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Reward Project Documentation

Nodra

Table of contents
  1. Data Processing Flow & Important Links:
  2. Plan for the Data
  3. Data Acquisition
  4. Download and Storage
  5. Curation Process
    1. BIDS Validation:
    2. BIDS Optimization:
  6. Preprocessing Pipelines
    1. fMRIPrep (version 20.2.3)
      1. Exemplar Testing:
      2. Production:
    2. XCP-ABCD (version 0.0.8)
      1. Production:

Data Processing Flow & Important Links:

  • Flow diagram that describes the lifecycle of this dataset curation and preprocessing:

flow

Plan for the Data

  • Why does PennLINC need this data?

    Acquired at UPenn

  • For which project(s) is it intended? Please link to project pages below:

    Reward Project

  • Goal:

    Curate and preprocess an amalgam of datasets for a harmonized PennLINC resource

Data Acquisition

  • Data acquired by Dan Wolf & Ted Satterthwaite
  • Describe the data:
    • number of subjects = 104
    • types of images = bold (2 runs task-ITC, 2 runs task-CARD, rest), T1w, fieldmaps

Download and Storage

  • Original data available on Flywheel
  • Source data (NIfTI) on CUBIC in /cbica/projects/wolf_satterthwaite_reward/original_data/bidsdatasets/nodra.
  • Data was copied to /cbica/projects/wolf_satterthwaite_reward/Curation/bidsdatasets/nodra and checked in to datalad after removing PHI (below)

  • JSON’s within origial_data were updated using cubids-add-nifti-info.

  • Listing metadata fields using cubids-print-metadata-fields gave the following fields:
Acknowledgements
AcquisitionDateTime
AcquisitionMatrixPE
AcquisitionNumber
AcquisitionTime
Authors
BIDSVersion
BandwidthPerPixelPhaseEncode
BaseResolution
CoilString
ConversionSoftware
ConversionSoftwareVersion
DatasetDOI
DeidentificationMethod
DerivedVendorReportedEchoSpacing
DeviceSerialNumber
DwellTime
EchoNumber
EchoTime
EchoTime1
EchoTime2
EchoTrainLength
EffectiveEchoSpacing
FlipAngle
Funding
HowToAcknowledge
ImageOrientationPatientDICOM
ImageType
ImagingFrequency
InPlanePhaseEncodingDirectionDICOM
InstitutionAddress
InstitutionName
InstitutionalDepartmentName
IntendedFor
InversionTime
License
MRAcquisitionType
MagneticFieldStrength
Manufacturer
ManufacturersModelName
Modality
Name
ParallelReductionFactorInPlane
PartialFourier
PatientPosition
PatientSex
PercentPhaseFOV
PhaseEncodingDirection
PhaseEncodingSteps
PhaseResolution
PixelBandwidth
ProcedureStepDescription
ProtocolName
PulseSequenceDetails
ReceiveCoilName
ReconMatrixPE
RefLinesPE
ReferencesAndLinks
RepetitionTime
SAR
ScanOptions
ScanningSequence
SequenceName
SequenceVariant
SeriesDescription
SeriesInstanceUID
SeriesNumber
ShimSetting
SliceThickness
SliceTiming
SoftwareVersions
SpacingBetweenSlices
StationName
StudyID
StudyInstanceUID
TaskName
TotalReadoutTime
TxRefAmp
template
ImageComments
MultibandAccelerationFactor

Offending fields were removed with cubids-remove-metadata-fields in /cbica/projects/wolf_satterthwaite_reward/Curation/code/metadatafields_remove.sh

Curation Process

  • Data curation by Tinashe Tapera on the CUBIC project user wolfsatterthwaitereward
  • Link to final CuBIDS csvs: /cbica/projects/wolf_satterthwaite_reward/Curation/code/iterations/iteration7/nodra/

BIDS Validation:

  • Data with short bold time series (<3mins) were removed with the Notebook /cbica/projects/wolf_satterthwaite_reward/Curation/code/RemoveShortBOLD.ipynb and cubids with /cbica/projects/wolf_satterthwaite_reward/Curation/code/iterations/cubids-testing_adjustments/nodra/purge_low_bold.txt as input

  • All validation outputs are available in chronological order in /cbica/projects/wolf_satterthwaite_reward/Curation/code/validate_outputs/nodra; most recent validation errors being:

    • EVENTS_TSV_MISSING ( Task scans should have a corresponding events.tsv file. If this is a resting state scan you can ignore this warning or rename the task to include the word “rest”. ) : 394 counts

    • README_FILE_MISSING ( The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. ) : 1 count

    • NO_AUTHORS ( 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. ) : 1 count

Data at this stage were approved for preprocessing.

BIDS Optimization:

  • All cubids optimization results are available in /cbica/projects/wolf_satterthwaite_reward/Curation/code/iterations/iter<ITERATION_NUMBER>/nodra/

  • Final optimization resulted in /cbica/projects/wolf_satterthwaite_reward/Curation/code/iterations/iter7/nodra/nodra_summary.csv

Preprocessing Pipelines

fMRIPrep (version 20.2.3)

  • Tinashe Tapera was responsible for running preprocessing pipelines/audits on CUBIC

Exemplar Testing:

  • Used cubids to create exemplar dataset: cubids-copy-exemplars /cbica/projects/wolf_satterthwaite_reward/Curation/bidsdatasets/nodra/BIDS /cbica/projects/wolf_satterthwaite_reward/Testing/nodra/exemplars_dir /cbica/projects/wolf_satterthwaite_reward/Curation/code/iterations/iter6/nodra/nodra_AcqGrouping.csv
  • Path to exemplar dataset (annexed to datalad): /cbica/projects/wolf_satterthwaite_reward/Testing/nodra/exemplars_dir

  • Path to fmriprep container: Original in ~/dropbox, datalad in /cbica/projects/wolf_satterthwaite_reward/Testing/exemplars_test/fmriprep-container

  • Adjustments:
    • During testing, some fieldmaps were found to be corrupt/unusable for the data, and were removed with cubids-purge. These files are in /cbica/projects/wolf_satterthwaite_reward/Curation/code/iterations/cubids-testing_adjustments/nodra/purge_fmaps.txt; likewise, one BOLD run was unusable (gzip error) and similarly removed with /cbica/projects/wolf_satterthwaite_reward/Curation/code/iterations/cubids-testing_adjustments/nodra/purge_broken_card<BBLID>.txt

Testing directory was deleted to save space on CUBIC on 12/2/21, once production completed

Production:

  • 103/104 subjects completed fMRIPrep successfully
  • Path to production inputs: /cbica/projects/wolf_satterthwaite_reward/Curation/bidsdatasets/nodra/BIDS
  • Path to fmriprep run command: /cbica/projects/wolf_satterthwaite_reward/Production/nodra/fmriprep/analysis/code/fmriprep_zip.sh
  • Path to production outputs: /cbica/projects/wolf_satterthwaite_reward/Production/nodra/fmriprep/output_ria
  • Path to fmriprep production audit: /cbica/projects/wolf_satterthwaite_reward/Production/nodra/fmriprep/-audit/FMRIPREP_AUDIT.csv
  • Path to freesurfer production audit: NA

XCP-ABCD (version 0.0.8)

Production:

  • 103/104 subjects completed XCP successfully
  • Path to production inputs: /cbica/projects/wolf_satterthwaite_reward/Curation/bidsdatasets/nodra/fmriprep/merge_ds
  • Path to xcp run command: /cbica/projects/wolf_satterthwaite_reward/Production/nodra/xcp/analysis/code/xcp_zip.sh
  • Path to production outputs: /cbica/projects/wolf_satterthwaite_reward/Production/nodra/xcp/output_ria
  • Path to xcp production audit: NA
  • Path to xcp derivatives: /cbica/projects/wolf_satterthwaite_reward/Production/nodra/xcp-derivatives/XCP
  • Path to xcp derivatives (concatenated): NA