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Reconstruction pipeline

The reconstruction pipeline was developed by the team at King’s College London.

Motion corrected volumetric reconstructions of multi-slice inversion recovery T1- and turbo spin echo T2-weighted images are obtained by extending the aligned sensitivity encoding (SENSE) method1 to the multi-slice case2. Corrections are performed for both within-plane and through-plane motion from partial k-space information. The two acquired orthogonal stacks are integrated by a super-resolution scheme3. Methods and example data for the aligned SENSE method are available at https://github.com/mriphysics/multiSliceAlignedSENSE/releases/tag/1.0.1.

Inputs and outputs

Path: rawdata/sub-{subid}/ses-{sesid}

The reconstruction pipeline generates the files listed in the Reconstruction pipeline section of the directory structure summary.

Standard magnitude and phase reconstructions are provided for all native acquired anatomical image stacks, with the different orientations and repeat acquisitions labelled by sequence run number as follows:

Description Filename
T1w magnitude image (native acquired stack) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_T1w.nii
T1w phase image (native acquired stack) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-phase_T1w.nii
T2w magnitude image (native acquired stack) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_T2w.nii
T2w phase image (native acquired stack) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-phase_T2w.nii

Motion corrected and super-resolved reconstructions, and phase images, are included for every acquired multislice stack:

Description Filename
T1w image (motion corrected) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-mc_T1w.nii
T2w image (motion corrected) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-mc_T2w.nii
T1w image (motion corrected and super resolved) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-mcsr_T1w.nii
T2w image (motion corrected and super resolved) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-mcsr_T2w.nii

Primary anatomical outputs

The final motion corrected slice-to-volume reconstructed T1w and T2w volumes are:

Description Filename
T1w image (combined Slice-to-Volume reconstruction) anat/sub-{subid}_ses-{sesid}_rec-SVR_T1w.nii
T2w image (combined Slice-to-Volume reconstruction) anat/sub-{subid}_ses-{sesid}_rec-SVR_T2w.nii

An additional T1 3D MPRAGE volume is also provided, but currently not used in processing pipelines:

Description Filename
T1w image (3D MPRAGE) anat/sub-{subid}_ses-{sesid}_run-{seqnum}_acq-MPRAGE_T1w.nii

For fMRI and dMRI, simultaneous multi-slice (SMS) echo planar imaging (EPI) is reconstructed using the extended SENSE technique4, with details described elsewhere5,6,7; sensitivity estimates from a conventional reference scan are refined with the information from non-SMS reference acquisitions with matched readouts to promote matched coil map and image distortions. As for dMRI, complex data retrieval is performed by the generalized singular value shrinkage (GSVS) denoising technique using noise measures performed during the acquisition8. Methods and example data for the GSVS method are available at https://github.com/mriphysics/complexSVDShrinkageDWI/releases/tag/1.1.0.

Primary dMRI outputs

dMRI reconstructions are provided with and without denoising, along with phase images, and additional chi^2 maps from the reconstruction required for the dMRI (SHARD) pipeline. A third reconstruction used by the dMRI (EDDY) pipeline is included, this matches the version from the 2nd data release, the main difference being that residual fat artefacts are suppressed in the reconstruction pipeline:

Description Filename
Multi-band dMRI EPI dwi/sub-{subid}_ses-{sesid}_run-{seqnum}_dwi.nii
Multi-band dMRI EPI (denoised reconstruction) dwi/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-denoised_dwi.nii
Multi-band dMRI EPI (Release 2 reconstruction) dwi/sub-{subid}_ses-{sesid}_rec-release2_dwi.nii

Primary outputs for fMRI

There is one primary reconstruction for the resting state fMRI data, along with single-band reference scans (typically one before and one after resting state run), and a spin-echo EPI with matched readout for field estimation. In addition, all phase images are provided.

Description Filename
Single-band Ref func/sub-{subid}_ses-{sesid}_run-{seqnum}_task-rest_sbref.nii
Resting fMRI func/sub-{subid}_ses-{sesid}_run-{seqnum}_task-rest_bold.nii
4D Spin Echo EPI with different phase encode directions (for topup fieldmap estimation) fmap/sub-{subid}_ses-{sesid}_run-{seqnum}_epi.nii

Primary outputs for field mapping

Data from calibration scans are provided for B1+ and B0 field estimates, using the DREAM and dual-gradient echo methods, respectively. Reconstructed magnitude and phase images are provided, along with the following calculated field maps as the primary outputs:

Description Filename
B0 field-map in (Hz) - unfiltered fmap/sub-{subid}_ses-{sesid}_run-{seqnum}_rec-raw_fieldmap.nii
B1+ field map (rel. nom. flip) B1/sub-{subid}_ses-{sesid}_run-{seqnum}_b1map.nii

The full output list can be found in the Reconstruction pipeline section of the directory structure summary.

References

  1. Cordero-Grande, L., Teixeira. R. P. A. G., Hughes, E. J., Hutter, J., Price, A. N., and Hajnal, J. V. Sensitivity encoding for aligned multishot magnetic resonance reconstruction IEEE Transactions on Computational Imaging (2016), 2(3): 266-280. DOI: 10.1109/TCI.2016.2557069

  2. Cordero-Grande, L., Hughes, E. J., Hutter, J., Hutter, J., Price, A. N., and Hajnal, J. V. Three-Dimensional Motion Corrected Sensitivity Encoding Reconstruction for Multi-Shot Multi-Slice MRI: Application to Neonatal Brain Imaging Magnetic Resonance in Medicine 2018, 79(3): 1365-1376. DOI: 10.1002/mrm.26796

  3. Kuklikova-Murgasova, M., Quaghebeur, G., Rutherford, M. A., Hajnal, J. V., and Schnabel, J. A. Reconstruction of fetal brain MRI with intensity matching and complete outlier removal Medical Image Analysis (2012), 16(8): 1550-1564. DOI: 10.1016/j.media.2012.07.004

  4. Zhu, K., Dougherty, R. F., Wu, H., Middione, M. J., Takahashi, A. M, Zhang, T., Pauly, J. M., Kerr, A. B. Hybrid-space SENSE reconstruction for simultaneous multi-slice MRI IEEE Transactions on Medical Imaging, 35(8) (2016):1824-1836. DOI: 10.1109/TMI.2016.2531635

  5. Cordero-Grande, L., Price, A. N., and Hajnal, J. V. Comprehensive CG-SENSE reconstruction of SMS-EPI ISMRM 2016: 3239.

  6. Cordero-Grande, L., Hutter, J., Price, A., Hughes, E., and Hajnal, J. V. Goodness of fit factor in SENSE reconstruction: a tool for pseudolesion detection and fat unfolding ESMRMB 2016: 458.

  7. Hennel, F.,Buehrer, M., von Deuster, C., Seuven, A., and Pruessmann, K. P. SENSE reconstruction for multiband EPI including slice-dependent N/2 ghost correction Magnetic Resonance in Medicine (2016), 76(3): 873-879. DOI: 10.1002/mrm.25915

  8. Cordero-Grande, L., Christiaens, D., Hutter, J., Price, A. N., and Hajnal, J. V. Complex diffusion-weighted image estimation via matrix recovery under general noise models Neuroimage (2019), 200: 391-404. DOI: 10.1016/j.neuroimage.2019.06.039