fMRIprep suddenly giving error code: 10 - REPETITION_TIME_MUST_DEFINE but the TR is already defined

ngfrye · July 5, 2023, 6:05pm

Summary of what happened:

I have been preprocessing a dataset with fMRIprep, and did this successfully for the first 11 subjects. However, last week, I launched fMRIprep for the next 5 subjects, and the first three ran and have now finished successfully, but the last two failed, with errors in the logs that the Repetition Time is not defined, as well as warnings that the slice timing is not defined. I now cannot get fMRIprep to run for any participants. But when I check their .json files, the “RepetitionTime” and “SliceTiming” fields are defined. I have compared them carefully to the .json files for subjects that ran successfully before this problem occurred, and they are exactly the same (aside from the acquisition time). I’m stumped about what could be going wrong, especially since nothing seems to have changed between the subjects that already ran successfully and all the rest of them. I would greatly appreciate any ideas! More details about what I’ve tried and noticed in the Screenshots/relevant information section.

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

I believe what I used is a helper script, so here is an example of the command generated by it:

 sbatch --no-requeue -n 1 --mem=100000 --time=40:0:0 --cpus-per-task=12 --job-name="sub-035_fmriprep" --output=/proj/lindquistgiovanello/projects/EPIC/logs/FMRIprep_logs/Output-sub-035_fmriprep-jobid-%j.out --wrap="unset PYTHONPATH; export SINGULARITYENV_TEMPLATEFLOW_HOME=/proj/hng/singularity_imgs/template_flow; singularity run -B ${TEMPLATEFLOW_HOME:-$HOME/.cache/templateflow}:/proj/hng/singularity_imgs/template_flow,/proj,/pine,/work,/nas02,/nas -e --no-home /proj/hng/singularity_imgs/fmriprep_1.5.3.sif /proj/lindquistgiovanello/projects/EPIC/data_BIDS /proj/lindquistgiovanello/projects/EPIC/data_fmriprep/fmriprep participant --participant-label 035 -w /work/users/n/g/ngfrye --fs-license-file /proj/hng/singularity_imgs/license.txt --nthreads 12  "

Version:

fMRIprep version 21.0.2, but have also tried with version 22.1.1 and version 1.5.3 with the same results.

Environment (Docker, Singularity, custom installation):

I’m a bit new to this and I’m not totally sure what this means, but I believe Singularity. I’m running fMRIprep through an fMRI processing pipeline that we use at my institution called clpipe. So it runs on an HPC, and it implements fMRIprep for preprocessing.

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

The data are in BIDS format. Some context on that in the relevant information section below - in short, I am working from nifti’s rather than DICOMS and manually created .json’s and put the data into BIDS format. Once I did this for one subject, I ran BIDS validator to check that it worked, and got the following output:

	e[33m1: [WARN] 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". (code: 25 - EVENTS_TSV_MISSING)e[39m
		./sub-001/func/sub-001_task-AR1_bold.nii.gz
			Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /task-AR1_events.tsv, /events.tsv, /sub-001/sub-001_task-AR1_events.tsv, /sub-001/sub-001_events.tsv, /sub-001/func/sub-001_task-AR1_events.tsv, /sub-001/func/sub-001_events.tsv
		./sub-001/func/sub-001_task-AR2_bold.nii.gz
			Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /task-AR2_events.tsv, /events.tsv, /sub-001/sub-001_task-AR2_events.tsv, /sub-001/sub-001_events.tsv, /sub-001/func/sub-001_task-AR2_events.tsv, /sub-001/func/sub-001_events.tsv
		./sub-001/func/sub-001_task-AR3_bold.nii.gz
			Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /task-AR3_events.tsv, /events.tsv, /sub-001/sub-001_task-AR3_events.tsv, /sub-001/sub-001_events.tsv, /sub-001/func/sub-001_task-AR3_events.tsv, /sub-001/func/sub-001_events.tsv
		./sub-001/func/sub-001_task-AR4_bold.nii.gz
			Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /task-AR4_events.tsv, /events.tsv, /sub-001/sub-001_task-AR4_events.tsv, /sub-001/sub-001_events.tsv, /sub-001/func/sub-001_task-AR4_events.tsv, /sub-001/func/sub-001_events.tsv
		./sub-001/func/sub-001_task-ER_bold.nii.gz
			Task scans should have a corresponding events.tsv file. It can be included one of the following locations: /task-ER_events.tsv, /events.tsv, /sub-001/sub-001_task-ER_events.tsv, /sub-001/sub-001_events.tsv, /sub-001/func/sub-001_task-ER_events.tsv, /sub-001/func/sub-001_events.tsv

	e[33m2: [WARN] Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT)e[39m
		./sub-001/anat/sub-001_T1w.nii.gz
			Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short
		./sub-001/anat/sub-001_T2w.nii.gz
			Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short

        e[34me[4mSummary:e[24me[39m                 e[34me[4mAvailable Tasks:e[24me[39m        e[34me[4mAvailable Modalities:e[24me[39m 
        21 Files, 16.27GB        AR1                     /participants         
        1 - Subject              AR2                     T1w                   
        1 - Session              AR4                     T2w                   
                                 AR3                     bold                  
                                 rest                                          
                                 ER

Then, about a month later, when this issue arose, I ran BIDS validator again (this time on all of our participants as I had at this point gotten them all into BIDS format). This is the output:

[31m1: [ERR] You have to define 'RepetitionTime' for this file. (code: 10 - REPETITION_TIME_MUST_DEFINE)e[39m
		./sub-008/func/sub-008_task-AR1_bold.nii.gz
		./sub-035/func/sub-035_task-AR3_bold.nii.gz
		./sub-035/func/sub-035_task-AR4_bold.nii.gz
		./sub-035/func/sub-035_task-AR5_bold.nii.gz
		./sub-035/func/sub-035_task-ER_bold.nii.gz
		./sub-036/func/sub-036_task-AR1_bold.nii.gz
		./sub-036/func/sub-036_task-AR2_bold.nii.gz
		./sub-036/func/sub-036_task-AR3_bold.nii.gz
		./sub-036/func/sub-036_task-ER_bold.nii.gz
		./sub-037/func/sub-037_task-AR1_bold.nii.gz
		e[31m... and 125 more files having this issue (Use --verbose to see them all).e[39m

	e[31m2: [ERR] Not a valid JSON file. (code: 27 - JSON_INVALID)e[39m
		./sub-016/anat/sub-016_T2w.json
			@ line: 2 character: 5
			Evidence:     "Modality": "MR",
		./sub-016/anat/sub-016_T2w.json
			@ line: 2 character: 15
			Evidence:     "Modality": "MR",
		./sub-016/anat/sub-016_T2w.json
			@ line: 3 character: 28
			Evidence:     "MagneticFieldStrength": 3,
		./sub-016/anat/sub-016_T2w.json
			@ line: 3 character: 5
		./sub-016/anat/sub-016_T2w.json
			@ line: 2 character: 15
			Evidence:     "Modality": "MR",
		./sub-016/anat/sub-016_T2w.json
			@ line: 3 character: 5
			Evidence:     "MagneticFieldStrength": 3,

	e[31m3: [ERR] You have to define 'TaskName' for this file. (code: 50 - TASK_NAME_MUST_DEFINE)e[39m
		./sub-008/func/sub-008_task-AR1_bold.nii.gz
		./sub-035/func/sub-035_task-AR3_bold.nii.gz
		./sub-035/func/sub-035_task-AR4_bold.nii.gz
		./sub-035/func/sub-035_task-AR5_bold.nii.gz
		./sub-035/func/sub-035_task-ER_bold.nii.gz
		./sub-036/func/sub-036_task-AR1_bold.nii.gz
		./sub-036/func/sub-036_task-AR2_bold.nii.gz
		./sub-036/func/sub-036_task-AR3_bold.nii.gz
		./sub-036/func/sub-036_task-ER_bold.nii.gz
		./sub-037/func/sub-037_task-AR1_bold.nii.gz
		e[31m... and 125 more files having this issue (Use --verbose to see them all).e[39m

	e[31m4: [ERR] A json sidecar file was found without a corresponding data file (code: 90 - SIDECAR_WITHOUT_DATAFILE)e[39m
		./sub-008/anat/sub-008_T1w.json
		./sub-008/anat/sub-008_T2w.json
		./sub-015/anat/sub-015_T1w.json
		./sub-015/anat/sub-015_T2w.json
		./sub-016/anat/sub-016_T1w.json

	e[33m1: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED)e[39m
		./sub-008/func/sub-008_task-AR1_bold.nii.gz
		./sub-035/func/sub-035_task-AR3_bold.nii.gz
		./sub-035/func/sub-035_task-AR4_bold.nii.gz
		./sub-035/func/sub-035_task-AR5_bold.nii.gz
		./sub-035/func/sub-035_task-ER_bold.nii.gz
		./sub-036/func/sub-036_task-AR1_bold.nii.gz
		./sub-036/func/sub-036_task-AR2_bold.nii.gz
		./sub-036/func/sub-036_task-AR3_bold.nii.gz
		./sub-036/func/sub-036_task-ER_bold.nii.gz
		./sub-037/func/sub-037_task-AR1_bold.nii.gz
		e[33m... and 125 more files having this issue (Use --verbose to see them all).e[39m

	e[33m2: [WARN] 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". (code: 25 - EVENTS_TSV_MISSING)e[39m
		./sub-001/func/sub-001_task-AR1_bold.nii.gz
		./sub-001/func/sub-001_task-AR2_bold.nii.gz
		./sub-001/func/sub-001_task-AR3_bold.nii.gz
		./sub-001/func/sub-001_task-AR4_bold.nii.gz
		./sub-001/func/sub-001_task-ER_bold.nii.gz
		./sub-002/func/sub-002_task-AR1_bold.nii.gz
		./sub-002/func/sub-002_task-AR2_bold.nii.gz
		./sub-002/func/sub-002_task-AR3_bold.nii.gz
		./sub-002/func/sub-002_task-AR4_bold.nii.gz
		./sub-003/func/sub-003_task-AR2_bold.nii.gz
		e[33m... and 246 more files having this issue (Use --verbose to see them all).e[39m

	e[33m3: [WARN] Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing. (code: 38 - INCONSISTENT_SUBJECTS)e[39m
		./sub-001/func/sub-001_task-AR5_bold.json
			Evidence: Subject: sub-001; Missing file: sub-001_task-AR5_bold.json
		./sub-001/func/sub-001_task-AR5_bold.nii.gz
			Evidence: Subject: sub-001; Missing file: sub-001_task-AR5_bold.nii.gz
		./sub-002/func/sub-002_task-AR5_bold.json
			Evidence: Subject: sub-002; Missing file: sub-002_task-AR5_bold.json
		./sub-002/func/sub-002_task-AR5_bold.nii.gz
			Evidence: Subject: sub-002; Missing file: sub-002_task-AR5_bold.nii.gz
		./sub-002/func/sub-002_task-ER_bold.json
			Evidence: Subject: sub-002; Missing file: sub-002_task-ER_bold.json
		./sub-002/func/sub-002_task-ER_bold.nii.gz
			Evidence: Subject: sub-002; Missing file: sub-002_task-ER_bold.nii.gz
		./sub-002/func/sub-002_task-resting_bold.json
			Evidence: Subject: sub-002; Missing file: sub-002_task-resting_bold.json
		./sub-002/func/sub-002_task-resting_bold.nii.gz
			Evidence: Subject: sub-002; Missing file: sub-002_task-resting_bold.nii.gz
		./sub-003/func/sub-003_task-AR1_bold.json
			Evidence: Subject: sub-003; Missing file: sub-003_task-AR1_bold.json
		./sub-003/func/sub-003_task-AR1_bold.nii.gz
			Evidence: Subject: sub-003; Missing file: sub-003_task-AR1_bold.nii.gz
		e[33m... and 92 more files having this issue (Use --verbose to see them all).e[39m

	e[33m4: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)e[39m
		./sub-003/func/sub-003_task-AR2_bold.nii.gz
		./sub-003/func/sub-003_task-AR3_bold.nii.gz
		./sub-003/func/sub-003_task-AR4_bold.nii.gz
		./sub-012/func/sub-012_task-ER_bold.nii.gz
		./sub-057/func/sub-057_task-ER_bold.nii.gz
		./sub-057/func/sub-057_task-resting_bold.nii.gz

	e[33m5: [WARN] Nifti file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT)e[39m
		./sub-001/anat/sub-001_T1w.nii.gz
		./sub-001/anat/sub-001_T2w.nii.gz
		./sub-004/anat/sub-004_T1w.nii.gz
		./sub-004/anat/sub-004_T2w.nii.gz
		./sub-005/anat/sub-005_T1w.nii.gz
		./sub-005/anat/sub-005_T2w.nii.gz
		./sub-006/anat/sub-006_T1w.nii.gz
		./sub-006/anat/sub-006_T2w.nii.gz
		./sub-007/anat/sub-007_T1w.nii.gz
		./sub-007/anat/sub-007_T2w.nii.gz
		e[33m... and 56 more files having this issue (Use --verbose to see them all).e[39m

        e[34me[4mSummary:e[24me[39m                   e[34me[4mAvailable Tasks:e[24me[39m        e[34me[4mAvailable Modalities:e[24me[39m 
        731 Files, 731.46GB        AR1                     /participants         
        46 - Subjects              AR2                     T1w                   
        1 - Session                AR4                     T2w                   
                                   ER                      bold                  
                                   AR3                                           
                                   rest                                          
                                   AR5

Relevant log outputs (up to 20 lines):

Here are the first 20 lines of the log output from fMRIprep for the last subject that was processed successfully (which was submitted at the same time as the first subjects that failed):

WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TEMPLATEFLOW_HOME as environment variable will not be supported in the future, use APPTAINERENV_TEMPLATEFLOW_HOME instead
INFO:    underlay of /etc/localtime required more than 50 (107) bind mounts
bids-validator@1.8.0

	e[33m1: [WARN] NIfTI file's header field for unit information for x, y, z, and t dimensions empty or too short (code: 41 - NIFTI_UNIT)e[39m
		./sub-031/anat/sub-031_T1w.nii.gz
		./sub-031/anat/sub-031_T2w.nii.gz

e[36m	Please visit https://neurostars.org/search?q=NIFTI_UNIT for existing conversations about this issue.e[39m

	e[33m2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)e[39m

e[36m	Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.e[39m

	e[33m3: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)e[39m

e[36m	Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.e[39m

Now here are the first 20 lines of the log output from fMRIprep for the first subject that failed:

WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TEMPLATEFLOW_HOME as environment variable will not be supported in the future, use APPTAINERENV_TEMPLATEFLOW_HOME instead
INFO:    underlay of /etc/localtime required more than 50 (107) bind mounts
bids-validator@1.8.0

	e[31m1: [ERR] You have to define 'RepetitionTime' for this file. (code: 10 - REPETITION_TIME_MUST_DEFINE)e[39m
		./sub-035/func/sub-035_task-AR3_bold.nii.gz
		./sub-035/func/sub-035_task-AR4_bold.nii.gz
		./sub-035/func/sub-035_task-AR5_bold.nii.gz
		./sub-035/func/sub-035_task-ER_bold.nii.gz

e[36m	Please visit https://neurostars.org/search?q=REPETITION_TIME_MUST_DEFINE for existing conversations about this issue.e[39m

	e[33m1: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. 'Slice Timing' is the time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. (code: 13 - SLICE_TIMING_NOT_DEFINED)e[39m
		./sub-035/func/sub-035_task-AR3_bold.nii.gz
		./sub-035/func/sub-035_task-AR4_bold.nii.gz
		./sub-035/func/sub-035_task-AR5_bold.nii.gz
		./sub-035/func/sub-035_task-ER_bold.nii.gz

e[36m	Please visit https://neurostars.org/search?q=SLICE_TIMING_NOT_DEFINED for existing conversations about this issue.e[39m

Screenshots / relevant information:

Background info on the data:

There are only nifti’s for these data, no DICOMS, so I have had to find a way to get the data into BIDS format to be compatable with fMRIprep and with my institution’s processing pipeline. Here are the steps I have done to do that: I created .json files for each task, using .json’s from another study as a template and filling in all the needed metadata, which I do have access to. I created a BIDS file structure and moved the nifti’s into the proper folders, renamed them according to BIDS conventions, and uploaded the .jsons to accompany them, aslo naming them according to BIDS conventions. Then, for the .jsons accompanying functional runs, I opened each and edited the ‘AcquisitionTime’ field according to study records, and sometimes changed the ‘SeriesNumber’ if the study records indicated the protocol was adjusted in a particular scan and tasks were re-ordered. The .jsons for the structural runs I was able to get straight from Flywheel where they were automatically generated (unlike our functional runs), so I didn’t change anything about them and just moved them into the appropriate folders. After doing that and running BIDS validator, there was an error indicating that the nifti headers on our functional runs did not contain the units for the TR or voxel dimensions, so I opened and edited each functional nifti header using flsedithd and adding those fields. After doing this, BIDS validator ran without errors, and I was able to process the first 11 participants with fmriprep.

Other notes:

On the first subject that failed, these errors/warnings pointed to only the last 4 tasks, and on the second subject that failed and all other subjects I have tried since, it points to all tasks.

I have also checked the nifti headers, and they are exactly the same as those for subjects that already ran successfully. When I ran BIDS validator again, it now shows a number of additional errors and warnings that similarly don’t make sense to me, such as needing to define ‘TaskName’ for the file, when it is also defined in all of the files and is the same as in the .json’s for subjects that ran successfully. I also see in the BIDS validator output that it is not giving errors/warnings for the subjects that already were ran successfully, even though I can’t find anything that’s different about them.

I have tried using different versions of fMRIprep, as well as different versions of the pipeline I am using to implement it (clpipe)

Steven · July 5, 2023, 6:42pm

Hi @ngfrye and welcome to neurostars!

Please share an example JSON for your BOLD images that is failing.

The difference in BIDS validation outputs could be from different versions of the validator. You should use the most recent version available, or at the earliest, the version included with the fMRIPrep version you want to use (which should probably be the most recent fMRIPrep version, 23.1.3 at this time).

Best,
Steven

ngfrye · July 5, 2023, 8:03pm

Hi @Steven, thank you! Here is an example JSON for a run that is failing:

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 123.248,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Prisma_fit",
    "InstitutionName": "University of North Carolina BRIC",
    "InstitutionalDepartmentName": "Department",
    "InstitutionAddress": "Mason Farm Rd 106,Chapel Hill,District,US,27599",
    "DeviceSerialNumber": "67094",
    "StationName": "Prisma",
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "PRISMA^HEAD",
    "SoftwareVersions": "syngo MR E11",
    "MRAcquisitionType": "2D", 
    "SeriesDescription": "mb3d_task3_wtp3_1mm_mb6x1_PA",
    "ProtocolName": "mb3d_task3_wtp3_1mm_mb6x1_PA",
    "ScanningSequence": "EP", 
    "SequenceVariant": "NONE", 
    "ScanOptions": "PFP", 
    "SequenceName": "epfid", 
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "MOSAIC"
    ],
    "NonlinearGradientCorrection": false, 
    "SeriesNumber": 9, 
    "AcquisitionTime": "17:49:00.000000", 
    "AcquisitionNumber": 1, 
    "ImageComments": "SMS; MB=6; FOVshift=3;", 
    "SliceThickness": 1,
    "SpacingBetweenSlices": 2.0, 
    "SAR": 0.0728032, 
    "EchoTime": 0.03, 
    "RepetitionTime": 2,
    "FlipAngle": 80,
    "PartialFourier": 0.75, 
    "BaseResolution": 192,
    "ShimSetting": [
        -1640,
        7538,
        6663,
        397,
        -49,
        -66,
        -66,
        7
    ],
    "TxRefAmp": 200, 
    "PhaseResolution": 1,
    "ReceiveCoilName": "Head_32",
    "ReceiveCoilActiveElements": "HEA;HEP",
    "PulseSequenceDetails": "%CustomerSeq%\\ep2d_bold_sms", 
    "WipMemBlock": "5213660f-c9a1-4bc1-8c49-b1455df5b94e", 
    "RefLinesPE": 24,
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE11C_LATEST_20160120", 
    "MultibandAccelerationFactor": 6, 
    "PercentPhaseFOV": 100,
    "PercentSampling": 100, 
    "EchoTrainLength": 192, 
    "PhaseEncodingSteps": 192, 
    "AcquisitionMatrixPE": 192, 
    "ReconMatrixPE": 192, 
    "BandwidthPerPixelPhaseEncode": 1302, 
    "EffectiveEchoSpacing": 0.00093,
    "DerivedVendorReportedEchoSpacing": 0.00093,
    "TotalReadoutTime": 0.067, 
    "PixelBandwidth": 1300,
    "DwellTime": 2e-06, 
    "PhaseEncodingDirection": "j",
    "SliceTiming": [ 
        1.0000, 
        0,
        1.1000,
        0.1000,
        1.2000,
        0.2000,
        1.3000,
        0.3000,
        1.4000,
        0.4000,
        1.5000,
        0.5000,
        1.6000,
        0.6000,
        1.7000,
        0.7000,
        1.8000,
        0.8000,
        1.9000,
        0.9000,
        1.0000,
        0,
        1.1000,
        0.1000,
        1.2000,
        0.2000,
        1.3000,
        0.3000,
        1.4000,
        0.4000,
        1.5000,
        0.5000,
        1.6000,
        0.6000,
        1.7000,
        0.7000,
        1.8000,
        0.8000,
        1.9000,
        0.9000,
        1.0000,
            0,
        1.1000,
        0.1000,
        1.2000,
        0.2000,
        1.3000,
        0.3000,
        1.4000,
        0.4000,
        1.5000,
        0.5000,
        1.6000,
        0.6000,
        1.7000,
        0.7000,
        1.8000,
        0.8000,
        1.9000,
        0.9000,
        1.0000,
            0,
        1.1000,
        0.1000,
        1.2000,
        0.2000,
        1.3000,
        0.3000,
        1.4000,
        0.4000,
        1.5000,
        0.5000,
        1.6000,
        0.6000,
        1.7000,
        0.7000,
        1.8000,
        0.8000,
        1.9000,
        0.9000,
        1.0000,
        0,
        1.1000,
        0.1000,
        1.2000,
        0.2000,
        1.3000,
        0.3000,
        1.4000,
        0.4000,
        1.5000,
        0.5000,
        1.6000,
        0.6000,
        1.7000,
        0.7000,
        1.8000,
        0.8000,
        1.9000,
        0.9000,
        1.0000,
        0,
        1.1000,
        0.1000,
        1.2000,
        0.2000,
        1.3000,
        0.3000,
        1.4000,
        0.4000,
        1.5000,
        0.5000,
        1.6000,
        0.6000,
        1.7000,
        0.7000,
        1.8000,
        0.8000,
        1.9000,
        0.9000
    ],
    "ImageOrientationPatientDICOM": [
        0.999803,
        0.00844561,
        0.017979,
        5.07885e-08,
        0.90511,
        -0.425177
    ],
    "ImageOrientationText": "Tra>Cor(-25.2)>Sag(1.1)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20220720",
    "Dcm2bidsVersion": "2.1.4",
    "TaskName": "AR3"
}

I’ll check which version of BIDS validator I’m using, it looks like it might be an older one so I might need to adjust that. In the fMRIprep output at least it looks like both were using BIDS validator 1.8.0.

Steven · July 5, 2023, 8:12pm

Hmm, this looks fine… what happens if you --skip-bids-validation?

ngfrye · July 5, 2023, 8:50pm

Aha, that seems to be getting somewhere – it’s running now and has created a folder in /fmriprep for the subject and a figures folder, when before it failed within a minute or two and never created a new directory. It usually takes about 24hrs to run fully for this study so I’ll have to check back tomorrow afternoon to see if it actually completed successfully and if the output looks right, but fingers crossed!

ngfrye · July 6, 2023, 2:18pm

It looks like the subject ran through fmriprep successfully! I’m not sure what’s going on with the bids validation but this seems to work as a workaround and the fmriprep output looks good. Thank you!