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

Optimized partial-coverage functional analysis pipeline (OPFAP): a semi-automated pipeline for... 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, demon- strating the goodness of the co-registration results. Furthermore, the greatest volume of group-level activation in the most http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Magnetic Resonance Materials in Physics, Biology and Medicine Springer Journals

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

Loading next page...
 
/lp/springer_journal/optimized-partial-coverage-functional-analysis-pipeline-opfap-a-semi-uPeaCEDrKr
Publisher
Springer Journals
Copyright
Copyright © 2018 by ESMRMB
Subject
Medicine & Public Health; Imaging / Radiology; Computer Appl. in Life Sciences; Solid State Physics; Biomedical Engineering; Health Informatics
ISSN
0968-5243
eISSN
1352-8661
D.O.I.
10.1007/s10334-018-0690-z
Publisher site
See Article on Publisher Site

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, demon- strating the goodness of the co-registration results. Furthermore, the greatest volume of group-level activation in the most

Journal

Magnetic Resonance Materials in Physics, Biology and MedicineSpringer Journals

Published: May 29, 2018

References

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Search

Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly

Organize

Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.

Access

Get unlimited, online access to over 18 million full-text articles from more than 15,000 scientific journals.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Elsevier, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve

Freelancer

DeepDyve

Pro

Price

FREE

$49/month
$360/year

Save searches from
Google Scholar,
PubMed

Create lists to
organize your research

Export lists, citations

Read DeepDyve articles

Abstract access only

Unlimited access to over
18 million full-text articles

Print

20 pages / month

PDF Discount

20% off