Summary of what happened:
Hello!
I have been trying to run fmriprep on some bids-validated data of mine, but I keep getting the * Phase-encoding (PE) direction: Could not be determined - assuming Anterior-Posterior and also
- Susceptibility distortion correction: None
my intended for fields seem ok, my PE fields seem o.k., i am not sure why it does not perform SDC nor recovers the PE direction. Data is bids compliant (beside my events for now, but should it should not impact fmriprep right?)
any idea on why PE is not recognized and SDC performed?
Command used (and if a helper script was used, a link to the helper script or the command generated):
# Run fMRIPrep
fmriprep-docker "${input_dir}" "${output_dir}" participant \
--skip-bids-validation \
--participant-label "${subj}" \
--fs-license-file "${license_dir}/license.txt" \
--longitudinal \
--user "${user_id}:${group_id}" \
--work-dir "${work_dir}" \
-v -v
Version:
fMRIPrep* 25.0.0
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
bids-validator@1.15.0
(node:236440) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
1: [ERR] A stimulus file was declared but not found in the dataset. (code: 52 - STIMULUS_FILE_MISSING)
1: [WARN] Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)
./sub-RGC901/ses-1/func/sub-RGC901_ses-1_task-BDM_run-1_bold.nii.gz
./sub-RGC901/ses-1/func/sub-RGC901_ses-1_task-BDM_run-3_bold.nii.gz
./sub-RGC901/ses-x/func/sub-RGC901_ses-x_task-BDM_run-2_bold.nii.gz
./sub-RGC901/ses-x/func/sub-RGC901_ses-x_task-BDM_run-3_bold.nii.gz
./sub-RGC902/ses-1/func/sub-RGC902_ses-1_task-BDM_run-1_bold.nii.gz
./sub-RGC902/ses-1/func/sub-RGC902_ses-1_task-BDM_run-2_bold.nii.gz
./sub-RGC902/ses-1/func/sub-RGC902_ses-1_task-BDM_run-3_bold.nii.gz
./sub-RGC902/ses-x/func/sub-RGC902_ses-x_task-BDM_run-1_bold.nii.gz
./sub-RGC902/ses-x/func/sub-RGC902_ses-x_task-BDM_run-2_bold.nii.gz
./sub-RGC902/ses-x/func/sub-RGC902_ses-x_task-BDM_run-3_bold.nii.gz
... and 96 more files having this issue (Use --verbose to see them all).
2: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION)
./sub-RGC901/ses-1/func/sub-RGC901_ses-1_task-BDM_run-1_events.tsv
3: [WARN] The onset of the last event is after the total duration of the corresponding scan. This design is suspiciously long. (code: 85 - SUSPICIOUSLY_LONG_EVENT_DESIGN)
./sub-RGC901/ses-x/func/sub-RGC901_ses-x_task-BDM_run-2_events.tsv
./sub-RGC906/ses-1/func/sub-RGC906_ses-1_task-BDM_run-1_events.tsv
./sub-RGC906/ses-1/func/sub-RGC906_ses-1_task-BDM_run-3_events.tsv
./sub-RGC906/ses-x/func/sub-RGC906_ses-x_task-BDM_run-1_events.tsv
./sub-RGC906/ses-x/func/sub-RGC906_ses-x_task-BDM_run-3_events.tsv
./sub-RGC910/ses-1/func/sub-RGC910_ses-1_task-BDM_run-2_events.tsv
./sub-RGC910/ses-x/func/sub-RGC910_ses-x_task-BDM_run-3_events.tsv
./sub-RGC914/ses-x/func/sub-RGC914_ses-x_task-BDM_run-2_events.tsv
./sub-RGC917/ses-1/func/sub-RGC917_ses-1_task-BDM_run-3_events.tsv
./sub-RGC924/ses-x/func/sub-RGC924_ses-x_task-BDM_run-1_events.tsv
Please visit https://neurostars.org/search?q=SUSPICIOUSLY_LONG_EVENT_DESIGN for existing conversations about this issue.
4: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
5: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS)
Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
761 Files, 5.44GB BDM MRI
20 - Subjects
2 - Sessions
Relevant log outputs (up to 20 lines) (from the html fmriprep report)
Summary
Anatomical
B0 field mapping
Functional
About
Summary
Subject ID: RGC901
Structural images: 2 T1-weighted
Functional series: 6
Task: BDM (6 runs)
Standard output spaces: MNI152NLin2009cAsym
Non-standard output spaces:
FreeSurfer reconstruction: Pre-existing directory
Anatomical
Anatomical Conformation
Input T1w images: 2
Output orientation: RAS
Output dimensions: 176x240x240
Output voxel size: 1mm x 1mm x 1mm
Discarded images: 0
B0 field mapping
Reports for: session 1, run 1, fmapid auto00000.
Preprocessed B0 mapping acquisition
Reports for: session 1, run 2, fmapid auto00001.
Preprocessed B0 mapping acquisition
Reports for: session x, run 1, fmapid auto00002.
Preprocessed B0 mapping acquisition
Reports for: session x, run 2, fmapid auto00003.
Preprocessed B0 mapping acquisition
Functional
Reports for: session 1, task BDM, run 1.
Summary
Original orientation: LAS
Repetition time (TR): 2.75s
Phase-encoding (PE) direction: Could not be determined - assuming Anterior-Posterior
Single-echo EPI sequence.
Slice timing correction: Applied
Susceptibility distortion correction: None
Registration: FreeSurfer bbregister (boundary-based registration, BBR) - 6 dof
Non-steady-state volumes: 0
Note on orientation: qform matrix overwritten
The qform has been copied from sform. The difference in angle is -1.2e-05 radians. The difference in translation is 1e-14mm.
Alignment of functional and anatomical MRI data (coregistration)
Note on orientation: qform matrix overwritten
The qform has been copied from sform. The difference in angle is 5.5e-06 radians. The difference in translation is 7.9e-15mm.
Alignment of functional and anatomical MRI data (coregistration)
Preprocessing of B0 inhomogeneity mappings
A total of 4 fieldmaps were found available within the input BIDS structure for this particular subject. A B0 nonuniformity map (or fieldmap) was directly measured with an MRI scheme designed with that purpose such as SEI (Spiral-Echo Imaging).
Screenshots / relevant information:
example fmap json
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 127.768,
"Manufacturer": "Philips",
"StationName": "PHILIPS-BQ9N6TK",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "5.3.1\\5.3.1.1",
"MRAcquisitionType": "2D",
"SeriesDescription": "B0 map (immediate)",
"ProtocolName": "WIP B0 map (immediate)",
"ScanningSequence": "RM",
"SequenceVariant": "SS",
"ScanOptions": "OTHER",
"PulseSequenceName": "FFE",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"T1",
"MIXED",
"REAL",
"FIELDMAPHZ"
],
"SeriesNumber": 301,
"AcquisitionTime": "09:52:22.070000",
"AcquisitionNumber": 3,
"PhilipsRWVSlope": 0.0815629,
"PhilipsRWVIntercept": -167,
"PhilipsRescaleSlope": 0.0815629,
"PhilipsRescaleIntercept": -167,
"PhilipsScaleSlope": 12.285,
"UsePhilipsFloatNotDisplayScaling": 1,
"Units": "Hz",
"SliceThickness": 3,
"SpacingBetweenSlices": 3,
"EchoNumber": 2,
"RepetitionTime": 0.649998,
"MTState": false,
"FlipAngle": 80,
"CoilString": "MULTI COIL",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingSteps": 80,
"AcquisitionMatrixPE": 80,
"ReconMatrixPE": 80,
"WaterFatShift": 0.998103,
"EstimatedEffectiveEchoSpacing": 0.0000145418,
"EstimatedTotalReadoutTime": 0.0011488,
"AcquisitionDuration": 105.3,
"PixelBandwidth": 435.237,
"PhaseEncodingAxis": "j",
"ImageOrientationPatientDICOM": [
0.999515,
-0.0205438,
0.0234043,
0.0301223,
0.828502,
-0.559176
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720",
"IntendedFor": [
"ses-1/func/sub-RGC901_ses-1_task-BDM_run-1_bold.nii.gz"
],
"PhaseEncodingDirection": "j"
}
example of a func json file
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 127.768,
"Manufacturer": "Philips",
"ManufacturersModelName": "Ingenia",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "5.3.1\\5.3.1.1",
"MRAcquisitionType": "2D",
"SeriesDescription": "fMRI_3mm_FOOD1",
"ProtocolName": "WIP fMRI_3mm_FOOD1",
"ScanningSequence": "GR",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"PulseSequenceName": "FEEPI",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"T2",
"NONE"
],
"SeriesNumber": 601,
"AcquisitionTime": "10:06:18.790000",
"AcquisitionNumber": 6,
"PhilipsRescaleSlope": 0.806593,
"PhilipsRescaleIntercept": 0,
"PhilipsScaleSlope": 0.0267301,
"UsePhilipsFloatNotDisplayScaling": 1,
"SliceThickness": 3,
"SpacingBetweenSlices": 3,
"EchoTime": 0.03,
"RepetitionTime": 2.75,
"MTState": false,
"FlipAngle": 80,
"CoilString": "MULTI COIL",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 39,
"PhaseEncodingSteps": 80,
"AcquisitionMatrixPE": 80,
"ReconMatrixPE": 80,
"ParallelReductionFactorInPlane": 2.1,
"ParallelAcquisitionTechnique": "SENSE",
"WaterFatShift": 10.5683,
"EstimatedEffectiveEchoSpacing": 0.000300251,
"EstimatedTotalReadoutTime": 0.0237198,
"AcquisitionDuration": 626.962,
"PixelBandwidth": 2104.91,
"PhaseEncodingAxis": "j",
"ImageOrientationPatientDICOM": [
0.999515,
-0.0205438,
0.0234043,
0.0301223,
0.828502,
-0.559176
],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720",
"TaskName": "BDM",
"SliceTiming": [
0E-8,
0.05978260,
0.11956520,
0.17934780,
0.23913040,
0.29891300,
0.35869560,
0.41847820,
0.47826080,
0.53804340,
0.59782600,
0.65760860,
0.71739120,
0.77717380,
0.83695640,
0.89673900,
0.95652160,
1.01630420,
1.07608680,
1.13586940,
1.19565200,
1.25543460,
1.31521720,
1.37499980,
1.43478240,
1.49456500,
1.55434760,
1.61413020,
1.67391280,
1.73369540,
1.79347800,
1.85326060,
1.91304320,
1.97282580,
2.03260840,
2.09239100,
2.15217360,
2.21195620,
2.27173880,
2.33152140,
2.39130400,
2.45108660,
2.51086920,
2.57065180,
2.63043440
],
"PhaseEncodingDirection": "j"
}
fslhd output for func file
sizeof_hdr 348
data_type INT16
dim0 4
dim1 80
dim2 80
dim3 45
dim4 173
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 -1.000000
pixdim1 3.000000
pixdim2 3.000000
pixdim3 3.000000
pixdim4 2.749998
pixdim5 0.000000
pixdim6 0.000000
pixdim7 0.000000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
scl_slope 37.411068
scl_inter 0.000000
phase_dim 2
freq_dim 1
slice_dim 3
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
toffset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -2.998544 0.090374 0.023731 120.402924
qto_xyz:2 0.061625 2.485505 -1.678828 -91.328682
qto_xyz:3 0.070236 1.677527 2.486156 -109.903519
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -2.998545 0.090367 0.023709 120.402924
sto_xyz:2 0.061631 2.485506 -1.678828 -91.328682
sto_xyz:3 0.070213 1.677527 2.486156 -109.903519
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip TE=30;Time=100618.790
aux_file