Dataset Information

Automatic cortical surface reconstruction of high-resolution T1 echo planar imaging data.

ABSTRACT: Echo planar imaging (EPI) is the method of choice for the majority of functional magnetic resonance imaging (fMRI), yet EPI is prone to geometric distortions and thus misaligns with conventional anatomical reference data. The poor geometric correspondence between functional and anatomical data can lead to severe misplacements and corruption of detected activation patterns. However, recent advances in imaging technology have provided EPI data with increasing quality and resolution. Here we present a framework for deriving cortical surface reconstructions directly from high-resolution EPI-based reference images that provide anatomical models exactly geometric distortion-matched to the functional data. Anatomical EPI data with 1mm isotropic voxel size were acquired using a fast multiple inversion recovery time EPI sequence (MI-EPI) at 7T, from which quantitative T1 maps were calculated. Using these T1 maps, volumetric data mimicking the tissue contrast of standard anatomical data were synthesized using the Bloch equations, and these T1-weighted data were automatically processed using FreeSurfer. The spatial alignment between T2(?)-weighted EPI data and the synthetic T1-weighted anatomical MI-EPI-based images was improved compared to the conventional anatomical reference. In particular, the alignment near the regions vulnerable to distortion due to magnetic susceptibility differences was improved, and sampling of the adjacent tissue classes outside of the cortex was reduced when using cortical surface reconstructions derived directly from the MI-EPI reference. The MI-EPI method therefore produces high-quality anatomical data that can be automatically segmented with standard software, providing cortical surface reconstructions that are geometrically matched to the BOLD fMRI data.

SUBMITTER: Renvall V

PROVIDER: S-EPMC5234090 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Automatic cortical surface reconstruction of high-resolution T1 echo planar imaging data.

Renvall Ville V Witzel Thomas T Wald Lawrence L LL Polimeni Jonathan R JR

NeuroImage 20160411

Echo planar imaging (EPI) is the method of choice for the majority of functional magnetic resonance imaging (fMRI), yet EPI is prone to geometric distortions and thus misaligns with conventional anatomical reference data. The poor geometric correspondence between functional and anatomical data can lead to severe misplacements and corruption of detected activation patterns. However, recent advances in imaging technology have provided EPI data with increasing quality and resolution. Here we presen ...[more]

PMID: 27079529

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Project description:BackgroundMagnetic resonance elastography (MRE) is an imaging technique that can noninvasively assess the shear properties of the intervertebral disc (IVD). Unlike the standard gradient recalled echo (GRE) MRE technique, a spin-echo echo-planar imaging (SE-EPI) sequence has the potential to improve imaging efficiency and patient compliance.PurposeTo validate the use of an SE-EPI sequence for MRE of the IVD compared against the standard GRE sequence.Study typeCross-over.SubjectsTwenty-eight healthy volunteers (15 males and 13 females, age range: 19-55).Field strength/sequence3 T; GRE, SE-EPI with breath holds (SE-EPI-BH) and SE-EPI with free breathing (SE-EPI-FB) MRE sequences.AssessmentMRE-derived shear stiffnesses were calculated via principal frequency analysis. SE-EPI derived shear stiffness and octahedral shear strain signal-to-noise ratios (OSS-SNR) were compared against those derived using the GRE sequence. The reproducibility and repeatability of SE-EPI stiffness measurements were determined. Shear stiffness was evaluated in the nucleus pulposus (NP) and annulus fibrosus (AF) regions of the disc. Scan times between sequences were compared.Statistical testsLinear mixed models, Bland-Altman plots, and Lin's concordance correlation coefficients (CCCs) were used with P < 0.05 considered statistically significant.ResultsGood correlation was observed between shear stiffnesses derived from the SE-EPI sequences with those derived from the GRE sequence with CCC values greater than 0.73 and 0.78 for the NP and AF regions, respectively. OSS-SNR was not significantly different between GRE and SE-EPI sequences (P > 0.05). SE-EPI sequences generated highly reproducible and repeatable stiffness measurements with CCC values greater than 0.97 in the NP and AF regions and reduced scan time by at least 51% compared to GRE. SE-EPI-BH and SE-EPI-FB stiffness measurements were similar with CCC values greater than 0.98 for both regions.Data conclusionSE-EPI-based MRE-derived stiffnesses were highly reproducible and repeatable and correlated with current standard GRE MRE-derived stiffness estimates while reducing scan times.Level of evidence1 TECHNICAL EFFICACY STAGE: 1.

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Dataset Information

Automatic cortical surface reconstruction of high-resolution T1 echo planar imaging data.

Publications

Automatic cortical surface reconstruction of high-resolution T1 echo planar imaging data.

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