Summary of what happened:
I can run fMRIPrep without error, but it does not run the susceptibility distortion correction.
I get the following message for each scan run: None of the available B0 fieldmaps are associated to </path/to/bold.nii.gz>
Despite this, I have an IntendedFor field in my fmap .json files indicating the func files with which they should be associated.
The field map I am using has two phase maps and two magnitude images. I’ve included an example .json file for the first phase map below.
Command used (and if a helper script was used, a link to the helper script or the command generated):
unset PYTHONPATH; singularity run --cleanenv -B /project/gottfried/samlyons/olfunc:/data \
-B /project/gottfried/samlyons/olfunc/derivatives:/olfunc/derivatives \
-B /project/gottfried/samlyons/work:/work \
-B /project/gottfried/samlyons/images/license.txt:/license.txt \
-B /project/gottfried/samlyons/olfunc \
/project/gottfried/samlyons/images/fmriprep-23.0.2.simg \
/project/gottfried/samlyons/olfunc/sub-olfunc007/ses-olfunc007 \
/project/gottfried/samlyons/olfunc/derivatives \
participant \
--participant-label olfunc007 \
--skip-bids-validation \
--fs-license-file /license.txt \
--stop-on-first-crash \
--nthreads 16 \
--omp-nthreads 16 \
-w /work \
--fs-no-reconall
Version:
23.0.2
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
No errors from BIDS validator.
Relevant log outputs (up to 20 lines):
230614-15:02:09,396 nipype.workflow CRITICAL:
None of the available B0 fieldmaps are associated to </project/gottfried/samlyons/olfunc/sub-olfunc007/ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-01_bold.nii.gz>
Screenshots / relevant information:
.json file for phase 1 of fieldmap. Phase 2 looks basically the same, except the echotime is different.
{
"AcquisitionMatrix": [
112,
0,
0,
112
],
"AcquisitionMatrixPE": 112,
"AcquisitionNumber": 1,
"AcquisitionTime": "11:21:22.980000",
"B0FieldIdentifier": "phases_fmap0",
"BaseResolution": 112,
"BodyPartExamined": "BRAIN",
"CoilCombinationMethod": "Adaptive Combine",
"Columns": 112,
"ConsistencyInfo": "N4_VE12U_LATEST_20181126",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20211006",
"DeviceSerialNumber": "79106",
"EchoNumber": 1,
"EchoTime": 0.00299,
"EchoTime1": 0.00299,
"EchoTime2": 0.00525,
"EchoTrainLength": 2,
"FlipAngle": 15,
"ImageComments": "007@gottfried:OlfUnc",
"ImageOrientationPatientDICOM": [
0.998864,
-0.0335361,
-0.0338444,
0.0071479,
0.807771,
-0.589454
],
"ImageType": [
"ORIGINAL",
"PRIMARY",
"P",
"ND",
"PHASE"
],
"ImagingFrequency": 296.942,
"InPlanePhaseEncodingDirection": "COL",
"InPlanePhaseEncodingDirectionDICOM": "COL",
"InstitutionAddress": "Curie Blvd 422,Philadelphia,PA,US,19104",
"InstitutionName": "SC7T",
"IntendedFor": [
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-01_bold.nii.gz",
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-02_bold.nii.gz",
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-03_bold.nii.gz",
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-04_bold.nii.gz",
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-05_bold.nii.gz",
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-06_bold.nii.gz",
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-07_bold.nii.gz",
"ses-olfunc007/func/sub-olfunc007_ses-olfunc007_task-olfunc_run-08_bold.nii.gz"
],
"MRAcquisitionType": "2D",
"MagneticFieldStrength": 7,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Investigational_Device_7T",
"MatrixCoilMode": "GRAPPA",
"Modality": "MR",
"ParallelReductionFactorInPlane": 2,
"PartialFourier": 1,
"PatientPosition": "HFS",
"PercentPhaseFOV": 100,
"PercentPhaseFieldOfView": 100.0,
"PercentSampling": 100.0,
"PhaseEncodingDirection": "j-",
"PhaseEncodingSteps": 112,
"PhaseResolution": 1,
"PixelBandwidth": 630,
"PixelSpacing": [
1.9642857313156,
1.9642857313156
],
"ProcedureStepDescription": "Research^Ludwig",
"ProtocolName": "B0map2D_2mm",
"PulseSequenceDetails": "%AdjustSeq%\\AdjGreSeq",
"ReceiveCoilActiveElements": "HE1-4;NE1,2",
"ReceiveCoilName": "1Tx32Rx_Head",
"ReconMatrixPE": 112,
"RefLinesPE": 24,
"RepetitionTime": 0.032,
"Rows": 112,
"SAR": 0.0172858,
"ScanningSequence": "GR",
"SequenceName": "*fl2d2",
"SequenceVariant": "SP",
"SeriesDescription": "AdjGre",
"SeriesNumber": 11,
"ShimSetting": [
27,
-70,
594,
17,
-151,
602,
-110,
163
],
"SliceThickness": 2,
"SliceTiming": [
0,
2.17969,
4.35156,
6.53125,
8.70312,
10.8828,
13.0547,
15.2344,
17.4141,
19.5859,
21.7656,
23.9375,
26.1172,
28.2891,
30.4688,
32.6406,
34.8203,
36.9922,
39.1719,
41.3438,
43.5234,
45.6953,
47.875,
50.0547,
0.00781,
2.1875,
4.36719,
6.53906,
8.71094,
10.8906,
13.0625,
15.2422,
17.4219,
19.5938,
21.7734,
23.9453,
26.125,
28.2969,
30.4766,
32.6484,
34.8281,
37,
39.1797,
41.3516,
43.5312,
45.7031,
47.8828,
50.0547,
0.01562,
2.19531,
4.36719,
6.54688,
8.72656,
10.8984,
13.0703,
15.25,
17.4297,
19.6016,
21.7812,
23.9531,
26.1328,
28.3047,
30.4844,
32.6562,
34.8359,
37.0078,
39.1875,
41.3672,
43.5391,
45.7109,
47.8906,
50.0625,
0.02344,
2.20312,
4.375,
6.55469,
8.73438,
10.9062,
13.0859,
15.2578,
17.4297,
19.6094,
21.7891,
23.9609,
26.1406,
28.3125,
30.4922,
32.6641,
34.8438,
37.0156,
39.1953,
41.3672,
43.5469,
45.7266,
47.8984,
50.0703
],
"SoftwareVersions": "syngo MR E12",
"SpacingBetweenSlices": 2.0,
"StationName": "AWP79106",
"TxRefAmp": 230.174
}