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Magnetic Resonance Materials in Physics, Biology and Medicine

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29.05.2018 | Research Article

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

verfasst von: 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

Erschienen in: Magnetic Resonance Materials in Physics, Biology and Medicine | Ausgabe 5/2018

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Abstract

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.

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Titel: 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
verfasst von: 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
Publikationsdatum: 29.05.2018
Verlag: Springer International Publishing
Erschienen in: Magnetic Resonance Materials in Physics, Biology and Medicine / Ausgabe 5/2018
Print ISSN: 0968-5243
Elektronische ISSN: 1352-8661
DOI: https://doi.org/10.1007/s10334-018-0690-z

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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