1. Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI at Ultra-high Field
Saskia Bollmann1, Steffen Bollmann1, Alexander Pucket2, Andrew Janke1, Markus Barth1
1Centre for Advanced Imaging, The University of Queensland, Brisbane, Australia
2Queensland Brain Institute, The University of Queensland, Brisbane, Australia

2. Realignment in fMRI Realignment = correct for motion
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Realignment in fMRI
Realignment = correct for motion
Affine coregistration: 3 translation + 3 rotation parameters
Realignment

3. Nonlinear Deformations in fMRI
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Nonlinear Deformations in fMRI
Through
Interaction with the main magnetic field1
Cardiac pulsation  tissue displacement of up to 2 mm2
Reduces
Temporal signal-to-noise-ratio (tSNR)
Spatial specificity
Can not be corrected using affine transformations
1Dymerska et al., 2016, NeuroImage; 2Soellinger, 2008, Zurich

4. Minimum Deformation Atlassing (MDA)1
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Minimum Deformation Atlassing (MDA)1
Non-linear realignment (NR) technique
Can average sub-voxel boundaries
Reduces partial-volume effects
Applied to single-subject fMRI time series
MDA
1Janke and Ullmann, 2015, Methods

5. Impact of Physiological Noise on Serial Correlations in Fast Simultaneous Multislice (SMS) EPI at 7T - Saskia Bollmann - # 5308
Data Acquisition
MAGNETOM 7T (Siemens) with a 32-channel head coil (Nova Medical)
CMRR SMS1,2 implementation (release 11a) + slice-GRAPPA2 + leak-block3
low-resolution sequence TR = 589 ms, voxel size = 2.5 mm isotropic, GRAPPA x SMS: 2 x 4, 581 volumes
high-resolution sequence TR = 1999 ms, voxel size = 1.3 mm isotropic, GRAPPA x SMS: 3 x 3, 188 volumes
1 participant performing a 6-minute rhythmic finger-tapping task using a block-design (18s block length)
1Feinberg et al., 2010, PLOS ONE; 2Setsompop et al., 2012, MRM; 3Cauley et al., 2014, MRM

6. 1Ashburner et al., 2005, NeuroImage, 2Penny et al., 2003, NeuroImage
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Data Analysis
MDA: Linear realignment + non-linear robust averaging of low resolution images
Data sets
Low resolution (LR)
High resolution (HR)
Low resolution low resolution + non-linear realignment (LRNR)
Outcome measure
tSNR maps
Segmentation1 results
Posterior probability maps2
MDA
1Ashburner et al., 2005, NeuroImage, 2Penny et al., 2003, NeuroImage

7. Spatial Specificity – Mean Images
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Spatial Specificity – Mean Images LR
LRNR HR
Low resolution (LR): pronounced partial volume effects between CSF, grey and white matter
Low resolution + non-linear realignment (LRNR): reduced partial volume effects, anatomical features match the high resolution reference image
High resolution (HR): clear delineation of CSF, grey and white matter

8. Sensitivity – Temporal SNR
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Sensitivity – Temporal SNR LR
LRNR HR
LR: highest tSNR
LRNR: slightly reduced tSNR, contains anatomical features
HR: substantially (~50 %) reduced tSNR

9. Spatial Specificity – Segmentation Results
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Spatial Specificity – Segmentation Results LR
LRNR HR
LR: course structures, only large gyri visible
LRNR: fine-grained structures discernible, matching high resolution images
HR: most detailed segmentation

10. Sensitivity – Posterior Probability Maps
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Sensitivity – Posterior Probability Maps LR
LRNR HR
threshold: effect size of 1% with log odds ratio of 10
LR: response in M1 and SMA
LRNR: similar spatial extent of activation, but better visibility of borders between gyri (circle)
HR: similar activation sides, but lower spatial extent

11. 1Dymerska et al., 2016, NeuroImage
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Discussion
Main disadvantage: long computation time of ~ 2 days
Correction of B0 effects might be possible with different techniques1
Reduction in tSNR unclear
Reduction of non-linear deformation through physiological effects remains to be assessed
1Dymerska et al., 2016, NeuroImage

12. Conclusion MDA for single-subject fMRI: Reduced partial volume effects
Non-linear Realignment Using Minimum Deformation Averaging for Single-subject fMRI - Saskia Bollmann - # 5338
Conclusion
MDA for single-subject fMRI:
Reduced partial volume effects
Improve segmentation results
Better delineation of activation patterns
Could enable advanced surface-based analysis schemes for low resolution data1
1Khan et al., 2011, Graph. Models.