Summary of what happened:
The flag --use-syn-sdc errors out. I am trying to process multi-band resting state data with a single scan - no field maps etc
Command used (and if a helper script was used, a link to the helper script or the command generated):
This is my command:
CMD="apptainer run --cleanenv \
-B /path:/data \
-B /data/Outputs/test4/fmriprep/sourcedata/freesurfer:/fs_subjects \
--env SUBJECTS_DIR=/fs_subjects \
${CONTAINER} \
/data/Outputs/test4/BIDS \
/data/Outputs/test4/fmriprep \
participant \
--participant-label ${subjID} \
--session-label 01 \
--fs-license-file /data/Software/license.txt \
--ignore slicetiming \
--output-spaces T1w MNI152NLin2009cAsym:res-native MNI152NLin2009cAsym:res-2 \
--skull-strip-t1w force \
--skull-strip-template MNI152NLin2009cAsym \
--skull-strip-fixed-seed \
--use-syn-sdc \
-w /data/Outputs/test4/fmriprep \
-vvv"
echo "${CMD}"
eval "${CMD}"
Version:
25.2.3
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
After which my log reports the following
251126-15:16:43,580 nipype.workflow VERBOSE:
fMRIPrep config:
[environment]
cpu_count = 8
exec_env = "singularity"
free_mem = 117.3
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.10.0"
templateflow_version = "25.0.4"
version = "25.2.3"
[execution]
bids_dir = "/data/Outputs/test4/BIDS"
bids_database_dir = "/data/Outputs/test4/fmriprep/20251126-151443_8c1b61b3-d241-46f8-8a7f-a4b127fcbe43/bids_db"
bids_description_hash = "04d959ebeba6eed8e555cb59d91e3885bbce597101f70936810cb66e6a9ea497"
boilerplate_only = false
sloppy = false
debug = []
fmriprep_dir = "/data/Outputs/test4/fmriprep"
fs_license_file = "/data/Software/license.txt"
fs_subjects_dir = "/data/Outputs/test4/fmriprep/sourcedata/freesurfer"
layout = "BIDS Layout: .../data/Outputs/test4/BIDS | Subjects: 1 | Sessions: 1 | Runs: 0"
log_dir = "/data/Outputs/test4/fmriprep/logs"
log_level = 10
low_mem = false
md_only_boilerplate = false
notrack = false
track_carbon = false
country_code = "CAN"
output_dir = "/data/Outputs/test4/fmriprep"
me_output_echos = false
aggr_ses_reports = 4
output_layout = "bids"
output_spaces = "T1w MNI152NLin2009cAsym:res-native MNI152NLin2009cAsym:res-2"
reports_only = false
run_uuid = "20251126-151443_8c1b61b3-d241-46f8-8a7f-a4b127fcbe43"
processing_groups = [ "sub-01_ses-01",]
participant_label = [ "01",]
session_label = [ "01",]
templateflow_home = "/path/user/.cache/templateflow"
work_dir = "/data/Outputs/test4/fmriprep"
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",]
force = []
level = "full"
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 = true
skull_strip_template = "MNI152NLin2009cAsym"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "T1w MNI152NLin2009cAsym:res-native MNI152NLin2009cAsym:res-2"
subject_anatomical_reference = "first-lex"
use_syn_sdc = "error"
me_t2s_fit_method = "curvefit"
[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 8
omp_nthreads = 7
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = false
[seeds]
master = 58299
ants = 23060
numpy = 5193
[execution.derivatives]
[execution.dataset_links]
raw = "/data/Outputs/test4/BIDS"
templateflow = "/path/user/.cache/templateflow"
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
251126-15:16:43,581 nipype.workflow IMPORTANT:
fMRIPrep started!
Screenshots / relevant information:
my rsfMRI metadata:
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.259,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "syngo MR E11",
"MRAcquisitionType": "2D",
"SeriesDescription": "ep2d_bold rest 1",
"ProtocolName": "ep2d_bold rest 1",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"SequenceName": "*epfid2d1_82",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM", "MOSAIC"],
"NonlinearGradientCorrection": false,
"SeriesNumber": 9,
"AcquisitionTime": "11:40:19.397500",
"AcquisitionNumber": 1,
"SliceThickness": 3,
"SpacingBetweenSlices": 3,
"SAR": 0.0600313,
"EchoTime": 0.029,
"RepetitionTime": 0.46,
"FlipAngle": 44,
"PartialFourier": 1,
"BaseResolution": 82,
"ShimSetting": [
2383,
-2874,
3668,
242,
47,
-179,
2,
-26 ],
"TxRefAmp": 247.915,
"PhaseResolution": 1,
"VendorReportedEchoSpacing": 0.00053,
"ReceiveCoilName": "Head_32",
"ReceiveCoilActiveElements": "HEA;HEP",
"PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold",
"RefLinesPE": 12,
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"MultibandAccelerationFactor": 8,
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 82,
"PhaseEncodingSteps": 82,
"AcquisitionMatrixPE": 82,
"ReconMatrixPE": 82,
"BandwidthPerPixelPhaseEncode": 23.01,
"EffectiveEchoSpacing": 0.000529992,
"DerivedVendorReportedEchoSpacing": 0.000529992,
"TotalReadoutTime": 0.0429294,
"PixelBandwidth": 2770,
"DwellTime": 2.2e-06,
"PhaseEncodingDirection": "j-",
"SliceTiming": [
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725,
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725,
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725,
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725,
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725,
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725,
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725,
0.2925,
0,
0.22,
0.1475,
0.3675,
0.0725 ],
"ImageOrientationPatientDICOM": [
0.999898,
0.00088967,
0.0142391,
-1.52671e-08,
0.998054,
-0.0623581 ],
"ImageOrientationText": "Tra>Cor(-3.6)>Sag(0.8)",
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720"
}