Summary of what happened:
I am trying to pre-process my fmri data using fmriprep and freesurfer on ComputeCanada. When I run my script (posted below), func and anat directories run successfully without errors, however does not preprocess the FMAPs (no output). When I try running this same data locally, I do not seem to get this error and seem to have FMAP folders in the output directory. I have also run the data files through BIDS Validator which generates a Check_Error message for all the FMAP files with no specific indication into what the error is. I have included a sample JSON file (pasted below) from the FMAP data for reference. Wondering if anyone has had a similar experience and could kindly shed some light on how to resolve this.
Command used (and if a helper script was used, a link to the helper script or the command generated):
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
#SBATCH --time=12:00:00
#SBATCH --account=def-xyz
#SBATCH --job-name=mrtrix_test
cd $SLURM_SUBMIT_DIR
echo $SLURM_SUBMIT_DIR
module load CCEnv
module load StdEnv/2020
module load fmriprep/23.1.3
module load singularity
#Begin:
#User inputs:
bids_root_dir=/path/to/patientdirectory/sub-AUD1
subj=AUD1
nthreads=16
mem_mb=19000
# Export necessary environment variables
export FS_LISENCE=/PATH/TO/LICENSEFILE/lisence.txt
export APPTAINERENV_TEMPLATEFLOW_HOME=/PATH/TO/TEMPLATEFLOW/templateflow
export APPTAINER_BIND=$bids_root_dir,$APPTAINERENV_TEMPLATEFLOW_HOME,path/to/home
#Run fmriprep
fmriprep $bids_root_dir $bids_root_dir/derivatives \
participant \
--participant-label AUD1 \
--skip-bids-validation \
--fs-license-file /path/to/licensefile/license.txt \
--output-spaces MNI152NLin2009cAsym:res-2 \
--omp-nthreads $nthreads \
--n_cpus 40 \
--fs-no-reconall \
--stop-on-first-crash \
--work-dir /path/to/workdir/workdir
~
Version:
fmriprep version 23.1.3
Environment (Docker, Singularity / Apptainer, custom installation):
I have tried running it with singularity and also by module loading Freesufer, fmriprep and FSL separately with the same result from each attempt
Data formatted according to a validatable standard? Please provide the output of the validator:
error: CHECK_ERROR
generic place holder for errors from failed `checks` evaluated from schema.
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-alcohol_run-1_dir-AP_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-alcohol_run-1_dir-PA_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-alcohol_run-2_dir-AP_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-alcohol_run-2_dir-PA_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-eyes_run-1_dir-AP_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-eyes_run-1_dir-PA_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-eyes_run-2_dir-AP_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-eyes_run-2_dir-PA_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-face_run-1_dir-AP_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-face_run-1_dir-PA_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-face_run-2_dir-AP_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-face_run-2_dir-PA_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-dwi_dir-AP_epi.nii.gz
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-dwi_dir-PA_epi.bval
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-dwi_dir-PA_epi.bvec
/ses-12mos/fmap/sub-AUD1_ses-12mos_acq-dwi_dir-PA_epi.nii.gz
Relevant log outputs (up to 20 lines):
no log output - given in the log folder
Screenshots / relevant information:
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.25,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma",
"InstitutionName": "Sunnybrook_Research_Institute",
"InstitutionalDepartmentName": "HEALTH_SCIENCE_CENTRE",
"InstitutionAddress":
"DeviceSerialNumber": "66049",
"StationName": "AWP66049",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"ProcedureStepDescription": "RESEARCH_DBSA1F",
"SoftwareVersions": "syngo_MR_E11",
"MRAcquisitionType": "2D",
"SeriesDescription": "ep2d_bold_p2_s2_iso2.5_P>>A_ref",
"ProtocolName": "ep2d_bold_p2_s2_iso2.5_P>>A_ref",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"SequenceName": "_epfid2d1_80",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "MOSAIC"],
"SeriesNumber": 6,
"AcquisitionTime": "13:24:57.980000",
"AcquisitionNumber": 1,
"SliceThickness": 2.5,
"SpacingBetweenSlices": 2.5,
"SAR": 0.0319858,
"EchoTime": 0.03,
"RepetitionTime": 1.75,
"FlipAngle": 40,
"PartialFourier": 1,
"BaseResolution": 80,
"ShimSetting": [
-245,
-9767,
2656,
-33,
-57,
-200,
-46,
37 ],
"TxRefAmp": 295.594,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_20",
"ReceiveCoilActiveElements": "HE1-4",
"PulseSequenceDetails": "%SiemensSeq%_ep2d_bold",
"RefLinesPE": 32,
"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
"MultibandAccelerationFactor": 2,
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 39,
"PhaseEncodingSteps": 79,
"AcquisitionMatrixPE": 80,
"ReconMatrixPE": 80,
"BandwidthPerPixelPhaseEncode": 51.02,
"ParallelReductionFactorInPlane": 2,
"EffectiveEchoSpacing": 0.000245002,
"DerivedVendorReportedEchoSpacing": 0.000490004,
"TotalReadoutTime": 0.0193552,
"PixelBandwidth": 2500,
"DwellTime": 2.5e-06,
"PhaseEncodingDirection": "j",
"SliceTiming": [
1.2675,
0,
0.8625,
0.0575,
0.9225,
0.115,
0.98,
0.1725,
1.0375,
0.23,
1.095,
0.2875,
1.1525,
0.345,
1.21,
0.46,
1.325,
0.5175,
1.3825,
0.575,
1.44,
0.6325,
1.4975,
0.69,
1.555,
0.7475,
1.6125,
0.805,
1.67,
0.4025,
1.2675,
0,
0.8625,
0.0575,
0.9225,
0.115,
0.98,
0.1725,
1.0375,
0.23,
1.095,
0.2875,
1.1525,
0.345,
1.21,
0.46,
1.325,
0.5175,
1.3825,
0.575,
1.44,
0.6325,
1.4975,
0.69,
1.555,
0.7475,
1.6125,
0.805,
1.67,
0.4025 ],
"ImageOrientationPatientDICOM": [
0.999326,
0.0366555,
0.00207091,
-0.036469,
0.997583,
-0.0591523 ],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20200331",
"IntendedFor": "func/sub-AUD1_ses-12mos_task-alcohol_acq-TR1750_run-1_bold.nii.gz"
}
Thank you in advance for any suggestions!