ETX_T1w.nii.gz
    │   ├── sub-LUNA017_ses-ETX_T2w.json
    │   └── sub-LUNA017_ses-ETX_T2w.nii.gz
    ├── fmap
    │   ├── sub-LUNA017_ses-ETX_run-01_fieldmap.json
    │   ├── sub-LUNA017_ses-ETX_run-01_fieldmap.nii.gz
    │   ├── sub-LUNA017_ses-ETX_run-01_magnitude.nii.gz
    │   ├── sub-LUNA017_ses-ETX_run-02_fieldmap.json
    │   ├── sub-LUNA017_ses-ETX_run-02_fieldmap.nii.gz
    │   └── sub-LUNA017_ses-ETX_run-02_magnitude.nii.gz
    └── func
        ├── sub-LUNA017_ses-ETX_task-con2_bold.json
        ├── sub-LUNA017_ses-ETX_task-con2_bold.nii.gz
        ├── sub-LUNA017_ses-ETX_task-emocon2_bold.json
        ├── sub-LUNA017_ses-ETX_task-emocon2_bold.nii.gz
        ├── sub-LUNA017_ses-ETX_task-emoreg_bold.json
        ├── sub-LUNA017_ses-ETX_task-emoreg_bold.nii.gz
        ├── sub-LUNA017_ses-ETX_task-gonogo2_bold.json
        ├── sub-LUNA017_ses-ETX_task-gonogo2_bold.nii.gz
        ├── sub-LUNA017_ses-ETX_task-noncon2_bold.json
        ├── sub-LUNA017_ses-ETX_task-noncon2_bold.nii.gz

And here is the tree from the fmriprep output (same note as above about ETX session being the one of interest, so for space, I’m just pasting the ses-ETX directory within the fmriprep derivatives):

.
├── anat
│   └── sub-LUNA017_ses-ETX_from-orig_to-T1w_mode-image_xfm.txt
├── fmap
│   ├── sub-LUNA017_ses-ETX_run-01_fmapid-b0fmap01_desc-coeff0_fieldmap.nii.gz
│   ├── sub-LUNA017_ses-ETX_run-01_fmapid-b0fmap01_desc-coeff1_fieldmap.nii.gz
│   ├── sub-LUNA017_ses-ETX_run-01_fmapid-b0fmap01_desc-magnitude_fieldmap.nii.gz
│   ├── sub-LUNA017_ses-ETX_run-01_fmapid-b0fmap01_desc-preproc_fieldmap.json
│   ├── sub-LUNA017_ses-ETX_run-01_fmapid-b0fmap01_desc-preproc_fieldmap.nii.gz
│   ├── sub-LUNA017_ses-ETX_run-02_fmapid-b0fmap02_desc-coeff0_fieldmap.nii.gz
│   ├── sub-LUNA017_ses-ETX_run-02_fmapid-b0fmap02_desc-coeff1_fieldmap.nii.gz
│   ├── sub-LUNA017_ses-ETX_run-02_fmapid-b0fmap02_desc-magnitude_fieldmap.nii.gz
│   ├── sub-LUNA017_ses-ETX_run-02_fmapid-b0fmap02_desc-preproc_fieldmap.json
│   └── sub-LUNA017_ses-ETX_run-02_fmapid-b0fmap02_desc-preproc_fieldmap.nii.gz
└── func
    ├── sub-LUNA017_ses-ETX_task-con2_AROMAnoiseICs.csv
    ├── sub-LUNA017_ses-ETX_task-con2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_desc-MELODIC_mixing.tsv
    ├── sub-LUNA017_ses-ETX_task-con2_desc-confounds_timeseries.json
    ├── sub-LUNA017_ses-ETX_task-con2_desc-confounds_timeseries.tsv
    ├── sub-LUNA017_ses-ETX_task-con2_from-T1w_to-scanner_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-con2_from-scanner_to-T1w_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-con2_from-scanner_to-boldref_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-L_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-L_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-L_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-L_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-R_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-R_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-R_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-con2_hemi-R_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_boldref.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin2009cAsym_res-2_desc-preproc_smoothed-6mm_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-T1w_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-T1w_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-T1w_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-T1w_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-T1w_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-T1w_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-con2_space-T1w_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-con2_space-fsLR_den-91k_bold.dtseries.nii
    ├── sub-LUNA017_ses-ETX_task-con2_space-fsLR_den-91k_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_AROMAnoiseICs.csv
    ├── sub-LUNA017_ses-ETX_task-emocon2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_desc-MELODIC_mixing.tsv
    ├── sub-LUNA017_ses-ETX_task-emocon2_desc-confounds_timeseries.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_desc-confounds_timeseries.tsv
    ├── sub-LUNA017_ses-ETX_task-emocon2_from-T1w_to-scanner_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-emocon2_from-scanner_to-T1w_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-emocon2_from-scanner_to-boldref_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-L_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-L_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-L_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-L_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-R_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-R_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-R_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emocon2_hemi-R_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_boldref.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin2009cAsym_res-2_desc-preproc_smoothed-6mm_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-T1w_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-T1w_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-T1w_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-T1w_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-T1w_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-T1w_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-T1w_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-fsLR_den-91k_bold.dtseries.nii
    ├── sub-LUNA017_ses-ETX_task-emocon2_space-fsLR_den-91k_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_AROMAnoiseICs.csv
    ├── sub-LUNA017_ses-ETX_task-emoreg_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_desc-MELODIC_mixing.tsv
    ├── sub-LUNA017_ses-ETX_task-emoreg_desc-confounds_timeseries.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_desc-confounds_timeseries.tsv
    ├── sub-LUNA017_ses-ETX_task-emoreg_from-T1w_to-scanner_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-emoreg_from-scanner_to-T1w_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-emoreg_from-scanner_to-boldref_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-L_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-L_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-L_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-L_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-R_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-R_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-R_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-emoreg_hemi-R_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_boldref.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin2009cAsym_res-2_desc-preproc_smoothed-6mm_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-T1w_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-T1w_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-T1w_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-T1w_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-T1w_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-T1w_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-T1w_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-fsLR_den-91k_bold.dtseries.nii
    ├── sub-LUNA017_ses-ETX_task-emoreg_space-fsLR_den-91k_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_AROMAnoiseICs.csv
    ├── sub-LUNA017_ses-ETX_task-gonogo2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_desc-MELODIC_mixing.tsv
    ├── sub-LUNA017_ses-ETX_task-gonogo2_desc-confounds_timeseries.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_desc-confounds_timeseries.tsv
    ├── sub-LUNA017_ses-ETX_task-gonogo2_from-T1w_to-scanner_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-gonogo2_from-scanner_to-T1w_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-gonogo2_from-scanner_to-boldref_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-L_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-L_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-L_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-L_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-R_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-R_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-R_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-gonogo2_hemi-R_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_boldref.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin2009cAsym_res-2_desc-preproc_smoothed-6mm_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-T1w_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-T1w_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-T1w_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-T1w_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-T1w_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-T1w_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-T1w_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-fsLR_den-91k_bold.dtseries.nii
    ├── sub-LUNA017_ses-ETX_task-gonogo2_space-fsLR_den-91k_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_AROMAnoiseICs.csv
    ├── sub-LUNA017_ses-ETX_task-noncon2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_desc-MELODIC_mixing.tsv
    ├── sub-LUNA017_ses-ETX_task-noncon2_desc-confounds_timeseries.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_desc-confounds_timeseries.tsv
    ├── sub-LUNA017_ses-ETX_task-noncon2_from-T1w_to-scanner_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-noncon2_from-scanner_to-T1w_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-noncon2_from-scanner_to-boldref_mode-image_xfm.txt
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-L_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-L_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-L_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-L_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-R_space-fsaverage5_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-R_space-fsaverage5_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-R_space-fsnative_bold.func.gii
    ├── sub-LUNA017_ses-ETX_task-noncon2_hemi-R_space-fsnative_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_boldref.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin2009cAsym_res-2_desc-preproc_smoothed-6mm_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-T1w_boldref.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-T1w_desc-aparcaseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-T1w_desc-aseg_dseg.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-T1w_desc-brain_mask.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-T1w_desc-brain_mask.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-T1w_desc-preproc_bold.json
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-T1w_desc-preproc_bold.nii.gz
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-fsLR_den-91k_bold.dtseries.nii
    ├── sub-LUNA017_ses-ETX_task-noncon2_space-fsLR_den-91k_bold.json

Finally, here is the BIDS validator output – we don’t have the events files since we’re doing our task modeling separately.

File Path: Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word "rest".

	Type:		Warning
	File:		sub-LUNA017_ses-BL_task-con2_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_task-con2_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-con2_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-con2_events.tsv, /sub-LUNA017/ses-BL/sub-LUNA017_ses-BL_events.tsv, /sub-LUNA017/ses-BL/sub-LUNA017_ses-BL_task-con2_events.tsv, /sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_events.tsv, /sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_task-con2_events.tsv
	Type:		Warning
	File:		sub-LUNA017_ses-BL_task-emoreg_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_task-emoreg_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-emoreg_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-emoreg_events.tsv, /sub-LUNA017/ses-BL/sub-LUNA017_ses-BL_events.tsv, /sub-LUNA017/ses-BL/sub-LUNA017_ses-BL_task-emoreg_events.tsv, /sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_events.tsv, /sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_task-emoreg_events.tsv
	Type:		Warning
	File:		sub-LUNA017_ses-BL_task-noncon2_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_task-noncon2_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-noncon2_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-noncon2_events.tsv, /sub-LUNA017/ses-BL/sub-LUNA017_ses-BL_events.tsv, /sub-LUNA017/ses-BL/sub-LUNA017_ses-BL_task-noncon2_events.tsv, /sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_events.tsv, /sub-LUNA017/ses-BL/func/sub-LUNA017_ses-BL_task-noncon2_events.tsv
	Type:		Warning
	File:		sub-LUNA017_ses-ETX_task-con2_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-con2_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-con2_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-con2_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_task-con2_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-con2_events.tsv
	Type:		Warning
	File:		sub-LUNA017_ses-ETX_task-emocon2_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-emocon2_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-emocon2_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-emocon2_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_task-emocon2_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-emocon2_events.tsv
	Type:		Warning
	File:		sub-LUNA017_ses-ETX_task-emoreg_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-emoreg_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-emoreg_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-emoreg_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_task-emoreg_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-emoreg_events.tsv
	Type:		Warning
	File:		sub-LUNA017_ses-ETX_task-gonogo2_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-gonogo2_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-gonogo2_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-gonogo2_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_task-gonogo2_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-gonogo2_events.tsv
	Type:		Warning
	File:		sub-LUNA017_ses-ETX_task-noncon2_bold.nii.gz
	Location:		LUNA/sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-noncon2_bold.nii.gz
	Reason:		Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /events.tsv, /task-noncon2_events.tsv, /sub-LUNA017/sub-LUNA017_events.tsv, /sub-LUNA017/sub-LUNA017_task-noncon2_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/sub-LUNA017_ses-ETX_task-noncon2_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_events.tsv, /sub-LUNA017/ses-ETX/func/sub-LUNA017_ses-ETX_task-noncon2_events.tsv

Again, very much appreciate your help!

Steven · September 26, 2023, 7:44pm

Hmm, looks good upon first glance. Can you share an example HTML output?

AJK · September 26, 2023, 7:59pm

Sure thing. There’s quite a bit, so I’ll try to only include relevant bits. Let me know if there’s more I can add.

Summary

Subject ID: LUNA017
Structural images: 2 T1-weighted (+ 1 T2-weighted)
Functional series: 12
    Task: con2 (2 runs)
    Task: emocon2 (1 run)
    Task: emoreg (2 runs)
    Task: gonogo2 (1 run)
    Task: noncon2 (2 runs)
    Task: restpe0 (3 runs)
    Task: restpe1 (1 run)
Standard output spaces: MNI152NLin2009cAsym, fsaverage, MNI152NLin6Asym
Non-standard output spaces: anat, fsnative
FreeSurfer reconstruction: Run by fMRIPrep

(Skipping Anatomical Section…)

B0 field mapping

Reports for: session ETX, run 1, fmapid b0fmap01.

Preprocessed B0 mapping acquisition

Hover over the panels with the mouse pointer to also visualize the intensity of the field inhomogeneity in Hertz.

Inhomogeneities of the B0 field introduce (oftentimes severe) spatial distortions along the phase-encoding direction of the image. Some scanners produce a B0 mapping of the field, using Spiral Echo Imaging (SEI) or postprocessing a “phase-difference” acquisition. The plot below shows an anatomical “magnitude” reference and the corresponding fieldmap.

Functional
Reports for: session ETX, task con2.
Summary

Original orientation: LAS
Repetition time (TR): 2s
Phase-encoding (PE) direction: Anterior-Posterior
Single-echo EPI sequence.
Slice timing correction: Applied
Susceptibility distortion correction: None
Registration: FreeSurfer bbregister (boundary-based registration, BBR) - 6 dof
Non-steady-state volumes: 3 (Warning: 2 automatically detected)

(Won’t post the other fmaps since I can only include one image upload per reply, or the reports for the other functional runs, as they all look like this. Generally, seems like fmaps are detected and processed but not associated with any functional runs for SDC.)

In case it’s helpful, I’ll post the sidecar file for this first fmap (sub-LUNA017_ses-ETX_run-01_fieldmap.nii.gz + sub-LUNA017_ses-ETX_run-01_magnitude.nii.gz). My best guess is that I’m doing something wrong here, but not sure what. I’m sure it’s obvious I’m just missing something!

{
  "acquisition_matrix": [
    2048, 
    256
  ], 
  "acquisition_number": 2, 
  "effective_echo_spacing": 0.0, 
  "exam_datetime": "20220605 091200", 
  "exam_number": 25297, 
  "flip_angle": 70.0, 
  "fov": [
    222.0, 
    222.0
  ], 
  "mt_offset_hz": 0, 
  "num_acquired_timepoints": 2, 
  "num_echos": 1, 
  "num_receivers": 32, 
  "num_slices": 45, 
  "operator": "pal217", 
  "partial_ky": 1.0, 
  "patient_id": "", 
  "phase_encode_direction": 0, 
  "phase_encode_undersample": 1.0, 
  "pixel_bandwidth": 125.0, 
  "protocol_name": "Luna 11.13.20", 
  "psd_name": "sprt", 
  "receive_coil_name": "RM:Nova32ch2", 
  "recon_command": "/flywheel/v0/spirec28 -l --rotate -90 --magfile --savefmap2 --b0navigator -r /tmp/pfiledc/25297_3_2_pfile.7/P51712.7 -t /tmp/recon/recon",
  "series_description": "spiral high-res fieldmap_run001", 
  "series_number": 3, 
  "slice_encode_undersample": 1.0, 
  "te": 0.0045, 
  "ti": 0.0, 
  "tr": 1.4,
  "B0FieldIdentifier": "b0_fmap01",
  "Units": "Hz",
  "IntendedFor": ["bids::ses-ETX/func/sub-LUNA017_ses-ETX_task-noncon2_bold.nii.gz","bids::ses-ETX/func/sub-LUNA017_ses-ETX_task-con2_bold.nii.gz",
    "bids::ses-ETX/func/sub-LUNA017_ses-ETX_task-emoreg_bold.nii.gz"]

}

Steven · September 26, 2023, 8:12pm

Just to make sure, you don’t see something like this in the functional report?

Steven · September 26, 2023, 8:13pm

Also,

This, while technically BIDS valid, is not supported by fmriprep yet. For now, every IntendedFor entry should begin in the path relative to the subject folder (so for you that begins with session level).

Best,
Steven

AJK · September 26, 2023, 8:16pm

Oh yes I’m sure this must be the issue, as I wasn’t sure about it when building out the sidecars. Will change and retry. Thank you for catching that. Many details in setting this up for the first time, and this one got overlooked.

Yunhong_Wang · March 27, 2024, 2:18pm

Hi @Steven

I meet the same issue that fieldmaps were not worked for SDC. My fieldmaps are consisted of one phase-difference map with two magnitude images. I did not see the html output of SDC and html gave me Susceptibility distortion correction: None.

According your conversation, the IntendedFor in .json is necessary for fmriprep calling SDC.

Should I manually add IntendedFor in _phasediff.json?

For example,

{
   "IntendedFor": [
        "bids::sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_bold.nii.gz",
        "bids::sub-001/ses-01/func/sub-001_ses-01_task-movie_run-1_bold.nii.gz"
    ]
}

By the way, I used heudiconv to conduct convention.

Best,
Yunhong

Steven · March 27, 2024, 2:20pm

Hi @Yunhong_Wang,

Yunhong_Wang:

{
   "IntendedFor": [
        "bids::sub-001/ses-01/func/sub-001_ses-01_task-rest_run-1_bold.nii.gz",
        "bids::sub-001/ses-01/func/sub-001_ses-01_task-movie_run-1_bold.nii.gz"
    ]
}

fMRIPrep does not yet (but will soon) support the BIDS URI for “IntendedFor”. Until it does, you can get it to work by removing bids::sub-001/ from each entry.

Phasediff is where IntendedFor should go.

You can also use the B0FieldSource/B0FieldIdentifier method (Magnetic Resonance Imaging - Brain Imaging Data Structure v1.9.0).

Best,
Steven

Yunhong_Wang · March 27, 2024, 2:27pm

Hi @Steven

Appreciate your help!

Could heudiconv automatically add IntendedFor in _phasediff.json?

And whether _magnitude1.json and _magnitude2.json need IntendedFor too?

Best,
Yunhong

Steven · March 27, 2024, 2:29pm

Hi @Yunhong_Wang,

I do not use heudiconv so I do not know, but I imagine you can use the json package in python to manipulate json files in the same heuristic you use in heudiconv (or just make a script that will add it in after running).

They do not, but there’s no harm in adding it in.

Best,
Steven

Yunhong_Wang · March 27, 2024, 2:36pm

Got it. Thank you! @Steven