Missing fieldmap workflow

Software Support
1

Summary of what happened:

Hi,

I have one subject that had no fieldmap work flow and only had “1503” nodes when others have “2119” nodes. But I can see the field maps in the subject’s BIDS input. Any clue how to debug?

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

/opt/conda/envs/fmriprep/bin/fmriprep \
/dartfs/rc/lab/D/DBIC/DBIC/archive/HBN/HBN_BIDS \
/dartfs/rc/lab/D/DBIC/DBIC/archive/HBN/nipoppy_HBN/derivatives/fmriprep/25.0.0/output \
participant \
--skip_bids_validation \
--participant-label NDARZP630WYL \
--bids-database-dir /dartfs/rc/lab/D/DBIC/DBIC/archive/HBN/nipoppy_HBN/scratch/pybids_db/fmriprep-25.0.0-NDARZP630WYL-HBNsiteRU \
--nprocs 8 --omp-nthreads 4 --mem 4G \
--level full \
--ignore slicetiming \
--output-spaces MNI152NLin2009cAsym:res-2 \
--bold2anat-init auto \
--bold2anat-dof 6 \
--random-seed 0 \
--me-t2s-fit-method curvefit \
--output-layout bids \
--aggregate-session-reports 4 \
--project-goodvoxels \
--cifti-output 91k \
--fd-spike-threshold 0.5 \
--dvars-spike-threshold 1.5 \
--skull-strip-template OASIS30ANTs \
--skull-strip-t1w force \
--use-syn-sdc warn \
--fs-license-file /dartfs/rc/lab/H/HaxbyLab/hybr/apptainer/apptainer_home/FS_license.txt \
--fs-subjects-dir /dartfs/rc/lab/D/DBIC/DBIC/archive/HBN/nipoppy_HBN/derivatives/freesurfer/6.0.1/output/ \
--country-code CAN \
-v \
-w /work \
--stop-on-first-crash \
--notrack

Version:

25.0.0

Environment (Docker, Singularity / Apptainer, custom installation):

singularity

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

not sure where to find it but it should be valid format and consistent with other successful subjects

Relevant log outputs (up to 20 lines):

INFO     [RUN STDOUT]          fMRIPrep 25.0.0                                  
INFO     [RUN STDOUT]          Copyright The NiPreps Developers.                
INFO     [RUN STDOUT]                                                           
INFO     [RUN STDOUT]          This product includes software developed by      
INFO     [RUN STDOUT]          the NiPreps Community (https://nipreps.org/).    
INFO     [RUN STDOUT]                                                           
INFO     [RUN STDOUT]          Portions of this software were developed at the  
         Department of                                                          
INFO     [RUN STDOUT]          Psychology at Stanford University, Stanford, CA, 
         US.                                                                    
INFO     [RUN STDOUT]                                                           
INFO     [RUN STDOUT]          This software is also distributed as a Docker    
         container image.                                                       
INFO     [RUN STDOUT]          The bootstrapping file for the image             
         ("Dockerfile") is licensed                                             
INFO     [RUN STDOUT]          under the MIT License.                           
INFO     [RUN STDOUT]                                                           
INFO     [RUN STDOUT]          This software may be distributed through an      
         add-on package called                                                  
INFO     [RUN STDOUT]          "Docker Wrapper" that is under the BSD 3-clause  
         License.                                                               
INFO     [RUN STDOUT]                                                           
         #################################################################      
INFO     [RUN STDOUT] 250908-14:09:47,420 nipype.workflow IMPORTANT:            
INFO     [RUN STDOUT]     Building fMRIPrep's workflow:                         
INFO     [RUN STDOUT]            * BIDS dataset path:                           
         /dartfs/rc/lab/D/DBIC/DBIC/archive/HBN/HBN_BIDS.                       
INFO     [RUN STDOUT]            * Participant list: ['NDARZP630WYL'].          
INFO     [RUN STDOUT]            * Run identifier:                              
         20250908-140923_7753f6ac-dd3f-4dca-8e95-2c99312a4c26.                  
INFO     [RUN STDOUT]            * Output spaces: MNI152NLin2009cAsym:res-2.    
INFO     [RUN STDOUT]            * Pre-run FreeSurfer's SUBJECTS_DIR:           
         /dartfs/rc/lab/D/DBIC/DBIC/archive/HBN/nipoppy_HBN/derivatives/freesurf
         er/6.0.1/output.                                                       
INFO     [RUN STDOUT] 250908-14:09:49,813 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 1: Adding template workflow                
INFO     [RUN STDOUT] 250908-14:09:52,66 nipype.workflow INFO:                  
INFO     [RUN STDOUT]     ANAT Stage 2: Preparing brain extraction workflow     
INFO     [RUN STDOUT] 250908-14:09:52,205 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 3: Preparing segmentation workflow         
INFO     [RUN STDOUT] 250908-14:09:52,209 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 4: Preparing normalization workflow for    
         ['MNI152NLin2009cAsym', 'MNI152NLin6Asym']                             
INFO     [RUN STDOUT] 250908-14:09:52,222 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 5: Preparing surface reconstruction        
         workflow                                                               
INFO     [RUN STDOUT] 250908-14:09:52,237 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 6: Preparing mask refinement workflow      
INFO     [RUN STDOUT] 250908-14:09:52,239 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 7: Creating T2w template                   
INFO     [RUN STDOUT] 250908-14:09:52,242 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 8: Creating GIFTI surfaces for ['white',   
         'pial', 'midthickness', 'sphere_reg', 'sphere']                        
INFO     [RUN STDOUT] 250908-14:09:52,254 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 8: Creating GIFTI metrics for ['thickness',
         'sulc']                                                                
INFO     [RUN STDOUT] 250908-14:09:52,258 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 8a: Creating cortical ribbon mask          
INFO     [RUN STDOUT] 250908-14:09:52,261 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 9: Creating fsLR registration sphere       
INFO     [RUN STDOUT] 250908-14:09:52,264 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     ANAT Stage 10: Creating MSM-Sulc registration sphere  
INFO     [RUN STDOUT] 250908-14:09:53,741 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     No single-band-reference found for                    
         sub-NDARZP630WYL_ses-HBNsiteRU_task-movieDM_bold.nii.gz.               
INFO     [RUN STDOUT] 250908-14:09:53,970 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 1: Adding HMC boldref workflow                  
INFO     [RUN STDOUT] 250908-14:09:53,976 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 2: Adding motion correction workflow            
INFO     [RUN STDOUT] 250908-14:09:53,980 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 3: Adding coregistration boldref workflow       
INFO     [RUN STDOUT] 250908-14:09:54,158 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     No single-band-reference found for                    
         sub-NDARZP630WYL_ses-HBNsiteRU_task-movieTP_bold.nii.gz.               
INFO     [RUN STDOUT] 250908-14:09:54,209 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 1: Adding HMC boldref workflow                  
INFO     [RUN STDOUT] 250908-14:09:54,213 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 2: Adding motion correction workflow            
INFO     [RUN STDOUT] 250908-14:09:54,216 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 3: Adding coregistration boldref workflow       
INFO     [RUN STDOUT] 250908-14:09:54,657 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     No single-band-reference found for                    
         sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-1_bold.nii.gz.            
INFO     [RUN STDOUT] 250908-14:09:54,707 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 1: Adding HMC boldref workflow                  
INFO     [RUN STDOUT] 250908-14:09:54,712 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 2: Adding motion correction workflow            
INFO     [RUN STDOUT] 250908-14:09:54,715 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 3: Adding coregistration boldref workflow       
INFO     [RUN STDOUT] 250908-14:09:55,30 nipype.workflow INFO:                  
INFO     [RUN STDOUT]     No single-band-reference found for                    
         sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-2_bold.nii.gz.            
INFO     [RUN STDOUT] 250908-14:09:55,81 nipype.workflow INFO:                  
INFO     [RUN STDOUT]     Stage 1: Adding HMC boldref workflow                  
INFO     [RUN STDOUT] 250908-14:09:55,86 nipype.workflow INFO:                  
INFO     [RUN STDOUT]     Stage 2: Adding motion correction workflow            
INFO     [RUN STDOUT] 250908-14:09:55,89 nipype.workflow INFO:                  
INFO     [RUN STDOUT]     Stage 3: Adding coregistration boldref workflow       
INFO     [RUN STDOUT] 250908-14:09:55,254 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     No single-band-reference found for                    
         sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-1_bold.nii.gz.            
INFO     [RUN STDOUT] 250908-14:09:55,305 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 1: Adding HMC boldref workflow                  
INFO     [RUN STDOUT] 250908-14:09:55,309 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 2: Adding motion correction workflow            
INFO     [RUN STDOUT] 250908-14:09:55,312 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 3: Adding coregistration boldref workflow       
INFO     [RUN STDOUT] 250908-14:09:55,475 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     No single-band-reference found for                    
         sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-2_bold.nii.gz.            
INFO     [RUN STDOUT] 250908-14:09:55,526 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 1: Adding HMC boldref workflow                  
INFO     [RUN STDOUT] 250908-14:09:55,530 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 2: Adding motion correction workflow            
INFO     [RUN STDOUT] 250908-14:09:55,533 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     Stage 3: Adding coregistration boldref workflow       
INFO     [RUN STDOUT] 250908-14:09:59,576 nipype.workflow INFO:                 
INFO     [RUN STDOUT]     fMRIPrep workflow graph with 1503 nodes built         
         successfully.

Screenshots / relevant information:

looked at the fieldmap .json file and it is correctly linked to BOLD

2

Hi @tu.j,

In the future please use the Software Support post category and template, which prompts you for important information. You can see I edited your post for you this time. You can add the important information by editing your post. Also, how did you associate your fmap with your BOLD? IntendedFor or B0FieldSource/B0FieldIdentifier?

Best,
Steven

3

Thanks! What do you mean by associate fmap with the BOLD? It’s just placed in the BIDS directory and I did not specify anything…

4

Hi @tu.j,

You need to specify metadata in the fmap and bold metadata to associate each fmap with bold. Read more here: Magnetic Resonance Imaging - Brain Imaging Data Structure 1.10.1

Best,
Steven

5

hmm okay, but all other subjects were able to find it automatically

6

Then they probably had the metadata specified correctly.

7

if you are talking about the json files, they have the field “IntendedFor” correct. Here is one example:

{
    "AcquisitionMatrixPE": 84,
    "BandwidthPerPixelPhaseEncode": 21.645,
    "BaseResolution": 84,
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20171204 (OpenJPEG build) GCC4.8.4",
    "DerivedVendorReportedEchoSpacing": 0.000550001,
    "DwellTime": 2.6e-06,
    "EchoTime": 0.0512,
    "EffectiveEchoSpacing": 0.000550001,
    "FlipAngle": 90,
    "ImageOrientationPatientDICOM": [
        0.998719,
        0.0492156,
        -0.0117248,
        -0.0505929,
        0.97153,
        -0.231451
    ],
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "MOSAIC"
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "IntendedFor": [
        "ses-HBNsiteRU/func/sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-2_bold.nii.gz",
        "ses-HBNsiteRU/func/sub-NDARZP630WYL_ses-HBNsiteRU_task-movieTP_bold.nii.gz",
        "ses-HBNsiteRU/func/sub-NDARZP630WYL_ses-HBNsiteRU_task-movieDM_bold.nii.gz",
        "ses-HBNsiteRU/func/sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-1_bold.nii.gz",
        "ses-HBNsiteRU/func/sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-2_bold.nii.gz",
        "ses-HBNsiteRU/func/sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-1_bold.nii.gz"
    ],
    "MRAcquisitionType": "2D",
    "MagneticFieldStrength": 3,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "TrioTim",
    "Modality": "MR",
    "PartialFourier": 1,
    "PatientPosition": "HFS",
    "PercentPhaseFOV": 100,
    "PhaseEncodingDirection": "j-",
    "PhaseEncodingSteps": 84,
    "PhaseResolution": 1,
    "PixelBandwidth": 2289,
    "ProcedureStepDescription": "CMI_HBN",
    "ProtocolName": "fMRI_DistortionMap_AP",
    "PulseSequenceDetails": "%CustomerSeq%_cmrr_mbep2d_se",
    "ReceiveCoilName": "32Ch_Head",
    "ReconMatrixPE": 84,
    "RepetitionTime": 5.301,
    "SAR": 0.430094,
    "ScanOptions": "FS",
    "ScanningSequence": "EP",
    "SequenceName": "epse2d1_84",
    "SequenceVariant": "SK",
    "SeriesDescription": "fMRI_DistortionMap_AP",
    "ShimSetting": [
        2061,
        -618,
        -7530,
        821,
        426,
        411,
        -97,
        13
    ],
    "SliceThickness": 2.4,
    "SliceTiming": [
        2.66,
        0,
        2.75,
        0.0875,
        2.8375,
        0.1775,
        2.9275,
        0.265,
        3.015,
        0.355,
        3.105,
        0.4425,
        3.1925,
        0.5325,
        3.2825,
        0.62,
        3.37,
        0.71,
        3.46,
        0.7975,
        3.5475,
        0.8875,
        3.635,
        0.975,
        3.725,
        1.065,
        3.8125,
        1.1525,
        3.9025,
        1.2425,
        3.99,
        1.33,
        4.08,
        1.42,
        4.1675,
        1.5075,
        4.2575,
        1.595,
        4.345,
        1.685,
        4.435,
        1.7725,
        4.5225,
        1.8625,
        4.6125,
        1.95,
        4.7,
        2.04,
        4.79,
        2.1275,
        4.8775,
        2.2175,
        4.9675,
        2.305,
        5.055,
        2.395,
        5.145,
        2.4825,
        5.2325,
        2.5725
    ],
    "SoftwareVersions": "syngo_MR_B19",
    "SpacingBetweenSlices": 2.4,
    "TotalReadoutTime": 0.04565,
    "TxRefAmp": 309.009,
    "Obliquity": "True",
    "VoxelSizeDim1": 2.404761791229248,
    "VoxelSizeDim3": 2.4000000953674316,
    "VoxelSizeDim2": 2.404761791229248,
    "Dim1Size": 84,
    "Dim2Size": 84,
    "Dim3Size": 60,
    "NumVolumes": 1.0,
    "ImageOrientation": "LAS+"
}
8

Hi @tu.j,

In the future, please format code/terminal outputs with the </> button in the text editor, or surround with three tickmarks. You can see I edited your post for you this time.

Does the failing subject have correct metadata?

Best,
Steven

9

okay. Yes if you can see the json file above that looks like correct metadata. It is formatted the same way as other subjects.

10

May you provide the rest of the information requested in the software support template?

11

just did please see above

12

You can get the BIDS validation report by not skipping bids validation in the code.

Can you confirm the BOLD and fmap for this subject have opposite phase encoding direction? May you also provide the tree directory structure for this subject’s raw data organization?

13 
sub-NDARZP630WYL
└── ses-HBNsiteRU
    ├── anat
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-HCP_T1w.json
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-HCP_T1w.nii.gz -> ../../../.git/annex/objects/Wv/wX/MD5E-s21430689--b5d2112dbbd0db76239b90201895475c.nii.gz/MD5E-s21430689--b5d2112dbbd0db76239b90201895475c.nii.gz
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-HCP_T2w.json
    │   └── sub-NDARZP630WYL_ses-HBNsiteRU_acq-HCP_T2w.nii.gz -> ../../../.git/annex/objects/2q/gm/MD5E-s19053776--a242e3badcbcbbfb3c3e080073b59e8a.nii.gz/MD5E-s19053776--a242e3badcbcbbfb3c3e080073b59e8a.nii.gz
    ├── dwi
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-64dir_dwi.bval
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-64dir_dwi.bvec
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-64dir_dwi.json
    │   └── sub-NDARZP630WYL_ses-HBNsiteRU_acq-64dir_dwi.nii.gz -> ../../../.git/annex/objects/qj/G6/MD5E-s96893104--6637b1701259adaa9783622ac50306a1.nii.gz/MD5E-s96893104--6637b1701259adaa9783622ac50306a1.nii.gz
    ├── fmap
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-dwi_dir-AP_epi.json
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-dwi_dir-AP_epi.nii.gz -> ../../../.git/annex/objects/X8/7g/MD5E-s899924--f6612d2b2603aa07ba1a3375f0c15342.nii.gz/MD5E-s899924--f6612d2b2603aa07ba1a3375f0c15342.nii.gz
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-dwi_dir-PA_epi.json
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-dwi_dir-PA_epi.nii.gz -> ../../../.git/annex/objects/Kv/zx/MD5E-s9    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-dwi_dir-PA_epi.nii.gz -> ../../../.git/annex/objects/Kv/zx/MD5E-s916683--730556c353b27cc4035e4a39fb0906d4.nii.gz/MD5E-s916683--730556c353b27cc4035e4a39fb0906d4.nii.gz
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-fMRI_dir-AP_epi.json
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-fMRI_dir-AP_epi.nii.gz -> ../../../.git/annex/objects/G8/xf/MD5E-s560908--40ad7c862ad7dde9cb5646d785bc6842.nii.gz/MD5E-s560908--40ad7c862ad7dde9cb5646d785bc6842.nii.gz
    │   ├── sub-NDARZP630WYL_ses-HBNsiteRU_acq-fMRI_dir-PA_epi.json
    │   └── sub-NDARZP630WYL_ses-HBNsiteRU_acq-fMRI_dir-PA_epi.nii.gz -> ../../../.git/annex/objects/Xw/Q4/MD5E-s558790--47872c6fe9e243f305e3f6eeb88960a9.nii.gz/MD5E-s558790--47872c6fe9e243f305e3f6eeb88960a9.nii.gz
    └── func
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-movieDM_bold.json
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-movieDM_bold.nii.gz -> ../../../.git/annex/objects/9M/k1/MD5E-s346061016--e80a5c2d6fe30d6c03d96f96c2709cdb.nii.gz/MD5E-s346061016--e80a5c2d6fe30d6c03d96f96c2709cdb.nii.gz
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-movieDM_events.tsv
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-movieTP_bold.json
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-movieTP_bold.nii.gz -> ../../../.git/annex/objects/wq/Fw/MD5E-s118101657--fa19e55b22c4f16d292d932a2fddcb6d.nii.gz/MD5E-s118101657--fa19e55b22c4f16d292d932a2fddcb6d.nii.gz
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-movieTP_events.tsv
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-1_bold.json
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-1_bold.nii.gz -> ../../../.git/annex/objects/xg/6Z/MD5E-s62458379--47ad936d7acca3d3f76594f01e6dc3b3.nii.gz/MD5E-s62458379--47ad936d7acca3d3f76594f01e6dc3b3.nii.gz
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-2_bold.json
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-peer_run-2_bold.nii.gz -> ../../../.git/annex/objects/m1/Ff/MD5E-s62476666--a03ebad152c9141c004b94ef9e28fab7.nii.gz/MD5E-s62476666--a03ebad152c9141c004b94ef9e28fab7.nii.gz
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-1_bold.json
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-1_bold.nii.gz -> ../../../.git/annex/objects/kj/MM/MD5E-s173104730--f814a25c082ca01c2cce7faf421bfacc.nii.gz/MD5E-s173104730--f814a25c082ca01c2cce7faf421bfacc.nii.gz
        ├── sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-2_bold.json
        └── sub-NDARZP630WYL_ses-HBNsiteRU_task-rest_run-2_bold.nii.gz -> ../../../.git/annex/objects/Wk/q3/MD5E-s174457236--7a743b573fb5225303256732c60e642d.nii.gz/MD5E-s174457236--7a743b573fb5225303256732c60e642d.nii.gz
14

Do both phase encoding direction fmaps have correct metadata? Can you confirm all the niftis have been retrieved with datalad, and are not just symlinks?

15

yes they are downloaded both encoding direction have very similar json files as copied above.

16

Do the two fieldmaps have opposite phase encoding directions? Is it possible the pybids db was not complete? What happens if you do not use a precomputed pybids db?

17

yes, I run into an error when I don’t specify pybids db, maybe I had a typo somewhere

Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/fmriprep/lib/python3.12/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/cli/workflow.py", line 126, in build_workflow
    retval['workflow'] = init_fmriprep_wf()
                         ^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/workflows/base.py", line 95, in init_fmriprep_wf
    single_subject_wf = init_single_subject_wf(subject_id)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/workflows/base.py", line 767, in init_single_subject_wf
    bold_wf = init_bold_wf(
              ^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/workflows/bold/base.py", line 253, in init_bold_wf
    bold_fit_wf = init_bold_fit_wf(
                  ^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/fmriprep/workflows/bold/fit.py", line 481, in init_bold_fit_wf
    enhance_boldref_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/niworkflows/func/util.py", line 427, in init_enhance_and_skullstrip_bold_wf
    AI(
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/ants/base.py", line 76, in __init__
    super().__init__(**inputs)
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 633, in __init__
    super().__init__(**inputs)
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 204, in __init__
    self.inputs.trait_set(**inputs)
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/traits/has_traits.py", line 1458, in trait_set
    setattr(self, name, value)
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/traits_extension.py", line 325, in validate
    value = super().validate(objekt, name, value, return_pathlike=True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/opt/conda/envs/fmriprep/lib/python3.12/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: The 'fixed_image' trait of an AIInputSpec instance must be a pathlike object or string representing an existing file, but a value of '[]' <class 'str'> was specified.