BIDS validation error

1

Hi there,
I’m persistently getting errors with the naming of my fieldmap images. Any help would be greatly appreciated!
Currently I’m using the following naming scheme:
sub-{subjectname}_ses-1_dir-PA_acq-resting.nii/.json
I wasn’t having errors until I added these field maps.
The error is [Code 1] NOT_INCLUDED

Thanks in advance!

2

There’s no suffix. I guess these are reverse-phase-encoded EPIs? If so, then add _epi just before the extension.

3

Thanks for your reply! I’m still getting the same error. Files are now called: sub-AUD4_ses-1_dir-PA_acq-alcohol_epi.json
sub-AUD4_ses-1_dir-PA_acq-alcohol_epi.nii
sub-AUD4_ses-1_dir-PA_acq-face_epi.json
sub-AUD4_ses-1_dir-PA_acq-face_epi.nii
sub-AUD4_ses-1_dir-PA_acq-resting_epi.json
sub-AUD4_ses-1_dir-PA_acq-resting_epi.nii
(I’m going to be using PA nifti files as well)
and the path to these files is derivatives/Nifti/sub-AUD4/ses-1/fmap
Any advice greatly appreciated!

4

The template is:

sub-<label>/[ses-<label>/]
    fmap/
        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_epi.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_epi.json

acq goes before dir here. According to the spec:

A summary of all entities in BIDS and the order in which they MUST be specified is available in the entity table in the appendix.

5

Thanks a lot! It was the ordering that got me. Really appreciate the help

6

I hope this question isn’t ignorant. When I add “IntendedFor”: “func/name_of_image”,
to my .JSON of the field maps, I start getting errors saying that I don’t have RepetitionTime and other variables listed in the .json. I find this odd, because I do, and was not getting this error prior to adding this line to the JSON…

7

Can you share an example json file?

8

Thank you, yes here’s one of the .json’s that only gave me a problem when I added the “IntendedFor”:
{
“Modality”: “MR”,
“MagneticFieldStrength”: 3,
“Manufacturer”: “Siemens”,
“ManufacturersModelName”: “Prisma”,
“DeviceSerialNumber”: “66049”,
“StationName”: “AWP66049”,
“BodyPartExamined”: “BRAIN”,
“PatientPosition”: “HFS”,
“ProcedureStepDescription”: “RESEARCH_DBSA1F”,
“SoftwareVersions”: “syngo_MR_E11”,
“MRAcquisitionType”: “2D”,
“SeriesDescription”: “ep2d_bold_p2_s2_iso2.5_P>>A_ref”,
“ProtocolName”: “ep2d_bold_p2_s2_iso2.5_P>>A_ref”,
“IntendedFor”: “func/sub-AUD4_ses-1_task-face_acq-TR1750_bold.nii”
“ScanningSequence”: “EP”,
“SequenceVariant”: “SK”,
“ScanOptions”: “FS”,
“SequenceName”: “_epfid2d1_80”,
“ImageType”: [“ORIGINAL”, “PRIMARY”, “M”, “ND”, “MOSAIC”],
“SeriesNumber”: 15,
“AcquisitionTime”: “09:48:21.120000”,
“AcquisitionNumber”: 1,
“SliceThickness”: 2.5,
“SpacingBetweenSlices”: 2.5,
“SAR”: 0.0339327,
“EchoTime”: 0.03,
“RepetitionTime”: 1.75,
“FlipAngle”: 40,
“PartialFourier”: 1,
“BaseResolution”: 80,
“ShimSetting”: [
-254,
-9666,
2642,
377,
-76,
18,
-38,
-17 ],
“TxRefAmp”: 301.512,
“PhaseResolution”: 1,
“ReceiveCoilName”: “HeadNeck_20”,
“ReceiveCoilActiveElements”: “HE1-4”,
“PulseSequenceDetails”: “%SiemensSeq%_ep2d_bold”,
“ConsistencyInfo”: “N4_VE11C_LATEST_20160120”,
“MultibandAccelerationFactor”: 2,
“PercentPhaseFOV”: 100,
“EchoTrainLength”: 39,
“PhaseEncodingSteps”: 79,
“AcquisitionMatrixPE”: 80,
“ReconMatrixPE”: 80,
“BandwidthPerPixelPhaseEncode”: 51.02,
“ParallelReductionFactorInPlane”: 2,
“EffectiveEchoSpacing”: 0.000245002,
“DerivedVendorReportedEchoSpacing”: 0.000490004,
“TotalReadoutTime”: 0.0193552,
“PixelBandwidth”: 2500,
“DwellTime”: 2.5e-06,
“PhaseEncodingDirection”: “j”,
“SliceTiming”: [
1.2675,
0,
0.865,
0.0575,
0.9225,
0.115,
0.98,
0.1725,
1.0375,
0.23,
1.095,
0.2875,
1.1525,
0.345,
1.21,
0.46,
1.325,
0.5175,
1.3825,
0.575,
1.44,
0.6325,
1.4975,
0.69,
1.555,
0.7475,
1.6125,
0.8075,
1.67,
0.4025,
1.2675,
0,
0.865,
0.0575,
0.9225,
0.115,
0.98,
0.1725,
1.0375,
0.23,
1.095,
0.2875,
1.1525,
0.345,
1.21,
0.46,
1.325,
0.5175,
1.3825,
0.575,
1.44,
0.6325,
1.4975,
0.69,
1.555,
0.7475,
1.6125,
0.8075,
1.67,
0.4025 ],
“ImageOrientationPatientDICOM”: [
0.996142,
0.0108095,
0.0870912,
-0.00347717,
0.996467,
-0.0839073 ],
“InPlanePhaseEncodingDirectionDICOM”: “COL”,
“ConversionSoftware”: “dcm2niix”,
“ConversionSoftwareVersion”: “v1.0.20171215 (OpenJPEG build) GCC7.3.0”
}

9

You’re missing a comma after the entry. And I usually see it as a list, as it can be intended for multiple files, but I’m not sure whether that’s mandatory or convention. If fixing the comma doesn’t resolve it, then I would try making it a list.

10

Thanks a lot! I was missing that comma, and i think I was also not including enough of the path in the “IntendedFor” (needed to add ses-1/ as well). Thanks very much for your help