Multi‐atlas and label fusion approach for patient‐specific MRI based skull estimation

Torrado‐Carvajal, Angel; Herraiz, Joaquín L.; Hernández-Tamames, Juan Antonio; Estépar, Raúl San Jośe; Eryaman, Yiğitcan; Rozenholc, Yves; Adalsteinsson, Elfar; Wald, Lawrence L.; Malpica, Norberto

doi:10.1002/mrm.25737

Cited by 23 publications

(17 citation statements)

References 35 publications

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“…Three‐dimensional printing was performed using the Dimension SST 1200 ES printer with ABS plastic as the printed material. The phantom was based on the 3T MRI scan of a healthy volunteer segmented into six tissue classes: air, white matter, gray matter, cerebrospinal fluid, skull, and “everything else” . The brain compartment was obtained by combining the white matter, gray matter and cerebrospinal fluid tissue classes.…”

Section: Methodsmentioning

confidence: 99%

Robust time-shifted spoke pulse design in the presence of large B0 variations with simultaneous reduction of through-plane dephasing, B1+ effects, and the specific absorption rate using parallel transmission

et al. 2015

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Purpose We design parallel transmission (pTx) spokes pulses with time-shifted sub-pulse profiles for joint mitigation of intensity variations due to B1+ effects, signal loss due to through-plane dephasing and the specific absorption rate (SAR) at 7 Tesla. Methods We derive a slice-averaged small tip-angle (SA-STA) approximation of the magnetization signal at echo time that depends on the B1+ transmit profiles, the through-plane B0 gradient and the amplitude and time-shifts of the spoke waveforms. We minimize a magnitude least-squares (MLS) objective based on this signal equation using a fast interior-point approach with analytical expressions of the Jacobian and Hessian. Results Our algorithm runs in less than three minutes for the design of 2-spoke pulses subject to hundreds of local SAR constraints (single CPU, Matlab implementation). On a B0/B1+ head phantom, joint optimization of the channel-dependent time-shifts and spoke amplitudes allowed signal recovery in high-B0 regions at no increase of SAR. Although the method creates uniform magnetization profiles (i.e., uniform intensity), the flip-angle varies across the image which makes it ill-suited to T1-weighted applications. Conclusions The SA-STA approach presented in this work is best suited to T2*-weighted applications with long echo times that require signal recovery around B0 “hotspots”.

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Section: Methodsmentioning

confidence: 99%

Robust time-shifted spoke pulse design in the presence of large B0 variations with simultaneous reduction of through-plane dephasing, B1+ effects, and the specific absorption rate using parallel transmission

et al. 2015

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“…They differ mainly in the type of semantic representation used to describe the image data, based on mathematic morphology (6), deformable models (7), MRI Dixon (8) or ultrashort-echo-time (TE) sequences (9,10), and multiatlas segmentation using label fusion (11). However, most of these methods showed limited accuracy when used to create AC maps (12).…”

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Fast Patch-Based Pseudo-CT Synthesis from T1-Weighted MR Images for PET/MR Attenuation Correction in Brain Studies

et al. 2015

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Attenuation correction in hybrid PET/MR scanners is still a challenging task. This paper describes a methodology for synthesizing a pseudo-CT volume from a single T1-weighted volume, thus allowing us to create accurate attenuation correction maps. Methods: We propose a fast pseudo-CT volume generation from a patient-specific MR T1-weighted image using a groupwise patch-based approach and an MRI-CT atlas dictionary. For every voxel in the input MR image, we compute the similarity of the patch containing that voxel to the patches of all MR images in the database that lie in a certain anatomic neighborhood. The pseudo-CT volume is obtained as a local weighted linear combination of the CT values of the corresponding patches. The algorithm was implemented in a graphical processing unit (GPU). Results: We evaluated our method both qualitatively and quantitatively for PET/MR correction. The approach performed successfully in all cases considered. We compared the SUVs of the PET image obtained after attenuation correction using the patient-specific CT volume and using the corresponding computed pseudo-CT volume. The patient-specific correlation between SUV obtained with both methods was high (R 2 5 0.9980, P , 0.0001), and the Bland-Altman test showed that the average of the differences was low (0.0006 ± 0.0594). A region-of-interest analysis was also performed. The correlation between SUV mean and SUV max for every region was high (R 2 5 0.9989, P , 0.0001, and R 2 5 0.9904, P , 0.0001, respectively). Conclusion:The results indicate that our method can accurately approximate the patient-specific CT volume and serves as a potential solution for accurate attenuation correction in hybrid PET/MR systems. The quality of the corrected PET scan using our pseudo-CT volume is comparable to having acquired a patient-specific CT scan, thus improving the results obtained with the ultrashort-echo-timebased attenuation correction maps currently used in the scanner. The GPU implementation substantially decreases computational time, making the approach suitable for real applications.

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“…The different tissues (white matter, gray matter, cerebrospinal fluid, skull, muscle, fat, and skin) were segmented using the automatic segmentation pipeline proposed in [10]. This method estimates the skull using a CT multi-atlas and label-fusion based approach [11]. Figure 2 shows both acquisitions and their correspondent tissue segmentations.…”

Section: Methodsmentioning

confidence: 99%

The Effect of Mouth Motion on the Attenuation Correction in Neurological PET Studies

Herraiz

Torrado‐Carvajal

Hernández-Tamames

et al. 2015

Computational Methods for Molecular Imaging

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In each new generation of PET scanners, the axial field-of-view (FOV) has been increased as a way to improve their sensitivity and obtain better images, faster and with lower injected doses. Nevertheless, in neurological studies, the use of larger axial FOV can introduce errors in the PET attenuation correction (AC), as possible movements of the patient's mouth are not currently considered. This effect happens when oblique PET sinograms containing both the jaw and the brain are used. In this work we have studied the bias that mouth motion can introduce in the PET AC, for two different scanners. The average effect over large regions in the brain is around 1 % for a moderate mouth motion, although some voxels show differences of up to 18 %. These results indicate that if scanners with large axial FOV and acceptance angles are going to be used in the future, possible movements of patient's mouth should be considered in the AC procedure.

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Multi‐atlas and label fusion approach for patient‐specific MRI based skull estimation

Cited by 23 publications

References 35 publications

Robust time-shifted spoke pulse design in the presence of large B0 variations with simultaneous reduction of through-plane dephasing, B1+ effects, and the specific absorption rate using parallel transmission

Robust time-shifted spoke pulse design in the presence of large B0 variations with simultaneous reduction of through-plane dephasing, B1+ effects, and the specific absorption rate using parallel transmission

Fast Patch-Based Pseudo-CT Synthesis from T1-Weighted MR Images for PET/MR Attenuation Correction in Brain Studies

The Effect of Mouth Motion on the Attenuation Correction in Neurological PET Studies

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