fMRIPrep Not Using Fmaps

ejdavid · October 15, 2024, 7:51pm

Summary of what happened:

Hi there,

I am trying to use fMRIPrep version 23.2.1 and I have several fmap files for my functional data found within the fmap folder for each subject. fMRIPrep is not recognizing them. Why might fMRIPrep fail to use my fmaps in this case? Any information you might have would be very helpful. Thanks again!

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

PASTE CODE HERE

Version:

23.2.1

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

Docker

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

ode --trace-warnings ...` to show where the warning was created)
        1: [ERR] Repetition time did not match between the scan's header and the associated JSON metadata file. (code: 12 - REPETITION_TIME_MISMATCH)
                ./sub-076/func/sub-076_task-fmri_acq-3D11mm_dir-PA_run-01_bold.nii.gz
                ./sub-076/func/sub-076_task-fmri_acq-3D11mm_run-03_bold.nii.gz
                ./sub-076/func/sub-076_task-fmri_acq-3D11mm_run-04_bold.nii.gz

        Please visit https://neurostars.org/search?q=REPETITION_TIME_MISMATCH for existing conversations about this issue.

        2: [ERR] You have to define 'TaskName' for this file. (code: 50 - TASK_NAME_MUST_DEFINE)
                ./sub-001/func/sub-001_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_phase.nii.gz
                ./sub-001/func/sub-001_task-cloudySCR_acq-ep2d19mm_run-02_echo-3_phase.nii.gz
                ./sub-001/func/sub-001_task-cloudySCR_acq-ep2d19mm_run-03_echo-3_bold.nii.gz
                ./sub-001/func/sub-001_task-cloudySCR_acq-ep2d19mm_run-04_echo-2_bold.nii.gz
                ./sub-001/func/sub-001_task-cloudySCR_acq-ep2d19mm_run-05_echo-1_bold.nii.gz
                ./sub-001/func/sub-001_task-cloudySCR_acq-ep2d19mm_run-06_echo-2_phase.nii.gz
                ./sub-001/func/sub-001_task-cloudy_acq-ep2d19mm_run-01_echo-3_bold.nii.gz
                ./sub-001/func/sub-001_task-cloudy_acq-ep2d19mm_run-02_echo-1_bold.nii.gz
                ./sub-001/func/sub-001_task-cloudy_acq-ep2d19mm_run-03_echo-2_bold.nii.gz
                ./sub-001/func/sub-001_task-cloudy_acq-ep2d19mm_run-04_echo-1_phase.nii.gz

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

Portion of JSON

     ...

	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20211006",
	"IntendedFor": ["func/sub-018_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz", "func/sub-018_task-cloudy_acq-ep2d19mm_run-02_echo-3_bold.nii.gz", "func/sub-018_task-cloudy_acq-ep2d19mm_run-03_echo-2_bold.nii.gz", "func/sub-018_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz", "func/sub-018_task-cloudySCR_acq-ep2d19mm_run-02_echo-3_bold.nii.gz", "func/sub-018_task-cloudySCR_acq-ep2d19mm_run-03_echo-2_bold.nii.gz", "func/sub-018_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz", "func/sub-018_task-present_acq-ep2d19mm_run-02_echo-3_bold.nii.gz", "func/sub-018_task-present_acq-ep2d19mm_run-03_echo-2_bold.nii.gz", "func/sub-018_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz", "func/sub-018_task-presentSCR_acq-ep2d19mm_run-02_echo-3_bold.nii.gz", "func/sub-018_task-presentSCR_acq-ep2d19mm_run-03_echo-2_bold.nii.gz", "func/sub-018_task-rest_acq-ep2d19mm_run-02_echo-3_bold.nii.gz", "func/sub-018_task-rest_acq-ep2d19mm_run-03_echo-1_bold.nii.gz", "func/sub-018_task-rest_acq-ep2d19mm_run-06_echo-2_bold.nii.gz"]
 }

Steven · October 15, 2024, 7:53pm

Hi @ejdavid,

In the future please do not delete the post template as it helps organize your post. Please edit your post to include the BIDS validation report.

Are these GRE or SE fieldmaps? If SE, are PhaseEncodingDirections properly set?

Best,
Steven

ejdavid · October 15, 2024, 8:31pm

Hi Steven,

These are SE fieldmaps. “PhaseEncodingDirection”: “j-” for dir-AP files and “PhaseEncodingDirection”: “j”, for dir-PA.

Sorry about that. Thanks for the response anyway. I’ve updated the BIDS validator information. The only problem seems to be that I don’t have a taskname header in the .json files. Is this what is causing the problem? Shouldn’t the IntendedFor somewhat accomodate an issue like this as it gives full file names?

Steven · October 15, 2024, 8:31pm

Thanks. while you should definitely fix those errors before running fMRIPrep, they don’t look relevant to the fmap error. Can you provide the tree output on a subject raw data directory? And the contents of a AP/PA pair of jsons? And your fmriprep code?

Best,
Steven

ejdavid · October 16, 2024, 1:43pm

Sure.

Directory Tree:

.
├── dataset_description.json
├── sub-001
│   ├── anat
│   │   ├── sub-001_acq-mprage8mma_T1w.json
│   │   ├── sub-001_acq-mprage8mma_T1w.nii.gz
│   │   ├── sub-001_acq-mprage8mmb_T1w.json
│   │   └── sub-001_acq-mprage8mmb_T1w.nii.gz
│   ├── fmap
│   │   ├── sub-001_acq-mbep2d14mm_dir-AP_epi.json
│   │   ├── sub-001_acq-mbep2d14mm_dir-AP_epi.nii.gz
│   │   ├── sub-001_acq-mbep2d14mm_dir-PA_epi.json
│   │   ├── sub-001_acq-mbep2d14mm_dir-PA_epi.nii.gz
│   │   ├── sub-001_acq-mbep2d19mm_dir-AP_epi.json
│   │   ├── sub-001_acq-mbep2d19mm_dir-AP_epi.nii.gz
│   │   ├── sub-001_acq-mbep2d19mm_dir-PA_epi.json
│   │   └── sub-001_acq-mbep2d19mm_dir-PA_epi.nii.gz
│   └── func
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-01_echo-3_bold.json
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-01_echo-3_bold.nii.gz
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-02_echo-1_bold.json
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-02_echo-1_bold.nii.gz
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-03_echo-2_bold.json
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-03_echo-2_bold.nii.gz
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-04_echo-1_phase.json
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-04_echo-1_phase.nii.gz
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-05_echo-3_phase.json
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-05_echo-3_phase.nii.gz
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-06_echo-2_phase.json
│       ├── sub-001_task-cloudy_acq-ep2d19mm_run-06_echo-2_phase.nii.gz
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_phase.json
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_phase.nii.gz
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-02_echo-3_phase.json
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-02_echo-3_phase.nii.gz
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-03_echo-3_bold.json
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-03_echo-3_bold.nii.gz
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-04_echo-2_bold.json
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-04_echo-2_bold.nii.gz
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-05_echo-1_bold.json
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-05_echo-1_bold.nii.gz
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-06_echo-2_phase.json
│       ├── sub-001_task-cloudySCR_acq-ep2d19mm_run-06_echo-2_phase.nii.gz
│       ├── sub-001_task-fmri_acq-3D12mm_dir-PA_run-01_bold.json
│       ├── sub-001_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz
│       ├── sub-001_task-fmri_acq-3D12mm_dir-PA_run-02_phase.json
│       ├── sub-001_task-fmri_acq-3D12mm_dir-PA_run-02_phase.nii.gz
│       ├── sub-001_task-fmri_acq-3D12mm_run-01_phase.json
│       ├── sub-001_task-fmri_acq-3D12mm_run-01_phase.nii.gz
│       ├── sub-001_task-fmri_acq-3D12mm_run-02_bold.json
│       ├── sub-001_task-fmri_acq-3D12mm_run-02_bold.nii.gz
│       ├── sub-001_task-fmri_acq-3D12mm_run-03_phase.json
│       ├── sub-001_task-fmri_acq-3D12mm_run-03_phase.nii.gz
│       ├── sub-001_task-fmri_acq-3D12mm_run-04_bold.json
│       ├── sub-001_task-fmri_acq-3D12mm_run-04_bold.nii.gz
│       ├── sub-001_task-present_acq-ep2d19mm_run-01_echo-2_phase.json
│       ├── sub-001_task-present_acq-ep2d19mm_run-01_echo-2_phase.nii.gz
│       ├── sub-001_task-present_acq-ep2d19mm_run-02_echo-1_bold.json
│       ├── sub-001_task-present_acq-ep2d19mm_run-02_echo-1_bold.nii.gz
│       ├── sub-001_task-present_acq-ep2d19mm_run-03_echo-2_bold.json
│       ├── sub-001_task-present_acq-ep2d19mm_run-03_echo-2_bold.nii.gz
│       ├── sub-001_task-present_acq-ep2d19mm_run-04_echo-3_bold.json
│       ├── sub-001_task-present_acq-ep2d19mm_run-04_echo-3_bold.nii.gz
│       ├── sub-001_task-present_acq-ep2d19mm_run-05_echo-3_phase.json
│       ├── sub-001_task-present_acq-ep2d19mm_run-05_echo-3_phase.nii.gz
│       ├── sub-001_task-present_acq-ep2d19mm_run-06_echo-1_phase.json
│       ├── sub-001_task-present_acq-ep2d19mm_run-06_echo-1_phase.nii.gz
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-01_echo-3_bold.json
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-01_echo-3_bold.nii.gz
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-02_echo-1_phase.json
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-02_echo-1_phase.nii.gz
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-03_echo-3_phase.json
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-03_echo-3_phase.nii.gz
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-04_echo-2_phase.json
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-04_echo-2_phase.nii.gz
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-05_echo-1_bold.json
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-05_echo-1_bold.nii.gz
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-06_echo-2_bold.json
│       ├── sub-001_task-presentSCR_acq-ep2d19mm_run-06_echo-2_bold.nii.gz
│       ├── sub-001_task-rest_acq-ep2d19mm_run-01_echo-2_phase.json
│       ├── sub-001_task-rest_acq-ep2d19mm_run-01_echo-2_phase.nii.gz
│       ├── sub-001_task-rest_acq-ep2d19mm_run-02_echo-3_bold.json
│       ├── sub-001_task-rest_acq-ep2d19mm_run-02_echo-3_bold.nii.gz
│       ├── sub-001_task-rest_acq-ep2d19mm_run-03_echo-1_phase.json
│       ├── sub-001_task-rest_acq-ep2d19mm_run-03_echo-1_phase.nii.gz
│       ├── sub-001_task-rest_acq-ep2d19mm_run-04_echo-1_bold.json
│       ├── sub-001_task-rest_acq-ep2d19mm_run-04_echo-1_bold.nii.gz
│       ├── sub-001_task-rest_acq-ep2d19mm_run-05_echo-2_bold.json
│       ├── sub-001_task-rest_acq-ep2d19mm_run-05_echo-2_bold.nii.gz
│       ├── sub-001_task-rest_acq-ep2d19mm_run-06_echo-3_phase.json
│       ├── sub-001_task-rest_acq-ep2d19mm_run-06_echo-3_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-01_echo-3_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-01_echo-3_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-02_echo-3_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-02_echo-3_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-03_echo-2_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-03_echo-2_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-04_echo-1_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-04_echo-1_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-05_echo-1_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-05_echo-1_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-06_echo-2_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_dir-PA_run-06_echo-2_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-01_echo-1_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_run-01_echo-1_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-02_echo-2_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_run-02_echo-2_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-03_echo-1_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_run-03_echo-1_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-04_echo-2_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_run-04_echo-2_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-05_echo-3_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_run-05_echo-3_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-06_echo-1_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_run-06_echo-1_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-07_echo-3_phase.json
│       ├── sub-001_task-rest_acq-megre14mm_run-07_echo-3_phase.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-08_echo-2_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_run-08_echo-2_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-09_echo-3_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_run-09_echo-3_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-10_echo-1_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_run-10_echo-1_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-11_echo-3_bold.json
│       ├── sub-001_task-rest_acq-megre14mm_run-11_echo-3_bold.nii.gz
│       ├── sub-001_task-rest_acq-megre14mm_run-12_echo-2_phase.json
│       └── sub-001_task-rest_acq-megre14mm_run-12_echo-2_phase.nii.gz

dir-PA .json

{
	"Modality": "MR",
	"MagneticFieldStrength": 7,
	"ImagingFrequency": 297.184,
	"Manufacturer": "Siemens",
	"ManufacturersModelName": "Investigational_Device_7T",
	"InstitutionName": "BIC",
	"InstitutionalDepartmentName": "Department",
	"InstitutionAddress": "Street StreetNo,City,District,CA,ZIP",
	"DeviceSerialNumber": "79017",
	"StationName": "AWP79017",
	"SeriesInstanceUID": "1.3.12.2.1107.5.2.0.79017.2024082711404237305481959.0.0.0",
	"StudyInstanceUID": "1.3.12.2.1107.5.2.0.79017.30000024082713145338700000001",
	"ReferringPhysicianName": "Dr.Spreng",
	"StudyID": "1",
	"PatientName": "EE20240827_02001",
	"PatientID": "24.08.27-10:01:38-DST-1.3.12.2.1107.5.2.0.79017",
	"PatientBirthDate": "1991-01-01",
	"PatientSex": "M",
	"PatientWeight": 80,
	"BodyPartExamined": "BRAIN",
	"PatientPosition": "HFS",
	"ProcedureStepDescription": "Functional^Dr.Spreng",
	"SoftwareVersions": "syngo MR E12",
	"MRAcquisitionType": "2D",
	"SeriesDescription": "fmap-fmri_acq-mbep2d_SE_14mm_dir-PA",
	"ProtocolName": "fmap-fmri_acq-mbep2d_SE_14mm_dir-PA",
	"ScanningSequence": "EP",
	"SequenceVariant": "SK",
	"ScanOptions": "PFP\\FS",
	"SequenceName": "epse2d1_144",
	"ImageType": ["ORIGINAL", "PRIMARY", "M", "MB", "ND", "MOSAIC"],
	"SeriesNumber": 35,
	"AcquisitionTime": "11:42:29.482500",
	"AcquisitionDateTime": "2024-08-27T11:42:29.482500",
	"AcquisitionNumber": 1,
	"ImageComments": "Unaliased MB3/PE4/LB",
	"SliceThickness": 1.4,
	"SpacingBetweenSlices": 1.4,
	"SAR": 0.12644,
	"EchoTime": 0.024,
	"RepetitionTime": 5,
	"FlipAngle": 90,
	"PartialFourier": 0.75,
	"BaseResolution": 144,
	"ShimSetting": [
		154,
		45,
		560,
		445,
		57,
		602,
		228,
		-237	],
	"TxRefAmp": 258.829,
	"PhaseResolution": 1,
	"ReceiveCoilName": "8Tx32Rx_Head",
	"CoilString": "AC",
	"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
	"WipMemBlock": "8ce70461-b151-45a0-8ba1-710ab78f4ad6||Sequence: R016 ve12u/SP01_R016a r/af3652dd; Apr  1 2021 14:29:52 by eja",
	"RefLinesPE": 54,
	"CoilCombinationMethod": "Sum of Squares",
	"ConsistencyInfo": "N4_VE12U_LATEST_20181126",
	"MatrixCoilMode": "GRAPPA",
	"MultibandAccelerationFactor": 3,
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"EchoTrainLength": 36,
	"PhaseEncodingSteps": 109,
	"AcquisitionMatrixPE": 144,
	"ReconMatrixPE": 144,
	"BandwidthPerPixelPhaseEncode": 32.552,
	"ParallelReductionFactorInPlane": 3,
	"EffectiveEchoSpacing": 0.000213334,
	"DerivedVendorReportedEchoSpacing": 0.000640002,
	"TotalReadoutTime": 0.0305067,
	"PixelBandwidth": 1930,
	"DwellTime": 1.8e-06,
	"PhaseEncodingDirection": "j",
	"SliceTiming": [
		0,
		1.1675,
		2.3325,
		3.5,
		4.6675,
		0.8325,
		2,
		3.1675,
		4.3325,
		0.5,
		1.6675,
		2.8325,
		4,
		0.1675,
		1.3325,
		2.5,
		3.6675,
		4.8325,
		1,
		2.1675,
		3.3325,
		4.5,
		0.6675,
		1.8325,
		3,
		4.1675,
		0.3325,
		1.5,
		2.6675,
		3.8325,
		0,
		1.1675,
		2.3325,
		3.5,
		4.6675,
		0.8325,
		2,
		3.1675,
		4.3325,
		0.5,
		1.6675,
		2.8325,
		4,
		0.1675,
		1.3325,
		2.5,
		3.6675,
		4.8325,
		1,
		2.1675,
		3.3325,
		4.5,
		0.6675,
		1.8325,
		3,
		4.1675,
		0.3325,
		1.5,
		2.6675,
		3.8325,
		0,
		1.1675,
		2.3325,
		3.5,
		4.6675,
		0.8325,
		2,
		3.1675,
		4.3325,
		0.5,
		1.6675,
		2.8325,
		4,
		0.1675,
		1.3325,
		2.5,
		3.6675,
		4.8325,
		1,
		2.1675,
		3.3325,
		4.5,
		0.6675,
		1.8325,
		3,
		4.1675,
		0.3325,
		1.5,
		2.6675,
		3.8325	],
	"ImageOrientationPatientDICOM": [
		1,
		0,
		0,
		0,
		0.809017,
		-0.587785	],
	"ImageOrientationText": "Tra>Cor(-36.0)",
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20211006", 
	"IntendedFor": ["func/sub-001_task-rest_acq-megre14mm_dir-PA_run-01_echo-3_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_dir-PA_run-05_echo-1_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_dir-PA_run-06_echo-2_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-02_echo-2_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-03_echo-1_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-08_echo-2_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-09_echo-3_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-10_echo-1_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-11_echo-3_bold.nii.gz"]
}

dir-AP .json:

{
	"Modality": "MR",
	"MagneticFieldStrength": 7,
	"ImagingFrequency": 297.184,
	"Manufacturer": "Siemens",
	"ManufacturersModelName": "Investigational_Device_7T",
	"InstitutionName": "BIC",
	"InstitutionalDepartmentName": "Department",
	"InstitutionAddress": "Street StreetNo,City,District,CA,ZIP",
	"DeviceSerialNumber": "79017",
	"StationName": "AWP79017",
	"SeriesInstanceUID": "1.3.12.2.1107.5.2.0.79017.2024082711383742602780958.0.0.0",
	"StudyInstanceUID": "1.3.12.2.1107.5.2.0.79017.30000024082713145338700000001",
	"ReferringPhysicianName": "Dr.Spreng",
	"StudyID": "1",
	"PatientName": "EE20240827_02001",
	"PatientID": "24.08.27-10:01:38-DST-1.3.12.2.1107.5.2.0.79017",
	"PatientBirthDate": "1991-01-01",
	"PatientSex": "M",
	"PatientWeight": 80,
	"BodyPartExamined": "BRAIN",
	"PatientPosition": "HFS",
	"ProcedureStepDescription": "Functional^Dr.Spreng",
	"SoftwareVersions": "syngo MR E12",
	"MRAcquisitionType": "2D",
	"SeriesDescription": "fmap-fmri_acq-mbep2d_SE_14mm_dir-AP",
	"ProtocolName": "fmap-fmri_acq-mbep2d_SE_14mm_dir-AP",
	"ScanningSequence": "EP",
	"SequenceVariant": "SK",
	"ScanOptions": "PFP\\FS",
	"SequenceName": "epse2d1_144",
	"ImageType": ["ORIGINAL", "PRIMARY", "M", "MB", "ND", "MOSAIC"],
	"SeriesNumber": 34,
	"AcquisitionTime": "11:40:20.915000",
	"AcquisitionDateTime": "2024-08-27T11:40:20.915000",
	"AcquisitionNumber": 1,
	"ImageComments": "Unaliased MB3/PE4/LB",
	"SliceThickness": 1.4,
	"SpacingBetweenSlices": 1.4,
	"SAR": 0.12644,
	"EchoTime": 0.024,
	"RepetitionTime": 5,
	"FlipAngle": 90,
	"PartialFourier": 0.75,
	"BaseResolution": 144,
	"ShimSetting": [
		154,
		45,
		560,
		445,
		57,
		602,
		228,
		-237	],
	"TxRefAmp": 258.829,
	"PhaseResolution": 1,
	"ReceiveCoilName": "8Tx32Rx_Head",
	"CoilString": "AC",
	"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
	"WipMemBlock": "2c784fd9-364a-419f-b465-8be18d6a26ee||Sequence: R016 ve12u/SP01_R016a r/af3652dd; Apr  1 2021 14:29:52 by eja",
	"RefLinesPE": 54,
	"CoilCombinationMethod": "Sum of Squares",
	"ConsistencyInfo": "N4_VE12U_LATEST_20181126",
	"MatrixCoilMode": "GRAPPA",
	"MultibandAccelerationFactor": 3,
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"EchoTrainLength": 36,
	"PhaseEncodingSteps": 109,
	"AcquisitionMatrixPE": 144,
	"ReconMatrixPE": 144,
	"BandwidthPerPixelPhaseEncode": 32.552,
	"ParallelReductionFactorInPlane": 3,
	"EffectiveEchoSpacing": 0.000213334,
	"DerivedVendorReportedEchoSpacing": 0.000640002,
	"TotalReadoutTime": 0.0305067,
	"PixelBandwidth": 1930,
	"DwellTime": 1.8e-06,
	"PhaseEncodingDirection": "j-",
	"SliceTiming": [
		0,
		1.1675,
		2.335,
		3.5,
		4.6675,
		0.835,
		2,
		3.1675,
		4.335,
		0.5,
		1.6675,
		2.835,
		4,
		0.1675,
		1.335,
		2.5,
		3.6675,
		4.835,
		1,
		2.1675,
		3.335,
		4.5,
		0.6675,
		1.835,
		3,
		4.1675,
		0.335,
		1.5,
		2.6675,
		3.835,
		0,
		1.1675,
		2.335,
		3.5,
		4.6675,
		0.835,
		2,
		3.1675,
		4.335,
		0.5,
		1.6675,
		2.835,
		4,
		0.1675,
		1.335,
		2.5,
		3.6675,
		4.835,
		1,
		2.1675,
		3.335,
		4.5,
		0.6675,
		1.835,
		3,
		4.1675,
		0.335,
		1.5,
		2.6675,
		3.835,
		0,
		1.1675,
		2.335,
		3.5,
		4.6675,
		0.835,
		2,
		3.1675,
		4.335,
		0.5,
		1.6675,
		2.835,
		4,
		0.1675,
		1.335,
		2.5,
		3.6675,
		4.835,
		1,
		2.1675,
		3.335,
		4.5,
		0.6675,
		1.835,
		3,
		4.1675,
		0.335,
		1.5,
		2.6675,
		3.835	],
	"ImageOrientationPatientDICOM": [
		1,
		0,
		0,
		0,
		0.809017,
		-0.587785	],
	"ImageOrientationText": "Tra>Cor(-36.0)",
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20211006", 
	"IntendedFor": ["func/sub-001_task-rest_acq-megre14mm_dir-PA_run-01_echo-3_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_dir-PA_run-05_echo-1_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_dir-PA_run-06_echo-2_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-02_echo-2_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-03_echo-1_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-08_echo-2_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-09_echo-3_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-10_echo-1_bold.nii.gz", "func/sub-001_task-rest_acq-megre14mm_run-11_echo-3_bold.nii.gz"]
}

fMRIPrep Script:

#!/bin/bash

# Check if subject number argument is provided
if [ $# -ne 1 ]; then
    echo "Usage: $0 <subject_number>"
    exit 1
fi

# Subject number provided as argument
subj=$1
echo "Starting subject ${subj}"

# Set paths
bids_root_dir="/lbc/lbc1/derivatives/brainstem_funk/BIDS_DAY2"
bids_deriv_dir="/lbc/lbc1/derivatives/brainstem_funk/fmriprep"
workdir="/lbc/lbc1/derivatives/brainstem_funk/work/sub-${subj}_wd"
license_dir="/lbc/lbc1/derivatives/brainstem_funk/license.txt"

# Create working directory
mkdir -p "$workdir"

# Run fMRIPrep with Docker
docker run --rm --user $(id -u):$(id -g) \
    -v $bids_root_dir:/data \
    -v $bids_deriv_dir:/out \
    -v $license_dir:/license.txt \
    -v $workdir:/work \
    nipreps/fmriprep:23.2.1 /data /out participant \
    --skip-bids-validation  \
    --participant-label $subj \
    --fs-license-file /license.txt \
    --use-aroma \
    --output-spaces fsnative \
    --n_cpus 8 \
    --omp-nthreads 8 \
    --mem-mb 204800 \
    --skull-strip-t1w force \
    --me-output-echos \
    --low-mem \
    --ignore slicetiming \
    -w /work

echo "Finished processing subject ${subj}"

# Clean up the work directory if desired
# rm -rf "$workdir"

Thanks again for your help on this!

Steven · October 16, 2024, 2:12pm

Hi @ejdavid,

Those field maps are paired to different func files according to the IntendedFor fields. Also AROMA will not work in that fmriprep version as it was removed in 23.1.0.

Best,
Steven

ejdavid · October 16, 2024, 2:29pm

Hi Steven,

Apologies for the confusion. I pasted the sub-018 .json files there but I’ve corrected it to the sub-001 files. The file names in the .json look correctly paired with the correct functional file names. Is it a formatting problem somehow?

I’ll take th AROMA out; thanks! I can’t imagine it is what is causing the field maps not to pair, though.

Steven · October 16, 2024, 2:56pm

Can you fix the bids validation errors, update to most recent version, and try again?

ejdavid · October 18, 2024, 2:18pm

Hi Steven,

I’ve eliminated the BIDS validation errors and updated to the latest version of fMRIPrep (v. 24.1.1). I’ve rerun subjects through fMRIPrep, and they are still coming out without Susceptibility Distortion Correction and no sign that the fmaps have been associated with their corresponding functional files.

Here is the code I used to run fMRIPrep:

#!/bin/bash

export DOCKER_CONTENT_TRUST=0

# Check if subject number argument is provided
if [ $# -ne 1 ]; then
    echo "Usage: $0 <subject_number>"
    exit 1
fi

# Subject number provided as argument
subj=$1
echo "Starting subject ${subj}"

# Set paths
bids_root_dir="/lbc/lbc1/derivatives/brainstem_funk/BIDS_DAY2"
bids_deriv_dir="/lbc/lbc1/derivatives/brainstem_funk/fmriprep"
workdir="/lbc/lbc1/derivatives/brainstem_funk/work/sub-${subj}_wd"
license_dir="/lbc/lbc1/derivatives/brainstem_funk/license.txt"

# Create working directory
mkdir -p "$workdir"

# Run fMRIPrep with Docker
docker run --rm --user $(id -u):$(id -g) \
    -v $bids_root_dir:/data \
    -v $bids_deriv_dir:/out \
    -v $license_dir:/license.txt \
    -v $workdir:/work \
    nipreps/fmriprep:24.1.1 /data /out participant \
    --skip-bids-validation  \
    --participant-label $subj \
    --fs-license-file /license.txt \
    --output-spaces fsnative \
    --n_cpus 8 \
    --omp-nthreads 8 \
    --mem-mb 204800 \
    --skull-strip-t1w force \
    --me-output-echos \
    --low-mem \
    --ignore slicetiming \
    -w /work

echo "Finished processing subject ${subj}"

# Clean up the work directory if desired
# rm -rf "$workdir"

Here is an example of the field map .json file with the IntendedFor header:

{
    "Modality": "MR",
    "MagneticFieldStrength": 7,
    "ImagingFrequency": 297.184,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Investigational_Device_7T",
    "InstitutionName": "BIC",
    "InstitutionalDepartmentName": "Department",
    "InstitutionAddress": "Street StreetNo,City,District,CA,ZIP",
    "DeviceSerialNumber": "79017",
    "StationName": "AWP79017",
    "SeriesInstanceUID": "1.3.12.2.1107.5.2.0.79017.2024082710382693595047946.0.0.0",
    "StudyInstanceUID": "1.3.12.2.1107.5.2.0.79017.30000024082713145338700000001",
    "ReferringPhysicianName": "Dr.Spreng",
    "StudyID": "1",
    "PatientName": "EE20240827_02001",
    "PatientID": "24.08.27-10:01:38-DST-1.3.12.2.1107.5.2.0.79017",
    "PatientBirthDate": "1991-01-01",
    "PatientSex": "M",
    "PatientWeight": 80,
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "Functional^Dr.Spreng",
    "SoftwareVersions": "syngo MR E12",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "fmap-fmri_acq-mbep2d_SE_19mm_dir-AP",
    "ProtocolName": "fmap-fmri_acq-mbep2d_SE_19mm_dir-AP",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "PFP\\FS",
    "SequenceName": "epse2d1_118",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "MB",
        "ND",
        "MOSAIC"
    ],
    "SeriesNumber": 13,
    "AcquisitionTime": "10:39:27.830000",
    "AcquisitionDateTime": "2024-08-27T10:39:27.830000",
    "AcquisitionNumber": 1,
    "ImageComments": "Unaliased MB3/PE4/LB",
    "SliceThickness": 1.9,
    "SpacingBetweenSlices": 1.9,
    "SAR": 0.1756,
    "EchoTime": 0.0184,
    "RepetitionTime": 3,
    "FlipAngle": 90,
    "PartialFourier": 0.75,
    "BaseResolution": 118,
    "ShimSetting": [
        154,
        45,
        560,
        445,
        57,
        602,
        228,
        -237
    ],
    "TxRefAmp": 258.829,
    "PhaseResolution": 1,
    "ReceiveCoilName": "8Tx32Rx_Head",
    "CoilString": "AC",
    "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
    "WipMemBlock": "85744b0f-11e1-40f6-82df-e6a9298b2cdc||Sequence: R016 ve12u/SP01_R016a r/af3652dd; Apr  1 2021 14:29:52 by eja",
    "RefLinesPE": 54,
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE12U_LATEST_20181126",
    "MatrixCoilMode": "GRAPPA",
    "MultibandAccelerationFactor": 3,
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 29,
    "PhaseEncodingSteps": 88,
    "AcquisitionMatrixPE": 118,
    "ReconMatrixPE": 118,
    "BandwidthPerPixelPhaseEncode": 47.969,
    "ParallelReductionFactorInPlane": 3,
    "EffectiveEchoSpacing": 0.000176668,
    "DerivedVendorReportedEchoSpacing": 0.000530003,
    "TotalReadoutTime": 0.0206701,
    "PixelBandwidth": 2355,
    "DwellTime": 1.8e-06,
    "PhaseEncodingDirection": "j-",
    "SliceTiming": [
        0,
        1.56,
        0.12,
        1.68,
        0.24,
        1.8,
        0.36,
        1.92,
        0.48,
        2.04,
        0.6,
        2.16,
        0.72,
        2.28,
        0.84,
        2.4,
        0.96,
        2.52,
        1.08,
        2.64,
        1.2,
        2.76,
        1.32,
        2.88,
        1.44,
        0,
        1.56,
        0.12,
        1.68,
        0.24,
        1.8,
        0.36,
        1.92,
        0.48,
        2.04,
        0.6,
        2.16,
        0.72,
        2.28,
        0.84,
        2.4,
        0.96,
        2.52,
        1.08,
        2.64,
        1.2,
        2.76,
        1.32,
        2.88,
        1.44,
        0,
        1.56,
        0.12,
        1.68,
        0.24,
        1.8,
        0.36,
        1.92,
        0.48,
        2.04,
        0.6,
        2.16,
        0.72,
        2.28,
        0.84,
        2.4,
        0.96,
        2.52,
        1.08,
        2.64,
        1.2,
        2.76,
        1.32,
        2.88,
        1.44
    ],
    "ImageOrientationPatientDICOM": [
        1,
        0,
        0,
        0,
        0.743145,
        -0.669131
    ],
    "ImageOrientationText": "Tra>Cor(-42.0)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Skullstripped": false,
    "IntendedFor": [
        "func/sub-001_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz",
        "func/sub-001_task-rest_acq-ep2d19mm_run-01_echo-1_phase.nii.gz",
        "func/sub-001_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz",
        "func/sub-001_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz",
        "func/sub-001_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz",
        "func/sub-001_task-presentSCR_acq-ep2d19mm_run-01_echo-1_phase.nii.gz",
        "func/sub-001_task-present_acq-ep2d19mm_run-01_echo-1_phase.nii.gz",
        "func/sub-001_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_phase.nii.gz",
        "func/sub-001_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz",
        "func/sub-001_task-cloudy_acq-ep2d19mm_run-01_echo-1_phase.nii.gz"
    ],
    "TaskName": [
        "cloudy",
        "cloudySCR",
        "present",
        "presentSCR",
        "rest"
    ]
}

Thanks again for your time!

Steven · October 18, 2024, 2:23pm

Can you attach or send the output log? You can also try using the B0FieldSource/Identifier method. Your fmap jsons get the B0FieldIdentifier tag (e.g., "B0FieldIdentifier":"fmap1" for both files for one pair of jsons), and the BOLD jsons you want to associate get "B0FieldSource":"fmap1" (or whatever you want to name the fmap).

ejdavid · October 18, 2024, 2:28pm

Is this the output log you were looking for?

[environment]
cpu_count = 48
exec_env = "docker"
free_mem = 239.0
overcommit_policy = "never"
overcommit_limit = "n/a"
nipype_version = "1.8.6"
templateflow_version = "24.2.0"
version = "24.1.1"

[execution]
bids_dir = "/data"
bids_database_dir = "/work/20241017-173157_9cb4b361-2119-4c02-ad31-932fadd4a448/bids_db"
bids_description_hash = "9b7ad57218b25718b8c639027bf4ae51e51ed007fe994faf80a2dc21cff88603"
boilerplate_only = false
sloppy = false
debug = []
fmriprep_dir = "/out"
fs_license_file = "/license.txt"
fs_subjects_dir = "/out/sourcedata/freesurfer"
layout = "BIDS Layout: .../data | Subjects: 1 | Sessions: 0 | Runs: 2"
log_dir = "/out/logs"
log_level = 25
low_mem = true
md_only_boilerplate = false
notrack = false
track_carbon = false
country_code = "CAN"
output_dir = "/out"
me_output_echos = true
aggr_ses_reports = 4
output_layout = "bids"
output_spaces = "fsnative"
reports_only = false
run_uuid = "20241017-173157_9cb4b361-2119-4c02-ad31-932fadd4a448"
participant_label = [ "001",]
templateflow_home = "/home/fmriprep/.cache/templateflow"
work_dir = "/work"
write_graph = false

[workflow]
anat_only = false
bold2anat_dof = 6
bold2anat_init = "t1w"
cifti_output = false
fmap_bspline = false
force_syn = false
hires = true
fs_no_resume = false
ignore = [ "slicetiming",]
level = "full"
longitudinal = false
run_msmsulc = true
medial_surface_nan = false
project_goodvoxels = false
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "fsnative MNI152NLin2009cAsym"
use_syn_sdc = false
me_t2s_fit_method = "curvefit"

[nipype]
crashfile_format = "txt"
get_linked_libs = false
memory_gb = 204.8
nprocs = 8
omp_nthreads = 8
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = false

[seeds]
master = 44407
ants = 9793
numpy = 22945

[execution.derivatives]

[execution.dataset_links]
raw = "/data"
templateflow = "/home/fmriprep/.cache/templateflow"

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

I can try your solution with the b0 identifier tag.

Steven · October 18, 2024, 2:30pm

I was referring to the terminal output when running or the .out file if using a job scheduler like SLURM.

ejdavid · October 18, 2024, 2:36pm

I’m not sure how to find this output. I’m not using any job scheduler; I’m just using the a bash script with the contents linked above.

Steven · October 18, 2024, 2:38pm

Then it would be what is output in the terminal.

ejdavid · October 18, 2024, 2:41pm

The terminal has been closed after it finished running. Is there a way to get access to this through a log stored somewhere?

Steven · October 18, 2024, 2:47pm

Unfortunately not to my knowledge, but I was mainly interested in the beginning block of the log.

ejdavid · October 18, 2024, 3:21pm

Well I’ve just started running a new participant using the B0FieldIdentifier tag. I don’t know what part you need, but here is the terminal output up until fMRIPrep starts:

emilyd@burgundy:/lbc/lbc1/derivatives/brainstem_funk/scripts$ ./run_fmriprep.sh 055
Starting subject 055
2024-10-18 15:15:49,234 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:15:56,841 [ WARNING] WARNING: `sentry_sdk.Hub` is deprecated and will be removed in a future major release. Please consult our 1.x to 2.x migration guide for details on how to migrate `Hub` usage to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x
2024-10-18 15:15:56,994 [ WARNING] WARNING: sentry_sdk.configure_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-configuring
2024-10-18 15:16:06,714 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:16:06,935 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:16:07,011 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:16:08,446 [IMPORTANT] Running fMRIPrep version 24.1.1

         License NOTICE ##################################################
         fMRIPrep 24.1.1
         Copyright The NiPreps Developers.

         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).

         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.

         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.

         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
241018-15:16:08,446 nipype.workflow IMPORTANT:
         Running fMRIPrep version 24.1.1

         License NOTICE ##################################################
         fMRIPrep 24.1.1
         Copyright The NiPreps Developers.

         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).

         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.

         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.

         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
241018-15:16:09,818 nipype.workflow IMPORTANT:
         Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['055'].
           * Run identifier: 20241018-151549_1545b225-1e87-4a05-9e9e-9d8e40a42222.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
2024-10-18 15:16:09,818 [IMPORTANT] Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['055'].
           * Run identifier: 20241018-151549_1545b225-1e87-4a05-9e9e-9d8e40a42222.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
241018-15:16:10,900 nipype.workflow INFO:
         ANAT Stage 1: Adding template workflow
2024-10-18 15:16:10,900 [    INFO] ANAT Stage 1: Adding template workflow
2024-10-18 15:16:10,993 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
2024-10-18 15:16:10,993 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
241018-15:16:11,268 nipype.workflow INFO:
         ANAT Stage 2: Preparing brain extraction workflow
2024-10-18 15:16:11,268 [    INFO] ANAT Stage 2: Preparing brain extraction workflow
241018-15:16:11,381 nipype.workflow INFO:
         ANAT Stage 3: Preparing segmentation workflow
2024-10-18 15:16:11,381 [    INFO] ANAT Stage 3: Preparing segmentation workflow
241018-15:16:11,386 nipype.workflow INFO:
         ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
2024-10-18 15:16:11,386 [    INFO] ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
2024-10-18 15:16:11,397 [    INFO] ANAT Stage 5: Preparing surface reconstruction workflow
241018-15:16:11,397 nipype.workflow INFO:
         ANAT Stage 5: Preparing surface reconstruction workflow
241018-15:16:11,420 nipype.workflow INFO:
         ANAT Stage 6: Preparing mask refinement workflow
2024-10-18 15:16:11,420 [    INFO] ANAT Stage 6: Preparing mask refinement workflow
241018-15:16:11,423 nipype.workflow INFO:
         ANAT No T2w images provided - skipping Stage 7
241018-15:16:11,423 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
2024-10-18 15:16:11,423 [    INFO] ANAT No T2w images provided - skipping Stage 7
2024-10-18 15:16:11,423 [    INFO] ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
241018-15:16:11,444 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
2024-10-18 15:16:11,444 [    INFO] ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
2024-10-18 15:16:11,453 [    INFO] ANAT Stage 8a: Creating cortical ribbon mask
241018-15:16:11,453 nipype.workflow INFO:
         ANAT Stage 8a: Creating cortical ribbon mask
241018-15:16:11,457 nipype.workflow INFO:
         ANAT Stage 9: Creating fsLR registration sphere
2024-10-18 15:16:11,457 [    INFO] ANAT Stage 9: Creating fsLR registration sphere
2024-10-18 15:16:11,461 [    INFO] ANAT Stage 10: Creating MSM-Sulc registration sphere
241018-15:16:11,461 nipype.workflow INFO:
         ANAT Stage 10: Creating MSM-Sulc registration sphere
2024-10-18 15:16:13,564 [    INFO] No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241018-15:16:13,564 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241018-15:16:13,686 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:16:13,686 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:13,697 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:13,697 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:13,708 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:13,708 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:13,710 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:16:14,56 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:14,056 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:14,358 [    INFO] No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241018-15:16:14,358 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:16:14,472 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:14,472 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
241018-15:16:14,481 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:14,481 [    INFO] Stage 2: Adding motion correction workflow
2024-10-18 15:16:14,488 [    INFO] Stage 3: Adding coregistration boldref workflow
241018-15:16:14,488 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:14,490 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:16:14,825 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:14,825 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:16:15,108 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
2024-10-18 15:16:15,108 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
241018-15:16:15,223 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:16:15,223 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:15,232 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:15,232 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:15,240 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:15,240 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:15,242 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:16:15,806 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
241018-15:16:15,806 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
241018-15:16:15,925 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:16:15,925 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:15,934 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:15,934 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:15,942 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:15,942 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:15,943 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:16:17,736 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
241018-15:16:17,736 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
2024-10-18 15:16:17,847 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:17,847 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
241018-15:16:17,857 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:17,857 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:17,865 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:17,865 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:17,867 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:16:18,219 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:16:18,219 [    INFO] No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241018-15:16:18,334 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:16:18,334 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:18,344 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:18,344 [    INFO] Stage 2: Adding motion correction workflow
2024-10-18 15:16:18,351 [    INFO] Stage 3: Adding coregistration boldref workflow
241018-15:16:18,351 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:18,353 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:16:18,692 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:16:18,692 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
241018-15:16:19,7 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:16:19,007 [    INFO] No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:16:19,123 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:19,123 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
241018-15:16:19,132 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:19,132 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:19,140 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:19,140 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:19,141 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:16:19,481 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:19,481 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:16:19,778 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:16:19,778 [    INFO] No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:16:19,898 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:19,898 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:16:19,907 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:19,907 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:19,914 [    INFO] Stage 3: Adding coregistration boldref workflow
241018-15:16:19,914 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:19,916 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:16:20,262 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:20,262 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:16:20,571 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
2024-10-18 15:16:20,571 [    INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
241018-15:16:20,686 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:16:20,686 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:20,696 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:20,696 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:20,703 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:20,703 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:20,705 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:16:21,48 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:21,048 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:16:21,555 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
2024-10-18 15:16:21,555 [    INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
241018-15:16:21,669 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:16:21,669 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:16:21,678 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:16:21,678 [    INFO] Stage 2: Adding motion correction workflow
241018-15:16:21,686 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:21,686 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:16:21,687 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:16:22,186 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:22,186 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:16:25,583 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:16:25,845 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:16:25,923 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:16:28,886 [    INFO] fMRIPrep workflow graph with 1820 nodes built successfully.
241018-15:16:28,886 nipype.workflow INFO:
         fMRIPrep workflow graph with 1820 nodes built successfully.
2024-10-18 15:16:32,246 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:16:32,322 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:16:42,109 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:16:42,324 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:16:42,401 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:16:45,985 [ WARNING] WARNING: sentry_sdk.configure_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-configuring
2024-10-18 15:16:47,971 [IMPORTANT] fMRIPrep started!
241018-15:16:47,971 nipype.workflow IMPORTANT:
         fMRIPrep started!

Here is a copy an associated .json field map with the identifier:

{
    "Modality": "MR",
    "MagneticFieldStrength": 7,
    "ImagingFrequency": 297.184,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Investigational_Device_7T",
    "InstitutionName": "BIC",
    "InstitutionalDepartmentName": "Department",
    "InstitutionAddress": "Street StreetNo,City,District,CA,ZIP",
    "DeviceSerialNumber": "79017",
    "StationName": "AWP79017",
    "SeriesInstanceUID": "1.3.12.2.1107.5.2.0.79017.2024092311543329320765566.0.0.0",
    "StudyInstanceUID": "1.3.12.2.1107.5.2.0.79017.30000024092311364606200000004",
    "ReferringPhysicianName": "Dr.Spreng",
    "StudyID": "1",
    "PatientName": "EE20240923_02055",
    "PatientID": "24.09.23-10:10:46-DST-1.3.12.2.1107.5.2.0.79017",
    "PatientBirthDate": "1999-01-01",
    "PatientSex": "M",
    "PatientWeight": 65,
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "Functional^Dr.Spreng",
    "SoftwareVersions": "syngo MR E12",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "fmap-fmri_acq-mbep2d_SE_14mm_dir-AP",
    "ProtocolName": "fmap-fmri_acq-mbep2d_SE_14mm_dir-AP",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "PFP\\FS",
    "SequenceName": "epse2d1_144",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "MB",
        "ND",
        "MOSAIC"
    ],
    "SeriesNumber": 30,
    "AcquisitionTime": "11:56:14.495000",
    "AcquisitionDateTime": "2024-09-23T11:56:14.495000",
    "AcquisitionNumber": 1,
    "ImageComments": "Unaliased MB3/PE4/LB",
    "SliceThickness": 1.4,
    "SpacingBetweenSlices": 1.4,
    "SAR": 0.163134,
    "EchoTime": 0.024,
    "RepetitionTime": 5,
    "FlipAngle": 90,
    "PartialFourier": 0.75,
    "BaseResolution": 144,
    "ShimSetting": [
        145,
        -28,
        499,
        444,
        290,
        494,
        131,
        -266
    ],
    "TxRefAmp": 267.232,
    "PhaseResolution": 1,
    "ReceiveCoilName": "8Tx32Rx_Head",
    "CoilString": "AC",
    "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
    "WipMemBlock": "ea0fdade-19e1-41d3-8864-142675b52e2b||Sequence: R016 ve12u/SP01_R016a r/af3652dd; Apr  1 2021 14:29:52 by eja",
    "RefLinesPE": 54,
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE12U_LATEST_20181126",
    "MatrixCoilMode": "GRAPPA",
    "MultibandAccelerationFactor": 3,
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 36,
    "PhaseEncodingSteps": 109,
    "AcquisitionMatrixPE": 144,
    "ReconMatrixPE": 144,
    "BandwidthPerPixelPhaseEncode": 32.552,
    "ParallelReductionFactorInPlane": 3,
    "EffectiveEchoSpacing": 0.000213334,
    "DerivedVendorReportedEchoSpacing": 0.000640002,
    "TotalReadoutTime": 0.0305067,
    "PixelBandwidth": 1930,
    "DwellTime": 1.8e-06,
    "PhaseEncodingDirection": "j-",
    "SliceTiming": [
        0,
        1.165,
        2.3325,
        3.4975,
        4.665,
        0.8325,
        2,
        3.165,
        4.3325,
        0.5,
        1.665,
        2.8325,
        3.9975,
        0.165,
        1.3325,
        2.5,
        3.665,
        4.8325,
        1,
        2.165,
        3.3325,
        4.4975,
        0.665,
        1.8325,
        3,
        4.165,
        0.3325,
        1.5,
        2.665,
        3.8325,
        0,
        1.165,
        2.3325,
        3.4975,
        4.665,
        0.8325,
        2,
        3.165,
        4.3325,
        0.5,
        1.665,
        2.8325,
        3.9975,
        0.165,
        1.3325,
        2.5,
        3.665,
        4.8325,
        1,
        2.165,
        3.3325,
        4.4975,
        0.665,
        1.8325,
        3,
        4.165,
        0.3325,
        1.5,
        2.665,
        3.8325,
        0,
        1.165,
        2.3325,
        3.4975,
        4.665,
        0.8325,
        2,
        3.165,
        4.3325,
        0.5,
        1.665,
        2.8325,
        3.9975,
        0.165,
        1.3325,
        2.5,
        3.665,
        4.8325,
        1,
        2.165,
        3.3325,
        4.4975,
        0.665,
        1.8325,
        3,
        4.165,
        0.3325,
        1.5,
        2.665,
        3.8325
    ],
    "ImageOrientationPatientDICOM": [
        1,
        0,
        0,
        0,
        0.838671,
        -0.544639
    ],
    "ImageOrientationText": "Tra>Cor(-33.0)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Skullstripped": false,
    "TaskName": [
        "rest"
    ],
    "B0FieldIdentifier": "fmap_14_j_2"
}

And an associated functional .json:

{
    "Modality": "MR",
    "MagneticFieldStrength": 7,
    "ImagingFrequency": 297.184,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Investigational_Device_7T",
    "InstitutionName": "BIC",
    "InstitutionalDepartmentName": "Department",
    "InstitutionAddress": "Street StreetNo,City,District,CA,ZIP",
    "DeviceSerialNumber": "79017",
    "StationName": "AWP79017",
    "SeriesInstanceUID": "1.3.12.2.1107.5.2.0.79017.2024092310432079705906167.0.0.0",
    "StudyInstanceUID": "1.3.12.2.1107.5.2.0.79017.30000024092311364606200000004",
    "ReferringPhysicianName": "Dr.Spreng",
    "StudyID": "1",
    "PatientName": "EE20240923_02055",
    "PatientID": "24.09.23-10:10:46-DST-1.3.12.2.1107.5.2.0.79017",
    "PatientBirthDate": "1999-01-01",
    "PatientSex": "M",
    "PatientWeight": 65,
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "Functional^Dr.Spreng",
    "SoftwareVersions": "syngo MR E12",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "func-cloudy_acq-ep2d_MJC_19mm",
    "ProtocolName": "func-cloudy_acq-ep2d_MJC_19mm",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "PFP\\FS",
    "SequenceName": "epfid2d3_118",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "MOSAIC"
    ],
    "SeriesNumber": 11,
    "AcquisitionTime": "10:43:49.480000",
    "AcquisitionDateTime": "2024-09-23T10:43:49.480000",
    "AcquisitionNumber": 1,
    "SliceThickness": 1.9,
    "SpacingBetweenSlices": 1.9,
    "SAR": 0.0966296,
    "EchoNumber": 1,
    "EchoTime": 0.0112,
    "RepetitionTime": 1.72,
    "FlipAngle": 67,
    "PartialFourier": 0.75,
    "BaseResolution": 118,
    "ShimSetting": [
        145,
        -28,
        499,
        444,
        290,
        494,
        131,
        -266
    ],
    "TxRefAmp": 267.232,
    "PhaseResolution": 1,
    "ReceiveCoilName": "8Tx32Rx_Head",
    "CoilString": "AC",
    "PulseSequenceDetails": "%CustomerSeq%\\ep2d_bold_me",
    "RefLinesPE": 54,
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE12U_LATEST_20181126",
    "MultibandAccelerationFactor": 3,
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 29,
    "PhaseEncodingSteps": 88,
    "AcquisitionMatrixPE": 118,
    "ReconMatrixPE": 118,
    "BandwidthPerPixelPhaseEncode": 47.969,
    "ParallelReductionFactorInPlane": 3,
    "EffectiveEchoSpacing": 0.000176668,
    "DerivedVendorReportedEchoSpacing": 0.000530003,
    "TotalReadoutTime": 0.0206701,
    "PixelBandwidth": 2230,
    "DwellTime": 1.9e-06,
    "PhaseEncodingDirection": "j-",
    "SliceTiming": [
        0,
        0.8925,
        0.0675,
        0.9625,
        0.1375,
        1.03,
        0.205,
        1.1,
        0.275,
        1.1675,
        0.3425,
        1.2375,
        0.4125,
        1.305,
        0.48,
        1.375,
        0.55,
        1.4425,
        0.6175,
        1.5125,
        0.6875,
        1.5825,
        0.755,
        1.65,
        0.825,
        0,
        0.8925,
        0.0675,
        0.9625,
        0.1375,
        1.03,
        0.205,
        1.1,
        0.275,
        1.1675,
        0.3425,
        1.2375,
        0.4125,
        1.305,
        0.48,
        1.375,
        0.55,
        1.4425,
        0.6175,
        1.5125,
        0.6875,
        1.5825,
        0.755,
        1.65,
        0.825,
        0,
        0.8925,
        0.0675,
        0.9625,
        0.1375,
        1.03,
        0.205,
        1.1,
        0.275,
        1.1675,
        0.3425,
        1.2375,
        0.4125,
        1.305,
        0.48,
        1.375,
        0.55,
        1.4425,
        0.6175,
        1.5125,
        0.6875,
        1.5825,
        0.755,
        1.65,
        0.825
    ],
    "ImageOrientationPatientDICOM": [
        1,
        0,
        0,
        0,
        0.743145,
        -0.669131
    ],
    "ImageOrientationText": "Tra>Cor(-42.0)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Skullstripped": false,
    "TaskName": "cloudy",
    "NumberOfVolumes": 189,
    "B0FieldSource": [
        "fmap_19_j_2",
        "fmap_19_j_1"
    ]
}

I don’t see anything about distortion correction in the fMRIPrep terminal output, but maybe this will be of some assistance in diagnosing what’s going wrong?

Steven · October 18, 2024, 3:23pm

Both the AP and PA fmaps should have the same B0FieldIdentifier tag. Based on your B0FieldSource tag, I am guessing you named the AP/PA differnetly.

ejdavid · October 18, 2024, 3:41pm

Ah, okay. I’ve made this adjustment and am rerunning it. I still don’t see anything in the terminal about my field maps:

emilyd@burgundy:/lbc/lbc1/derivatives/brainstem_funk/scripts$ ./run_fmriprep.sh 055
Starting subject 055
2024-10-18 15:38:15,095 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:38:22,949 [ WARNING] WARNING: `sentry_sdk.Hub` is deprecated and will be removed in a future major release. Please consult our 1.x to 2.x migration guide for details on how to migrate `Hub` usage to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x
2024-10-18 15:38:23,111 [ WARNING] WARNING: sentry_sdk.configure_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-configuring
2024-10-18 15:38:32,887 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:38:33,103 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:38:33,179 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:38:34,619 [IMPORTANT] Running fMRIPrep version 24.1.1

         License NOTICE ##################################################
         fMRIPrep 24.1.1
         Copyright The NiPreps Developers.

         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).

         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.

         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.

         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
241018-15:38:34,619 nipype.workflow IMPORTANT:
         Running fMRIPrep version 24.1.1

         License NOTICE ##################################################
         fMRIPrep 24.1.1
         Copyright The NiPreps Developers.

         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).

         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.

         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.

         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
241018-15:38:35,920 nipype.workflow IMPORTANT:
         Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['055'].
           * Run identifier: 20241018-153815_67dc983f-e34e-4d3f-9dda-07f86b2c2b63.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
2024-10-18 15:38:35,920 [IMPORTANT] Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['055'].
           * Run identifier: 20241018-153815_67dc983f-e34e-4d3f-9dda-07f86b2c2b63.
           * Output spaces: fsnative.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
241018-15:38:36,993 nipype.workflow INFO:
         ANAT Stage 1: Adding template workflow
2024-10-18 15:38:36,993 [    INFO] ANAT Stage 1: Adding template workflow
2024-10-18 15:38:37,087 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
2024-10-18 15:38:37,087 [ WARNING] WARNING: 'locale.getdefaultlocale' is deprecated and slated for removal in Python 3.15. Use setlocale(), getencoding() and getlocale() instead.
2024-10-18 15:38:37,368 [    INFO] ANAT Stage 2: Preparing brain extraction workflow
241018-15:38:37,368 nipype.workflow INFO:
         ANAT Stage 2: Preparing brain extraction workflow
241018-15:38:37,493 nipype.workflow INFO:
         ANAT Stage 3: Preparing segmentation workflow
2024-10-18 15:38:37,493 [    INFO] ANAT Stage 3: Preparing segmentation workflow
2024-10-18 15:38:37,499 [    INFO] ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
241018-15:38:37,499 nipype.workflow INFO:
         ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
2024-10-18 15:38:37,509 [    INFO] ANAT Stage 5: Preparing surface reconstruction workflow
241018-15:38:37,509 nipype.workflow INFO:
         ANAT Stage 5: Preparing surface reconstruction workflow
241018-15:38:37,533 nipype.workflow INFO:
         ANAT Stage 6: Preparing mask refinement workflow
2024-10-18 15:38:37,533 [    INFO] ANAT Stage 6: Preparing mask refinement workflow
2024-10-18 15:38:37,536 [    INFO] ANAT No T2w images provided - skipping Stage 7
2024-10-18 15:38:37,536 [    INFO] ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
241018-15:38:37,536 nipype.workflow INFO:
         ANAT No T2w images provided - skipping Stage 7
241018-15:38:37,536 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
241018-15:38:37,557 nipype.workflow INFO:
         ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
2024-10-18 15:38:37,557 [    INFO] ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
241018-15:38:37,566 nipype.workflow INFO:
         ANAT Stage 8a: Creating cortical ribbon mask
2024-10-18 15:38:37,566 [    INFO] ANAT Stage 8a: Creating cortical ribbon mask
241018-15:38:37,570 nipype.workflow INFO:
         ANAT Stage 9: Creating fsLR registration sphere
2024-10-18 15:38:37,570 [    INFO] ANAT Stage 9: Creating fsLR registration sphere
241018-15:38:37,575 nipype.workflow INFO:
         ANAT Stage 10: Creating MSM-Sulc registration sphere
2024-10-18 15:38:37,575 [    INFO] ANAT Stage 10: Creating MSM-Sulc registration sphere
241018-15:38:39,591 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:38:39,591 [    INFO] No single-band-reference found for sub-055_task-cloudySCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:38:39,709 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:39,709 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:39,719 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:39,719 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:39,730 [    INFO] Stage 3: Adding coregistration boldref workflow
241018-15:38:39,730 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:39,732 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:38:40,78 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:38:40,078 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:38:40,381 [    INFO] No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241018-15:38:40,381 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-cloudy_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:38:40,497 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:40,497 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:40,506 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:40,506 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:40,514 [    INFO] Stage 3: Adding coregistration boldref workflow
241018-15:38:40,514 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:40,515 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:38:40,848 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:38:40,848 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
241018-15:38:41,123 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
2024-10-18 15:38:41,123 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_dir-PA_run-01_bold.nii.gz.
2024-10-18 15:38:41,235 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:41,235 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:41,244 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:41,244 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:41,252 [    INFO] Stage 3: Adding coregistration boldref workflow
241018-15:38:41,252 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:41,254 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:38:41,786 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
241018-15:38:41,786 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-01_bold.nii.gz.
241018-15:38:41,883 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:41,883 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:41,891 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:41,891 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:41,896 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:41,896 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:41,898 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:38:43,560 [    INFO] No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
241018-15:38:43,560 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-fmri_acq-3D12mm_run-02_bold.nii.gz.
241018-15:38:43,671 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:43,671 [    INFO] Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:43,682 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:43,682 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
241018-15:38:43,689 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:43,689 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:43,691 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:38:44,33 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:38:44,033 [    INFO] No single-band-reference found for sub-055_task-presentSCR_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241018-15:38:44,151 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:44,151 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:44,160 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:44,160 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:44,168 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:44,168 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:44,169 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:38:44,510 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:38:44,510 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:38:44,816 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:38:44,816 [    INFO] No single-band-reference found for sub-055_task-present_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:38:44,930 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:44,930 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
241018-15:38:44,940 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:44,940 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:44,947 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:44,947 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:44,949 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

241018-15:38:45,293 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:38:45,293 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:38:45,584 [    INFO] No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
241018-15:38:45,584 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-rest_acq-ep2d19mm_run-01_echo-1_bold.nii.gz.
2024-10-18 15:38:45,705 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:45,705 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
241018-15:38:45,714 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:45,714 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:45,721 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:45,721 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:45,723 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:38:46,059 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:38:46,59 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:38:46,347 [    INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
241018-15:38:46,347 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-rest_acq-megre14mm_dir-PA_run-01_echo-1_bold.nii.gz.
241018-15:38:46,465 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:46,465 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:46,474 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:46,474 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:46,482 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:46,482 [    INFO] Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:46,483 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:38:46,825 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:38:46,825 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
241018-15:38:47,120 nipype.workflow INFO:
         No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
2024-10-18 15:38:47,120 [    INFO] No single-band-reference found for sub-055_task-rest_acq-megre14mm_run-02_echo-1_bold.nii.gz.
2024-10-18 15:38:47,238 [    INFO] Stage 1: Adding HMC boldref workflow
241018-15:38:47,238 nipype.workflow INFO:
         Stage 1: Adding HMC boldref workflow
2024-10-18 15:38:47,248 [    INFO] Stage 2: Adding motion correction workflow
241018-15:38:47,248 nipype.workflow INFO:
         Stage 2: Adding motion correction workflow
2024-10-18 15:38:47,255 [    INFO] Stage 3: Adding coregistration boldref workflow
241018-15:38:47,255 nipype.workflow INFO:
         Stage 3: Adding coregistration boldref workflow
2024-10-18 15:38:47,257 [ WARNING] WARNING: niworkflows.interfaces.nibabel.BinaryDilation is deprecated in favor of
niworkflows.interfaces.morphology.BinaryDilation. Please validate that
interface for your use case and switch.

2024-10-18 15:38:47,609 [IMPORTANT] Generating T2* map and optimally combined ME-EPI time series.
241018-15:38:47,609 nipype.workflow IMPORTANT:
         Generating T2* map and optimally combined ME-EPI time series.
2024-10-18 15:38:50,831 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:38:51,049 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:38:51,126 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:38:53,987 [    INFO] fMRIPrep workflow graph with 1820 nodes built successfully.
241018-15:38:53,987 nipype.workflow INFO:
         fMRIPrep workflow graph with 1820 nodes built successfully.
2024-10-18 15:38:57,326 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:38:57,405 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:39:07,227 [ WARNING] WARNING: SOCKS support in urllib3 requires the installation of optional dependencies: specifically, PySocks.  For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#socks-proxies
2024-10-18 15:39:07,446 [ WARNING] WARNING: Niworkflows will be deprecating reporting in favor of a standalone library "nireports".
2024-10-18 15:39:07,522 [ WARNING] WARNING: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
2024-10-18 15:39:09,946 [ WARNING] WARNING: sentry_sdk.configure_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-configuring
241018-15:39:11,585 nipype.workflow IMPORTANT:
         fMRIPrep started!
2024-10-18 15:39:11,585 [IMPORTANT] fMRIPrep started!

Example fmap .json:

{
    "Modality": "MR",
    "MagneticFieldStrength": 7,
    "ImagingFrequency": 297.184,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Investigational_Device_7T",
    "InstitutionName": "BIC",
    "InstitutionalDepartmentName": "Department",
    "InstitutionAddress": "Street StreetNo,City,District,CA,ZIP",
    "DeviceSerialNumber": "79017",
    "StationName": "AWP79017",
    "SeriesInstanceUID": "1.3.12.2.1107.5.2.0.79017.2024092310582087428063610.0.0.0",
    "StudyInstanceUID": "1.3.12.2.1107.5.2.0.79017.30000024092311364606200000004",
    "ReferringPhysicianName": "Dr.Spreng",
    "StudyID": "1",
    "PatientName": "EE20240923_02055",
    "PatientID": "24.09.23-10:10:46-DST-1.3.12.2.1107.5.2.0.79017",
    "PatientBirthDate": "1999-01-01",
    "PatientSex": "M",
    "PatientWeight": 65,
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "Functional^Dr.Spreng",
    "SoftwareVersions": "syngo MR E12",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "fmap-fmri_acq-mbep2d_SE_19mm_dir-AP",
    "ProtocolName": "fmap-fmri_acq-mbep2d_SE_19mm_dir-AP",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "PFP\\FS",
    "SequenceName": "epse2d1_118",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "MB",
        "ND",
        "MOSAIC"
    ],
    "SeriesNumber": 13,
    "AcquisitionTime": "10:59:22.137500",
    "AcquisitionDateTime": "2024-09-23T10:59:22.137500",
    "AcquisitionNumber": 1,
    "ImageComments": "Unaliased MB3/PE4/LB",
    "SliceThickness": 1.9,
    "SpacingBetweenSlices": 1.9,
    "SAR": 0.227775,
    "EchoTime": 0.0184,
    "RepetitionTime": 3,
    "FlipAngle": 90,
    "PartialFourier": 0.75,
    "BaseResolution": 118,
    "ShimSetting": [
        145,
        -28,
        499,
        444,
        290,
        494,
        131,
        -266
    ],
    "TxRefAmp": 267.232,
    "PhaseResolution": 1,
    "ReceiveCoilName": "8Tx32Rx_Head",
    "CoilString": "AC",
    "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
    "WipMemBlock": "f499b073-206e-46f7-af7a-dbcb26a4ca12||Sequence: R016 ve12u/SP01_R016a r/af3652dd; Apr  1 2021 14:29:52 by eja",
    "RefLinesPE": 54,
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE12U_LATEST_20181126",
    "MatrixCoilMode": "GRAPPA",
    "MultibandAccelerationFactor": 3,
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 29,
    "PhaseEncodingSteps": 88,
    "AcquisitionMatrixPE": 118,
    "ReconMatrixPE": 118,
    "BandwidthPerPixelPhaseEncode": 47.969,
    "ParallelReductionFactorInPlane": 3,
    "EffectiveEchoSpacing": 0.000176668,
    "DerivedVendorReportedEchoSpacing": 0.000530003,
    "TotalReadoutTime": 0.0206701,
    "PixelBandwidth": 2355,
    "DwellTime": 1.8e-06,
    "PhaseEncodingDirection": "j-",
    "SliceTiming": [
        0,
        1.56,
        0.12,
        1.68,
        0.24,
        1.8,
        0.36,
        1.92,
        0.48,
        2.04,
        0.6,
        2.16,
        0.72,
        2.28,
        0.84,
        2.4,
        0.96,
        2.52,
        1.08,
        2.64,
        1.2,
        2.76,
        1.32,
        2.88,
        1.44,
        0,
        1.56,
        0.12,
        1.68,
        0.24,
        1.8,
        0.36,
        1.92,
        0.48,
        2.04,
        0.6,
        2.16,
        0.72,
        2.28,
        0.84,
        2.4,
        0.96,
        2.52,
        1.08,
        2.64,
        1.2,
        2.76,
        1.32,
        2.88,
        1.44,
        0,
        1.56,
        0.12,
        1.68,
        0.24,
        1.8,
        0.36,
        1.92,
        0.48,
        2.04,
        0.6,
        2.16,
        0.72,
        2.28,
        0.84,
        2.4,
        0.96,
        2.52,
        1.08,
        2.64,
        1.2,
        2.76,
        1.32,
        2.88,
        1.44
    ],
    "ImageOrientationPatientDICOM": [
        1,
        0,
        0,
        0,
        0.743145,
        -0.669131
    ],
    "ImageOrientationText": "Tra>Cor(-42.0)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Skullstripped": false,
    "TaskName": [
        "cloudy",
        "cloudySCR",
        "present",
        "presentSCR",
        "rest"
    ],
    "B0FieldIdentifier": "fmap_19"
}

Example func file .json:

{
    "Modality": "MR",
    "MagneticFieldStrength": 7,
    "ImagingFrequency": 297.184,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Investigational_Device_7T",
    "InstitutionName": "BIC",
    "InstitutionalDepartmentName": "Department",
    "InstitutionAddress": "Street StreetNo,City,District,CA,ZIP",
    "DeviceSerialNumber": "79017",
    "StationName": "AWP79017",
    "SeriesInstanceUID": "1.3.12.2.1107.5.2.0.79017.2024092310432079705906167.0.0.0",
    "StudyInstanceUID": "1.3.12.2.1107.5.2.0.79017.30000024092311364606200000004",
    "ReferringPhysicianName": "Dr.Spreng",
    "StudyID": "1",
    "PatientName": "EE20240923_02055",
    "PatientID": "24.09.23-10:10:46-DST-1.3.12.2.1107.5.2.0.79017",
    "PatientBirthDate": "1999-01-01",
    "PatientSex": "M",
    "PatientWeight": 65,
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "Functional^Dr.Spreng",
    "SoftwareVersions": "syngo MR E12",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "func-cloudy_acq-ep2d_MJC_19mm",
    "ProtocolName": "func-cloudy_acq-ep2d_MJC_19mm",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "PFP\\FS",
    "SequenceName": "epfid2d3_118",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "MOSAIC"
    ],
    "SeriesNumber": 11,
    "AcquisitionTime": "10:43:49.480000",
    "AcquisitionDateTime": "2024-09-23T10:43:49.480000",
    "AcquisitionNumber": 1,
    "SliceThickness": 1.9,
    "SpacingBetweenSlices": 1.9,
    "SAR": 0.0966296,
    "EchoNumber": 1,
    "EchoTime": 0.0112,
    "RepetitionTime": 1.72,
    "FlipAngle": 67,
    "PartialFourier": 0.75,
    "BaseResolution": 118,
    "ShimSetting": [
        145,
        -28,
        499,
        444,
        290,
        494,
        131,
        -266
    ],
    "TxRefAmp": 267.232,
    "PhaseResolution": 1,
    "ReceiveCoilName": "8Tx32Rx_Head",
    "CoilString": "AC",
    "PulseSequenceDetails": "%CustomerSeq%\\ep2d_bold_me",
    "RefLinesPE": 54,
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE12U_LATEST_20181126",
    "MultibandAccelerationFactor": 3,
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 29,
    "PhaseEncodingSteps": 88,
    "AcquisitionMatrixPE": 118,
    "ReconMatrixPE": 118,
    "BandwidthPerPixelPhaseEncode": 47.969,
    "ParallelReductionFactorInPlane": 3,
    "EffectiveEchoSpacing": 0.000176668,
    "DerivedVendorReportedEchoSpacing": 0.000530003,
    "TotalReadoutTime": 0.0206701,
    "PixelBandwidth": 2230,
    "DwellTime": 1.9e-06,
    "PhaseEncodingDirection": "j-",
    "SliceTiming": [
        0,
        0.8925,
        0.0675,
        0.9625,
        0.1375,
        1.03,
        0.205,
        1.1,
        0.275,
        1.1675,
        0.3425,
        1.2375,
        0.4125,
        1.305,
        0.48,
        1.375,
        0.55,
        1.4425,
        0.6175,
        1.5125,
        0.6875,
        1.5825,
        0.755,
        1.65,
        0.825,
        0,
        0.8925,
        0.0675,
        0.9625,
        0.1375,
        1.03,
        0.205,
        1.1,
        0.275,
        1.1675,
        0.3425,
        1.2375,
        0.4125,
        1.305,
        0.48,
        1.375,
        0.55,
        1.4425,
        0.6175,
        1.5125,
        0.6875,
        1.5825,
        0.755,
        1.65,
        0.825,
        0,
        0.8925,
        0.0675,
        0.9625,
        0.1375,
        1.03,
        0.205,
        1.1,
        0.275,
        1.1675,
        0.3425,
        1.2375,
        0.4125,
        1.305,
        0.48,
        1.375,
        0.55,
        1.4425,
        0.6175,
        1.5125,
        0.6875,
        1.5825,
        0.755,
        1.65,
        0.825
    ],
    "ImageOrientationPatientDICOM": [
        1,
        0,
        0,
        0,
        0.743145,
        -0.669131
    ],
    "ImageOrientationText": "Tra>Cor(-42.0)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Skullstripped": false,
    "TaskName": "cloudy",
    "NumberOfVolumes": 189,
    "B0FieldSource": [
        "fmap_19"
    ]
}

Steven · October 18, 2024, 3:54pm

Would it be possible to send a zipped subject folder? Steven.meisler@pennmedicine.upenn.edu