Fieldmap correction gone wrong

Steve_Wilson · November 25, 2023, 4:04pm

Hi Chris,
I’ve been testing 23.2.0a2. For some reason, my fieldmaps don’t seem to be detected and no sdc is performed. The data includes blip-up/blip-down scans, and I believe that all the correct information is included in the json files (PE direction, “IntendedFor” field). The fieldmaps are recognized and used with previous versions. I’m using a singularity container with the command included below submitted in a batch script. Do you have any idea what I might be doing wrong?


singularity run --cleanenv /storage/group/sjw42/default/sjw42_collab/sw/singularity/fmriprep/fmriprep_v23.2.0a2.sif \
--participant_label 108 \
--nthreads 2 \
--omp-nthreads 1 \
--low-mem \
--mem 39000 \
--level full \
--use-aroma \
--output-layout legacy \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin6Asym:res-native \
--fs-license-file /storage/group/sjw42/default/sjw42_collab/sw/freesurfer-6.0.1/license.txt \
--work /storage/group/sjw42/default/ASH/LAPS/work \
/storage/group/sjw42/default/ASH/LAPS/bids \
/storage/group/sjw42/default/ASH/LAPS/bids/derivatives \
participants

Steven · November 25, 2023, 4:20pm

Hi @Steve_Wilson,

Please share an example field map JSON contents. Also, AROMA is deprecated and mo longer a function of fmriprep (a separate app is in development for it).

Best,
Steven

Steve_Wilson · November 25, 2023, 4:41pm

Hi Steven - I’ve pasted the JSON contents for one of the field maps below. Thanks for letting me know about the change with AROMA!
Steve


{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 123.252515,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "MAGNETOM Prisma Fit",
    "InstitutionName": "Penn State SLEIC",
    "InstitutionAddress": "University Park Chandlee Laboratory,State College,PA,US,16802",
    "DeviceSerialNumber": "67039",
    "StationName": "AWP67039",
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "SoftwareVersions": "syngo MR XA30",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "sms_distortion_map_PA_68_51",
    "ProtocolName": "sms_distortion_map_PA_68_51",
    "ScanningSequence": "GR\\EP",
    "SequenceVariant": "SK",
    "ScanOptions": "FS\\PER",
    "SequenceName": "*epse2d1_92",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "NORM",
        "MFSPLIT"
    ],
    "ImageTypeText": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "NONE"
    ],
    "NonlinearGradientCorrection": false,
    "SeriesNumber": 17,
    "AcquisitionTime": "13:37:1.482500",
    "AcquisitionNumber": 1,
    "SliceThickness": 2.4,
    "SpacingBetweenSlices": 2.4,
    "SAR": 0.127954,
    "EchoTime": 0.058,
    "RepetitionTime": 7.06,
    "FlipAngle": 90,
    "PartialFourier": 1,
    "BaseResolution": 92,
    "ShimSetting": [
        -1950,
        8279,
        9491,
        311,
        0,
        -409,
        53,
        23
    ],
    "TxRefAmp": 256.527,
    "PhaseResolution": 1,
    "VendorReportedEchoSpacing": 0.00051,
    "ReceiveCoilName": "HeadNeck_64",
    "ReceiveCoilActiveElements": "HC1-7;NC1",
    "CoilString": "HeadNeck_64",
    "PulseSequenceDetails": "%SiemensSeq%\\ep2d_se",
    "CoilCombinationMethod": "Sum of Squares",
    "MatrixCoilMode": "SENSE",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 92,
    "PhaseEncodingSteps": 92,
    "AcquisitionMatrixPE": 92,
    "ReconMatrixPE": 92,
    "BandwidthPerPixelPhaseEncode": 21.313,
    "EffectiveEchoSpacing": 0.000509997,
    "DerivedVendorReportedEchoSpacing": 0.000509997,
    "TotalReadoutTime": 0.0464097,
    "PixelBandwidth": 2470,
    "DwellTime": 2.2e-06,
    "PhaseEncodingDirection": "j",
    "SliceTiming": [
        3.53,
        0,
        3.6325,
        0.1025,
        3.7375,
        0.2075,
        3.84,
        0.31,
        3.945,
        0.415,
        4.0475,
        0.52,
        4.1525,
        0.6225,
        4.2575,
        0.7275,
        4.36,
        0.83,
        4.465,
        0.935,
        4.5675,
        1.0375,
        4.6725,
        1.1425,
        4.775,
        1.245,
        4.88,
        1.35,
        4.9825,
        1.4525,
        5.0875,
        1.5575,
        5.19,
        1.66,
        5.295,
        1.765,
        5.3975,
        1.8675,
        5.5025,
        1.9725,
        5.605,
        2.075,
        5.71,
        2.18,
        5.8125,
        2.2825,
        5.9175,
        2.3875,
        6.02,
        2.4925,
        6.125,
        2.595,
        6.23,
        2.7,
        6.3325,
        2.8025,
        6.4375,
        2.9075,
        6.54,
        3.01,
        6.645,
        3.115,
        6.7475,
        3.2175,
        6.8525,
        3.3225,
        6.955,
        3.425
    ],
    "ImageOrientationPatientDICOM": [
        0.998511,
        -0.0335475,
        0.0430195,
        0.0402788,
        0.985198,
        -0.166619
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20230411",
    "Dcm2bidsVersion": "3.1.0",
    "IntendedFor": [
        "bids::sub-108/func/sub-108_task-lapse_run-01_bold.nii.gz",
        "bids::sub-108/func/sub-108_task-lapse_run-02_bold.nii.gz",
        "bids::sub-108/func/sub-108_itask-iat_run-01_bold.nii.gz",
        "bids::sub-108/func/sub-108_task-iat_run-02_bold.nii.gz"
    ]
}

Steve_Wilson · November 25, 2023, 4:50pm

I just noticed the different format dcm2bids is using for the IntendedFor field. I wonder if that might be the issue.

Steven · November 25, 2023, 4:59pm

Yes, fmriprep does not support BIDS URI at the moment. Please remove bids::sub-XXX/ from your fields.

Best,
Steven

Steve_Wilson · November 25, 2023, 5:03pm

Ah, sounds good - I should have caught that before. Thanks, Steven!

Patricia_Fernandes · November 29, 2023, 7:46pm

Hello,

I had SDC problems similar to the reported in the beggining of the thread. So i’ve tried running version 23.2.0a2 but I ran into this error that leads to a crash of fmriprep. Do you know what I might’ve done wrong?

Node: fmriprep_23_2_wf.sub_05_wf.bold_task_subriskrun1_wf.bold_native_wf.boldref_fmap
Working directory: /tmp/work/fmriprep_23_2_wf/sub_05_wf/bold_task_subriskrun1_wf/bold_native_wf/boldref_fmap

Node inputs:

fmap_ref_file =
in_coeffs =
inverse = [True]
target_ref_file =
transforms =

Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 645, in _run_interface
return self._run_command(execute)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node boldref_fmap.

Traceback:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/interfaces/resampling.py”, line 169, in _run_interface
fieldmap = reconstruct_fieldmap(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/interfaces/resampling.py”, line 661, in reconstruct_fieldmap
raise ValueError(‘Reference passed is not aligned with spline grids’)
ValueError: Reference passed is not aligned with spline grids

Steven · November 29, 2023, 7:51pm

Hi @Patricia_Fernandes and welcome to neurostars!

We will need more information to address your issue Please open a new issue under the Software Support category and fill in all of the information in the prepopulated post template.

Best,
Steven

Steve_Wilson · November 29, 2023, 9:49pm

Just a quick update that the sdc results look very good with version 23.2.0a2!

jsein · November 29, 2023, 10:02pm

another quick update:

The PEPOLAR method for SDC works well with 23.2.0a2 on our data (it was also doing a good job with previous fmriprep version)

For testing purposed I ran also the Fieldmap-Less method on the same subject and unfortunately the correction is still quite a bit off for this method in 23.2.0a2. Here are some examples below of the HMTL output from fmriprep 23.2.0a2 with the fieldmap-less method:

This is confirmed in another report (even if for us the result is really not that bad with the Fieldmap- Less method!) : fieldmap-less SDC in v. 23.2.0a2 producing odd/distorted results · Issue #3158 · nipreps/fmriprep · GitHub