Optimized partial-coverage functional analysis pipeline (OPFAP): a semi-automated pipeline for skull stripping and co-registration of partial-coverage, ultra-high-field functional images

Peter E. Yoo, Jon O. Cleary, Scott C. Kolbe, Roger J. Ordidge, Terence J. O’Brien, Nicholas L. Opie, Sam E. John, Thomas J. Oxley, Bradford A. Moffat

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3 Citations (Scopus)


Objective: Ultra-high-field functional MRI (UHF-fMRI) allows for higher spatiotemporal resolution imaging. However, higher-resolution imaging entails coverage limitations. Processing partial-coverage images using standard pipelines leads to sub-optimal results. We aimed to develop a simple, semi-automated pipeline for processing partial-coverage UHF-fMRI data using widely used image processing algorithms. Materials and methods: We developed automated pipelines for optimized skull stripping and co-registration of partial-coverage UHF functional images, using built-in functions of the Centre for Functional Magnetic Resonance Imaging of the Brain's (FMRIB’s) Software library (FSL) and advanced normalization tools. We incorporated the pipelines into the FSL’s functional analysis pipeline and provide a semi-automated optimized partial-coverage functional analysis pipeline (OPFAP). Results: Compared to the standard pipeline, the OPFAP yielded images with 15 and 30% greater volume of non-zero voxels after skull stripping the functional and anatomical images, respectively (all p = 0.0004), which reflected the conservation of cortical voxels lost when the standard pipeline was used. The OPFAP yielded the greatest Dice and Jaccard coefficients (87 and 80%, respectively; all p < 0.0001) between the co-registered participant gyri maps and the template gyri maps, demonstrating the goodness of the co-registration results. Furthermore, the greatest volume of group-level activation in the most number of functionally relevant regions was observed when the OPFAP was used. Importantly, group-level activations were not observed when using the standard pipeline. Conclusion: These results suggest that the OPFAP should be used for processing partial-coverage UHF-fMRI data for detecting high-resolution macroscopic blood oxygenation level-dependent activations.

Original languageEnglish
Pages (from-to)621-632
Number of pages12
JournalMagnetic Resonance Materials in Physics, Biology and Medicine
Issue number5
Publication statusPublished - 1 Oct 2018
Externally publishedYes


  • 7 T
  • ANTs
  • Co-registration
  • fMRI
  • FSL
  • Partial coverage
  • Segmentation
  • Targeted
  • UHF

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