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This repo has moved to https://gitlab.com/flywheel-io/flywheel-apps/bids-hcp

flywheel/hcp-struct

Flywheel Gear that runs the structural preprocessing steps of the Human Connectome Project Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013. Currently, this includes v4.0.1 release of PreFreeSurfer, FreeSurfer, and PostFreeSurfer pipelines, as well as generating some helpful QC images. For more info on the pipelines, see HCP Pipelines.

Important notes

• T1w and T2w volumes should not have any online bias-correction (e.g.: no "Pre-scan Normalize" option on Siemens scanners). If on-scanner bias-correction was applied, it must be applied to BOTH T1w and T2w inputs.
• All MRI inputs (T1w, T2w, FieldMaps) must include BIDS-conformed DICOM metadata!
• Gradient nonlinearity correction (using coefficient file) is currently only available for data from Siemens scanners.
• Readout distortion correction using B0 field maps (Field map "Option 1", below) is currently only available for data from Siemens scanners. "TOPUP"-style correction (Field map "Option 2", below) should work for all data (but has not yet been tested).

Required inputs

1. T1-weighted anatomical volume (eg: MPRAGE), <= 1mm spatial resolution
2. T2-weighted anatomical volume (eg: SPACE, FLAIR), <= 1mm spatial resolution
3. FreeSurfer license.txt file (found in $FREESURFER_HOME/license.txt)

Optional inputs

1. Field map for correcting readout distortion
   • Option 1: "typical" GRE B0 field map including magnitude and phase volumes
   • Option 2: a pair of spin echo with opposite phase-encode directions ("Positive" = R>>L or P>>A, and "Negative" = L>>R or A>>P) for "TOPUP"-style distortion estimation
   • Note 1: If readout distortion correction is performed, user must specify the correct "StructualUnwarpDirection" config option. For HCP scans (sagittal slices with A>>P phase-encoding), this should be "z", corresponding to readout in the F>>H direction.
   • Note 2: This effect is very small, at most 0.35mm in a few high-susceptibility areas (e.g., orbitofrontal)
2. Gradient nonlinearity coefficients copied from scanner. See FAQ 8. What is gradient nonlinearity correction?
   • If needed, this file can be obtained from the console at C:\MedCom\MriSiteData\GradientCoil\coeff.grad for Siemens scanners
   • Note: This effect is significant for HCP data collected on custom Siemens "ConnectomS" scanner, and for 7T scanners. It is relatively minor for production 3T scanners (Siemens Trio, Prisma, etc.)

Configuration options

1. Subject: Subject ID to use for outputs
2. RegName: Surface registration type: either 'FS' (freesurfer) or 'MSMSulc' (HCP default). (See FSL MSM for details on MSMSulc)
3. BrainSize: Brain size in mm (in Superior-Inferior axis), typically 150 (default) for adults
4. TemplateSize: Voxel size of HCP anatomical template. Best if matches input. (Options = 0.7mm, 0.8mm (default), 1mm)
5. StructuralUnwarpDirection: Readout direction for structural scans ( 'x', 'x-', 'y', 'y-', 'z', 'z-' ). HCP default = 'z' (Only used when providing fieldmaps to correct readout distortion)

Outputs

• <subject>_hcpstruct.zip: Zipped output directory containing complete MNINonLinear/, T1w/, and T2w/ folders.
• <subject>_hcpstruct_QC.*.png: QC images for visual inspection of output quality (details to come...)
• Logs (details to come...)

Gear Release Notes

The latest iteration of the hcp gears use a common docker base image to consolidate both library installations and common functionality across gears. See HCP Base Docker Image for details.

Important HCP Pipeline links

• HCP Pipelines
• HCP Pipelines FAQ
• HCP Pipelines v3.4.0 release notes