Pushing MP2RAGE boundaries: Ultimate time-efficient parameterization combined with exhaustive T1 synthetic contrasts

PURPOSE

MP2RAGE parameter optimization is redefined to allow more time-efficient MR acquisitions, whereas the T1 -based synthetic imaging framework is used to obtain on-demand T1 -weighted contrasts. Our aim was to validate this concept on healthy volunteers and patients with multiple sclerosis, using plug-and-play parallel-transmission brain imaging at 7 T.

METHODS

A "time-efficient" MP2RAGE sequence was designed with optimized parameters including TI and TR set as small as possible. Extended phase graph formalism was used to set flip-angle values to maximize the gray-to-white-matter contrast-to-noise ratio (CNR). Several synthetic contrasts (UNI, EDGE, FGATIR, FLAWSMIN , FLAWSHCO ) were generated online based on the acquired T1 maps. Experimental validation was performed on 4 healthy volunteers at various spatial resolutions. Clinical applicability was evaluated on 6 patients with multiple sclerosis, scanned with both time-efficient and conventional MP2RAGE parameterizations.

RESULTS

The proposed time-efficient MP2RAGE protocols reduced acquisition time by 40%, 30%, and 19% for brain imaging at (1 mm)3 , (0.80 mm)3 and (0.65 mm)3 , respectively, when compared with conventional parameterizations. They also provided all synthetic contrasts and comparable contrast-to-noise ratio on UNI images. The flexibility in parameter selection allowed us to obtain a whole-brain (0.45 mm)3 acquisition in 19 min 56 s. On patients with multiple sclerosis, a (0.67 mm)3 time-efficient acquisition enhanced cortical lesion visualization compared with a conventional (0.80 mm)3 protocol, while decreasing the scan time by 15%.

CONCLUSION

The proposed optimization, associated with T1 -based synthetic contrasts, enabled substantial decrease of the acquisition time or higher spatial resolution scans for a given time budget, while generating all typical brain contrasts derived from MP2RAGE.

Optimal control in a magnetization-prepared rapid acquisition gradient-echo sequence

This article proposes a numerical framework to determine the optimal magnetization preparation in a three-dimensional magnetization-prepared rapid gradient-echo (MP-RAGE) sequence to obtain the best achievable contrast between target tissues based on differences in their relaxation times. The benefit lies in the adaptation of the algorithm of optimal control, GRAdient Ascent Pulse Engineering (GRAPE), to the optimization of magnetization preparation in a cyclic sequence without full recovery between each cycle. This numerical approach optimizes magnetization preparation of an arbitrary number of radio frequency pulses to enhance contrast, taking into account the establishment of a steady state in the longitudinal component of the magnetization. The optimal control preparation offers an optimized mixed T 1 / T 2 contrast in this traditional T 1 -weighted sequence. To show the versatility of the proposed method, numerical and in vitro results are described. Examples of contrasts acquired on brain regions of a healthy volunteer are presented for potential applications at 3 T.

Multi T1-weighted contrast imaging and T1 mapping with compressed sensing FLAWS at 3 T

OBJECTIVE

The Fluid And White matter Suppression (FLAWS) MRI sequence provides multiple T1-weighted contrasts of the brain in a single acquisition. However, the FLAWS acquisition time is approximately 8 min with a standard GRAPPA 3 acceleration factor at 3 T. This study aims at reducing the FLAWS acquisition time by providing a new sequence optimization based on a Cartesian phyllotaxis k-space undersampling and a compressed sensing (CS) reconstruction. This study also aims at showing that T1 mapping can be performed with FLAWS at 3 T.

MATERIALS AND METHODS

The CS FLAWS parameters were determined using a method based on a profit function maximization under constraints. The FLAWS optimization and T1 mapping were assessed with in-silico, in-vitro and in-vivo (10 healthy volunteers) experiments conducted at 3 T.

RESULTS

In-silico, in-vitro and in-vivo experiments showed that the proposed CS FLAWS optimization allows the acquisition time of a 1 mm-isotropic full-brain scan to be reduced from [Formula: see text] to [Formula: see text] without decreasing image quality. In addition, these experiments demonstrate that T1 mapping can be performed with FLAWS at 3 T.

DISCUSSION

The results obtained in this study suggest that the recent advances in FLAWS imaging allow to perform multiple T1-weighted contrast imaging and T1 mapping in a single [Formula: see text] sequence acquisition.

Accurate Diagnosis of Cortical and Infratentorial Lesions in Multiple Sclerosis Using Accelerated Fluid and White Matter Suppression Imaging

OBJECTIVES

The precise location of multiple sclerosis (MS) cortical lesions can be very challenging at 3 T, yet distinguishing them from subcortical lesions is essential for the diagnosis and prognosis of the disease. Compressed sensing-accelerated fluid and white matter suppression imaging (CS-FLAWS) is a new magnetic resonance imaging sequence derived from magnetization-prepared 2 rapid acquisition gradient echo with promising features for the detection and classification of MS lesions. The objective of this study was to compare the diagnostic performances of CS-FLAWS (evaluated imaging) and phase sensitive inversion recovery (PSIR; reference imaging) for classification of cortical lesions (primary objective) and infratentorial lesions (secondary objective) in MS, in combination with 3-dimensional (3D) double inversion recovery (DIR).

MATERIALS AND METHODS

Prospective 3 T scans (MS first diagnosis or follow-up) acquired between March and August 2021 were retrospectively analyzed. All underwent 3D CS-FLAWS, axial 2D PSIR, and 3D DIR. Double-blinded reading sessions exclusively in axial plane and final consensual reading were performed to assess the number of cortical and infratentorial lesions. Wilcoxon test was used to compare the 2 imaging datasets (FLAWS + DIR and PSIR + DIR), and intraobserver and interobserver agreement was assessed using the intraclass correlation coefficient.

RESULTS

Forty-two patients were analyzed (38 with relapsing-remitting MS, 29 women, 42.7 ± 12.6 years old). Compressed sensing-accelerated FLAWS allowed the identification of 263 cortical lesions versus 251 with PSIR ( P = 0.74) and 123 infratentorial lesions versus 109 with PSIR ( P = 0.63), corresponding to a nonsignificant difference between the 2 sequences. Compressed sensing-accelerated FLAWS exhibited fewer false-negative findings than PSIR either for cortical lesions (1 vs 13; P < 0.01) or infratentorial lesions (1 vs 15; P < 0.01). No false-positive findings were found with any of the 2 sequences. Diagnostic confidence was high for each contrast.

CONCLUSION

Three-dimensional CS-FLAWS is as accurate as 2D PSIR imaging for classification of cortical and infratentorial MS lesions, with fewer false-negative findings, opening the way to a reliable full brain MS exploration in a clinically acceptable duration (5 minutes 15 seconds).

Simultaneous Optimization of MP2RAGE T1 -weighted (UNI) and FLuid And White matter Suppression (FLAWS) brain images at 7T using Extended Phase Graph (EPG) Simulations

PURPOSE

The MP2RAGE sequence is typically optimized for either T1 -weighted uniform image (UNI) or gray matter-dominant fluid and white matter suppression (FLAWS) contrast images. Here, the purpose was to optimize an MP2RAGE protocol at 7 Tesla to provide UNI and FLAWS images simultaneously in a clinically applicable acquisition time at <0.7 mm isotropic resolution.

METHODS

Using the extended phase graph formalism, the signal evolution of the MP2RAGE sequence was simulated incorporating T2 relaxation, diffusion, RF spoiling, and B1 + variability. Flip angles and TI were optimized at different TRs (TRMP2RAGE ) to produce an optimal contrast-to-noise ratio for UNI and FLAWS images. Simulation results were validated by comparison to MP2RAGE brain scans of 5 healthy subjects, and a final protocol at TRMP2RAGE  = 4000 ms was applied in 19 subjects aged 8-62 years with and without epilepsy.

RESULTS

FLAWS contrast images could be obtained while maintaining >85% of the optimal UNI contrast-to-noise ratio. Using TI1 /TI2 /TRMP2RAGE of 650/2280/4000 ms, 6/8 partial Fourier in the inner phase-encoding direction, and GRAPPA factor = 4 in the other, images with 0.65 mm isotropic resolution were produced in <7.5 min. The contrast-to-noise ratio was around 20% smaller at TRMP2RAGE  = 4000 ms compared to that at TRMP2RAGE  = 5000 ms; however, the 20% shorter duration makes TRMP2RAGE  = 4000 ms a good candidate for clinical applications example, pediatrics.

CONCLUSION

FLAWS and UNI images could be obtained in a single scan with 0.65 mm isotropic resolution, providing a set of high-contrast images and full brain coverage in a clinically applicable scan time. Images with excellent anatomical detail were demonstrated over a wide age range using the optimized parameter set.

Mapping Resection Progress by Tool-Tip Tracking during Brain Tumor Surgery for Real-Time Estimation of Residual Tumor

Surgical resection continues to be the primary initial therapeutic strategy in the treatment of patients with brain tumors. Computerized cranial neuronavigation based on preoperative imaging offers precision guidance during craniotomy and early tumor resection but progressively loses validity with brain shift. Intraoperative MRI (iMRI) and intraoperative ultrasound (iUS) can update the imaging used for guidance and navigation but are limited in terms of temporal and spatial resolution, respectively. We present a system that uses time-stamped tool-tip positions of surgical instruments to generate a map of resection progress with high spatial and temporal accuracy. We evaluate this system and present results from 80 cranial tumor resections. Regions of the preoperative tumor segmentation that are covered by the resection map (True Positive Tracking) and regions of the preoperative tumor segmentation not covered by the resection map (True Negative Tracking) are determined for each case. We compare True Negative Tracking, which estimates the residual tumor, with the actual residual tumor identified using iMRI. We discuss factors that can cause False Positive Tracking and False Negative Tracking, which underestimate and overestimate the residual tumor, respectively. Our method provides good estimates of the residual tumor when there is minimal brain shift, and line-of-sight is maintained. When these conditions are not met, surgeons report that it is still useful for identifying regions of potential residual.

Fluid and White Matter Suppression: New Sensitive 3 T Magnetic Resonance Imaging Contrasts for Cortical Lesion Detection in Multiple Sclerosis

OBJECTIVE

Cortical lesions are common in multiple sclerosis (MS), but their visualization is challenging on conventional magnetic resonance imaging. The uniform image derived from magnetization prepared 2 rapid acquisition gradient echoes (MP2RAGE uni ) detects cortical lesions with a similar rate as the criterion standard sequence, double inversion recovery. Fluid and white matter suppression (FLAWS) provides multiple reconstructed contrasts acquired during a single acquisition. These contrasts include FLAWS minimum image (FLAWS min ), which provides an exquisite sensitivity to the gray matter signal and therefore may facilitate cortical lesion identification, as well as high contrast FLAWS (FLAWS hco ), which gives a contrast that is similar to one of MP2RAGE uni . In this study, we compared the manual detection rate of cortical lesions on MP2RAGE uni , FLAWS min , and FLAWS hco in MS patients. Furthermore, we assessed whether the combined detection rate on FLAWS min and FLAWS hco was superior to MP2RAGE uni for cortical lesions identification. Last, we compared quantitative T1 maps (qT1) provided by both MP2RAGE and FLAWS in MS lesions.

MATERIALS AND METHODS

We included 30 relapsing-remitting MS patients who underwent MP2RAGE and FLAWS magnetic resonance imaging with isotropic spatial resolution of 1 mm at 3 T. Cortical lesions were manually segmented by consensus of 3 trained raters and classified as intracortical or leukocortical lesions on (1) MP2RAGE uniform/flat images, (2) FLAWS min , and (3) FLAWS hco . In addition, segmented lesions on FLAWS min and FLAWS hco were merged to produce a union lesion map (FLAWS min + hco ). Number and volume of all cortical, intracortical, and leukocortical lesions were compared among MP2RAGE uni , FLAWS min , and FLAWS hco using Friedman test and between MP2RAGE uni and FLAWS min + hco using Wilcoxon signed rank test. The FLAWS T1 maps were then compared with the reference MP2RAGE T1 maps using relative differences in percentage. In an exploratory analysis, individual cortical lesion counts of the 3 raters were compared, and interrater variability was quantified using Fleiss ϰ.

RESULTS

In total, 633 segmentations were made on the 3 contrasts, corresponding to 355 cortical lesions. The median number and volume of single cortical, intracortical, and leukocortical lesions were comparable among MP2RAGE uni , FLAWS min , and FLAWS hco . In patients with cortical lesions (22/30), median cumulative lesion volume was larger on FLAWS min (587 μL; IQR, 1405 μL) than on MP2RAGE uni (490 μL; IQR, 990 μL; P = 0.04), whereas there was no difference between FLAWS min and FLAWS hco , or FLAWS hco and MP2RAGE uni . FLAWS min + hco showed significantly greater numbers of cortical (median, 4.5; IQR, 15) and leukocortical (median, 3.5; IQR, 12) lesions than MP2RAGE uni (median, 3; IQR, 10; median, 2.5; IQR, 7; both P < 0.001). Interrater agreement was moderate on MP2RAGE uni (ϰ = 0.582) and FLAWS hco (ϰ = 0.584), but substantial on FLAWS min (ϰ = 0.614). qT1 in lesions was similar between MP2RAGE and FLAWS.

CONCLUSIONS

Cortical lesions identification in FLAWS min and FLAWS hco was comparable to MP2RAGE uni . The combination of FLAWS min and FLAWS hco allowed to identify a higher number of cortical lesions than MP2RAGE uni , whereas qT1 maps did not differ between the 2 acquisition schemes.

Neuroimaging at 7 Tesla: a pictorial narrative review

Neuroimaging using the 7-Tesla (7T) human magnetic resonance (MR) system is rapidly gaining popularity after being approved for clinical use in the European Union and the USA. This trend is the same for functional MR imaging (MRI). The primary advantages of 7T over lower magnetic fields are its higher signal-to-noise and contrast-to-noise ratios, which provide high-resolution acquisitions and better contrast, making it easier to detect lesions and structural changes in brain disorders. Another advantage is the capability to measure a greater number of neurochemicals by virtue of the increased spectral resolution. Many structural and functional studies using 7T have been conducted to visualize details in the white matter and layers of the cortex and hippocampus, the subnucleus or regions of the putamen, the globus pallidus, thalamus and substantia nigra, and in small structures, such as the subthalamic nucleus, habenula, perforating arteries, and the perivascular space, that are difficult to observe at lower magnetic field strengths. The target disorders for 7T neuroimaging range from tumoral diseases to vascular, neurodegenerative, and psychiatric disorders, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, epilepsy, major depressive disorder, and schizophrenia. MR spectroscopy has also been used for research because of its increased chemical shift that separates overlapping peaks and resolves neurochemicals more effectively at 7T than a lower magnetic field. This paper presents a narrative review of these topics and an illustrative presentation of images obtained at 7T. We expect 7T neuroimaging to provide a new imaging biomarker of various brain disorders.

3-Dimensional Fluid and White Matter Suppression Magnetic Resonance Imaging Sequence Accelerated With Compressed Sensing Improves Multiple Sclerosis Cervical Spinal Cord Lesion Detection Compared With Standard 2-Dimensional Imaging

OBJECTIVES

Fluid and white matter suppression (FLAWS) is a recently proposed magnetic resonance sequence derived from magnetization-prepared 2 rapid acquisition gradient-echo providing 2 coregistered datasets with white matter- and cerebrospinal fluid-suppressed signal, enabling synthetic imaging with amplified contrast. Although these features are high potential for brain multiple sclerosis (MS) imaging, spinal cord has never been evaluated with this sequence to date. The objective of this work was therefore to assess diagnostic performance and self-confidence provided by compressed-sensing (CS) 3-dimensional (3D) FLAWS for cervical MS lesion detection on a head scan that includes the cervical cord without changing standard procedures.

MATERIALS AND METHODS

Prospective 3 T scans (MS first diagnosis or follow-up) acquired between 2019 and 2020 were retrospectively analyzed. All patients underwent 3D CS-FLAWS (duration: 5 minutes 40 seconds), axial T2 turbo spin echo covering cervical spine from cervicomedullary junction to the same inferior level as FLAWS, and sagittal cervical T2/short tau inversion recovery imaging. Two readers performed a 2-stage double-blind reading, followed by consensus reading. Wilcoxon tests were used to compare the number of detected spinal cord lesions and the reader's diagnostic self-confidence when using FLAWS versus the reference 2D T2-weighted imaging.

RESULTS

Fifty-eight patients were included (mean age, 40 ± 13 years, 46 women, 7 ± 6 years mean disease duration). The CS-FLAWS detected significantly more lesions than the reference T2-weighted imaging (197 vs 152 detected lesions, P < 0.001), with a sensitivity of 98% (T2-weighted imaging sensitivity: 90%) after consensual reading. Considering the subgroup of patients who underwent sagittal T2 + short tau inversion recovery imaging (Magnetic Resonance Imaging for Multiple Sclerosis subgroup), +250% lesions were detected with FLAWS (63 vs 25 lesions detected, P < 0.001). Mean reading self-confidence was significantly better with CS-FLAWS (median, 5 [interquartile range, 1] [no doubt for diagnosis] vs 4 [interquartile range, 1] [high confidence]; P < 0.001).

CONCLUSIONS

Imaging with CS-FLAWS provides an improved cervical spinal cord exploration for MS with increased self-confidence compared with conventional T2-weighted imaging, in a clinically acceptable time.

MRI of focal cortical dysplasia

Focal cortical dysplasia (FCD) are histopathologically categorized in ILAE type I to III. Mild malformations of cortical development (mMCD) including those with oligodendroglial hyperplasia (MOGHE) are to be integrated into this classification yet. Only FCD type II have distinctive MRI and molecular genetics alterations so far. Subtle FCD including FCD type II located in the depth of a sulcus are often overlooked requiring the use of dedicated sequences (MP2RAGE, FLAWS, EDGE) and/or voxel (VBM)- or surface-based (SBM) postprocessing. The added value of 7 Tesla MRI has to be proven yet.

The brainstem in multiple sclerosis: MR identification of tracts and nuclei damage

Objective

To evaluate the 3D Fast Gray Acquisition T1 Inversion Recovery (FGATIR) sequence for MRI identification of brainstem tracts and nuclei damage in multiple sclerosis (MS) patients.

Methods

From april to december 2020, 10 healthy volunteers and 50 patients with remitted-relapsing MS (58% female, mean age 36) underwent MR imaging in the Neuro-imaging department of the C.H.N.O. des Quinze-Vingts, Paris, France. MRI was achieved on a 3 T system (MAGNETOM Skyra) using a 64-channel coil. 3D FGATIR sequence was first performed on healthy volunteers to classify macroscopically identifiable brainstem structures. Then, FGATIR was assessed in MS patients to locate brainstem lesions detected with Proton Density/T2w (PD/T2w) sequence.

Results

In healthy volunteers, FGATIR allowed a precise visualization of tracts and nuclei according to their myelin density. Including FGATIR in MR follow-up of MS patients helped to identify structures frequently involved in the inflammatory process. Most damaged tracts were the superior cerebellar peduncle and the transverse fibers of the pons. Most frequently affected nuclei were the vestibular nuclei, the trigeminal tract, the facial nerve and the solitary tract.

Conclusion

Combination of FGATIR and PD/T2w sequences opened prospects to define MS elective injury in brainstem tracts and nuclei, with particular lesion features suggesting variations of the inflammatory process within brainstem structures. In a further study, hypersignal quantification and microstructure information should be evaluated using relaxometry and diffusion tractography. Technical improvements would bring novel parameters to train an artificial neural network for accurate automated labeling of MS lesions within the brainstem.

"Within a minute" detection of focal cortical dysplasia

PURPOSE

To evaluate a MRI postprocessing tool for the enhanced and rapid detection of focal cortical dysplasia (FCD).

METHODS

MP2RAGE sequences of 40 consecutive, so far MRI-negative patients and of 32 healthy controls were morphometrically analyzed to highlight typical FCD features. The resulting morphometric maps served as input for an artificial neural network generating a FCD probability map. The FCD probability map was inversely normalized, co-registered to the MPRAGE2 sequence, and re-transferred into the PACS system. Co-registered images were scrolled through "within a minute" to determine whether a FCD was present or not.

RESULTS

Fifteen FCD, three subcortical band heterotopias (SBH), and one periventricular nodular heterotopia were identified. Of those, four FCD and one SBH were only detected by MRI postprocessing while one FCD and one focal polymicrogryia were missed, respectively. False-positive results occurred in 21 patients and 22 healthy controls. However, true positive cluster volumes were significantly larger than volumes of false-positive clusters (p < 0.001). The area under the curve of the receiver operating curve was 0.851 with a cut-off volume of 0.05 ml best indicating a FCD.

CONCLUSION

Automated MRI postprocessing and presentation of co-registered output maps in the PACS allowed for rapid (i.e., "within a minute") identification of FCDs in our clinical setting. The presence of false-positive findings currently requires a careful comparison of postprocessing results with conventional MR images but may be reduced in the future using a neural network better adapted to MP2RAGE images.

Making the Invisible Visible: Advanced Neuroimaging Techniques in Focal Epilepsy

It has been a clinically important, long-standing challenge to accurately localize epileptogenic focus in drug-resistant focal epilepsy because more intensive intervention to the detected focus, including resection neurosurgery, can provide significant seizure reduction. In addition to neurophysiological examinations, neuroimaging plays a crucial role in the detection of focus by providing morphological and neuroanatomical information. On the other hand, epileptogenic lesions in the brain may sometimes show only subtle or even invisible abnormalities on conventional MRI sequences, and thus, efforts have been made for better visualization and improved detection of the focus lesions. Recent advance in neuroimaging has been attracting attention because of the potentials to better visualize the epileptogenic lesions as well as provide novel information about the pathophysiology of epilepsy. While the progress of newer neuroimaging techniques, including the non-Gaussian diffusion model and arterial spin labeling, could non-invasively detect decreased neurite parameters or hypoperfusion within the focus lesions, advances in analytic technology may also provide usefulness for both focus detection and understanding of epilepsy. There has been an increasing number of clinical and experimental applications of machine learning and network analysis in the field of epilepsy. This review article will shed light on recent advances in neuroimaging for focal epilepsy, including both technical progress of images and newer analytical methodologies and discuss about the potential usefulness in clinical practice.

Localization of the Epileptogenic Zone by Multimodal Neuroimaging and High-Frequency Oscillation

Accurate localization of the epileptogenic zone (EZ) is a key factor to obtain good surgical outcome for refractory epilepsy patients. However, no technique, so far, can precisely locate the EZ, and there are barely any reports on the combined application of multiple technologies to improve the localization accuracy of the EZ. In this study, we aimed to explore the use of a multimodal method combining PET-MRI, fluid and white matter suppression (FLAWS)—a novel MRI sequence, and high-frequency oscillation (HFO) automated analysis to delineate EZ. We retrospectively collected 15 patients with refractory epilepsy who underwent surgery and used the above three methods to detect abnormal brain areas of all patients. We compared the PET-MRI, FLAWS, and HFO results with traditional methods to evaluate their diagnostic value. The sensitivities, specificities of locating the EZ, and marking extent removed versus not removed [RatioChann(ev)] of each method were compared with surgical outcome. We also tested the possibility of using different combinations to locate the EZ. The marked areas in every patient established using each method were also compared to determine the correlations among the three methods. The results showed that PET-MRI, FLAWS, and HFOs can provide more information about potential epileptic areas than traditional methods. When detecting the EZs, the sensitivities of PET-MRI, FLAWS, and HFOs were 68.75, 53.85, and 87.50%, and the specificities were 80.00, 33.33, and 100.00%. The RatioChann(ev) of HFO-marked contacts was significantly higher in patients with good outcome than those with poor outcome (p< 0.05). When intracranial electrodes covered all the abnormal areas indicated by neuroimaging with the overlapping EZs being completely removed referred to HFO analysis, patients could reach seizure-free (p < 0.01). The periphery of the lesion marked by neuroimaging may be epileptic, but not every lesion contributes to seizures. Therefore, approaches in multimodality can detect EZ more accurately, and HFO analysis may help in defining real epileptic areas that may be missed in the neuroimaging results. The implantation of intracranial electrodes guided by non-invasive PET-MRI and FLAWS findings as well as HFO analysis would be an optimized multimodal approach for locating EZ.

Fluid and White Matter Suppression Imaging and Voxel-Based Morphometric Analysis in Conventional Magnetic Resonance Imaging-Negative Epilepsy

Purpose: Delineation of subtle lesions in magnetic resonance imaging (MRI)-negative patients is of great importance in preoperative epilepsy evaluation. The aim of our study was to explore the diagnostic value of the novel fluid and white matter suppression (FLAWS) sequence in comparison with a voxel-based MRI postprocessing morphometric analysis program (MAP) in a consecutive cohort of non-lesional patients.

Methods: Surgical candidates with a negative finding on an official neuroradiology report were enrolled. High-resolution FLAWS image and MAP maps generated based on high-resolution three-dimensional (3D) T1 image were visually inspected for each patient. The findings of FLAWS or MAP-positive (FLAWS/MAP+) regions were compared with the surgical resection cavity in correlation with surgical outcome and pathology.

Results: Forty-five patients were enrolled; the pathological examination revealed focal cortical dysplasia (FCD) in 32 patients and other findings in 13 patients. The positive rate, sensitivity, and specificity were 48.9%, 0.43, and 0.87, respectively, for FLAWS and 64.4%, 0.57, and 0.8, respectively, for MAP. Concordance between surgical resection and FLAWS+ or MAP+ regions was significantly associated with a seizure-free outcome (FLAWS: p = 0.002; MAP: p = 0.0003). A positive finding in FLAWS and MAP together with abnormalities in the same gyrus (FLAWS–MAP gyral+) was detected in 31.1% of patients. FLAWS+ only and MAP+ only were found in 7 (15.5%) and 14 (31.1%) patients, respectively.

Conclusions: FLAWS showed a promising value for identifying subtle epileptogenic lesions and can be used as a complement to current MAP in patients with MRI-negative epilepsy.

Development and evaluation of a manual segmentation protocol for deep grey matter in multiple sclerosis: Towards accelerated semi-automated references

BACKGROUND

Deep grey matter (dGM) structures, particularly the thalamus, are clinically relevant in multiple sclerosis (MS). However, segmentation of dGM in MS is challenging; labeled MS-specific reference sets are needed for objective evaluation and training of new methods.

OBJECTIVES

This study aimed to (i) create a standardized protocol for manual delineations of dGM; (ii) evaluate the reliability of the protocol with multiple raters; and (iii) evaluate the accuracy of a fast-semi-automated segmentation approach (FASTSURF).

METHODS

A standardized manual segmentation protocol for caudate nucleus, putamen, and thalamus was created, and applied by three raters on multi-center 3D T1-weighted MRI scans of 23 MS patients and 12 controls. Intra- and inter-rater agreement was assessed through intra-class correlation coefficient (ICC); spatial overlap through Jaccard Index (JI) and generalized conformity index (CIgen). From sparse delineations, FASTSURF reconstructed full segmentations; accuracy was assessed both volumetrically and spatially.

RESULTS

All structures showed excellent agreement on expert manual outlines: intra-rater JI > 0.83; inter-rater ICC ≥ 0.76 and CIgen ≥ 0.74. FASTSURF reproduced manual references excellently, with ICC ≥ 0.97 and JI ≥ 0.92.

CONCLUSIONS

The manual dGM segmentation protocol showed excellent reproducibility within and between raters. Moreover, combined with FASTSURF a reliable reference set of dGM segmentations can be produced with lower workload.

Automated detection and segmentation of focal cortical dysplasias (FCDs) with artificial intelligence: Presentation of a novel convolutional neural network and its prospective clinical validation

PURPOSE

Focal cortical dysplasias (FCDs) represent one of the most frequent causes of pharmaco-resistant focal epilepsies. Despite improved clinical imaging methods over the past years, FCD detection remains challenging, as FCDs vary in location, size, and shape and commonly blend into surrounding tissues without clear definable boundaries. We developed a novel convolutional neural network for FCD detection and segmentation and validated it prospectively on daily-routine MRIs.

MATERIAL AND METHODS

The neural network was trained on 201 T1 and FLAIR 3 T MRI volume sequences of 158 patients with mainly FCDs, regardless of type, and 7 focal PMG. Non-FCD/PMG MRIs, drawn from 100 normal MRIs and 50 MRIs with non-FCD/PMG pathologies, were added to the training. We applied the algorithm prospectively on 100 consecutive MRIs of patients with focal epilepsy from daily clinical practice. The results were compared with corresponding neuroradiological reports and morphometric MRI analyses evaluated by an experienced epileptologist.

RESULTS

Best training results reached a sensitivity (recall) of 70.1 % and a precision of 54.3 % for detecting FCDs. Applied on the daily-routine MRIs, 7 out of 9 FCDs were detected and segmented correctly with a sensitivity of 77.8 % and a specificity of 5.5 %. The results of conventional visual analyses were 33.3 % and 94.5 %, respectively (3/9 FCDs detected); the results of morphometric analyses with overall epileptologic evaluation were both 100 % (9/9 FCDs detected) and thus served as reference.

CONCLUSION

We developed a 3D convolutional neural network with autoencoder regularization for FCD detection and segmentation. Our algorithm employs the largest FCD training dataset to date with various types of FCDs and some focal PMG. It provided a higher sensitivity in detecting FCDs than conventional visual analyses. Despite its low specificity, the number of false positively predicted lesions per MRI was lower than with morphometric analysis. We consider our algorithm already useful for FCD pre-screening in everyday clinical practice.

An MRI protocol for anatomical and functional evaluation of the California sea lion brain

BACKGROUND

Domoic acid (DOM) is a neurotoxin produced by some harmful algae blooms in coastal waters. California sea lions (Zalophus californianus) exposed to DOM often strand on beaches where they exhibit a variety of symptoms, including seizures. These animals typically show hippocampal atrophy on MRI scans.

NEW METHOD

We describe an MRI protocol for comprehensive evaluation of DOM toxicosis in the sea lion brain. We intend to study brain development in pups exposed in utero. The protocol depicts the hippocampal formation as the primary region of interest. We include scans for quantitative morphometry, functional and structural connectivity, and a cerebral blood flow map.

RESULTS

High-resolution 3D anatomical scans facilitate post hoc slicing in arbitrary planes and accurate morphometry. We demonstrate the first cerebral blood flow map using MRI, and the first structural tractography from a live sea lion brain.

COMPARISON WITH EXISTING METHODS

Scans were compared to prior anatomical and functional studies in live sea lions, and structural connectivity in post mortem specimens. Hippocampal volumes were broadly in line with prior studies, with differences likely attributable to the 3D approach used here. Functional connectivity of the dorsal left hippocampus matched that found in a prior study conducted at a lower magnetic field, while structural connectivity in the live brain agreed with findings observed in post mortem studies.

CONCLUSIONS

Our protocol provides a comprehensive, longitudinal view of the functional and anatomical changes expected to result from DOM toxicosis. It can also screen for other common neurological pathologies and is suitable for any pinniped that can fit inside an MRI scanner.

T1-Based Synthetic Magnetic Resonance Contrasts Improve Multiple Sclerosis and Focal Epilepsy Imaging at 7 T

OBJECTIVES

Ultra-high field magnetic resonance imaging (MRI) (≥7 T) is a unique opportunity to improve the clinical diagnosis of brain pathologies, such as multiple sclerosis or focal epilepsy. However, several shortcomings of 7 T MRI, such as radiofrequency field inhomogeneities, could degrade image quality and hinder radiological interpretation. To address these challenges, an original synthetic MRI method based on T1 mapping achieved with the magnetization-prepared 2 rapid acquisition gradient echo (MP2RAGE) sequence was developed. The radiological quality of on-demand T1-based contrasts generated by this technique was evaluated in multiple sclerosis and focal epilepsy imaging at 7 T.

MATERIALS AND METHODS

This retrospective study was carried out from October 2017 to September 2019 and included 21 patients with different phenotypes of multiple sclerosis and 35 patients with focal epilepsy who underwent MRI brain examinations using a whole-body investigative 7 T magnetic resonance system. The quality of 2 proposed synthetic contrast images were assessed and compared with conventional images acquired at 7 T using the MP2RAGE sequence by 4 radiologists, evaluating 3 qualitative criteria: signal homogeneity, contrast intensity, and lesion visualization. Statistical analyses were performed on reported quality scores using Wilcoxon rank tests and further multiple comparisons tests. Intraobserver and interobserver reliabilities were calculated as well.

RESULTS

Radiological quality scores were reported higher for synthetic images when compared with original images, regardless of contrast, pathologies, or raters considered, with significant differences found for all 3 criteria (P < 0.0001, Wilcoxon rank test). None of the 4 radiologists ever rated a synthetic image "markedly worse" than an original image. Synthetic images were rated slightly less satisfying for only 3 epileptic patients, without precluding lesion identification.

CONCLUSION

T1-based synthetic MRI with the MP2RAGE sequence provided on-demand contrasts and high-quality images to the radiologist, facilitating lesion visualization in multiple sclerosis and focal epilepsy, while reducing the magnetic resonance examination total duration by removing an additional sequence.

Assessment of myelination in infants and young children by T1 relaxation time measurements using the magnetization-prepared 2 rapid acquisition gradient echoes sequence

BACKGROUND

Axonal myelination is an important maturation process in the developing brain. Increasing myelin content correlates with the longitudinal relaxation rate (R1=1/T1) in magnetic resonance imaging (MRI).

OBJECTIVE

By using magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) on a 3-T MRI system, we provide R1 values and myelination rates for infants and young children.

MATERIALS AND METHODS

Average R1 values in white and grey matter regions in 94 children without pathological MRI findings (age range: 3 months to 6 years) were measured and fitted by a saturating-exponential growth model. For comparison, R1 values of 36 children with different brain pathologies are presented. The findings were related to a qualitative evaluation using T2, magnetization-prepared rapid acquisition gradient echo (MP-RAGE) and MP2RAGE.

RESULTS

R1 changes rapidly in the first 16 months of life, then much slower thereafter. R1 is highest in pre-myelinated structures in the youngest subjects, such as the posterior limb of the internal capsule (0.74-0.76±0.04 s^-1) and lowest for the corpus callosum (0.37-0.44±0.03 s^-1). The myelination rate is fastest in the corpus callosum and slowest in the deep grey matter. R1 is decreased in hypo- and dysmyelination disorders. Myelin maturation is clearly visible on MP2RAGE, especially in the first year of life.

CONCLUSION

MP2RAGE permits a quantitative R1 mapping method with an examination time of approximately 6 min. The age-dependent R1 values for children without MRI-identified brain pathologies are well described by a saturating-exponential function with time constants depending on the investigated brain region. This model can serve as a reference for this age group and to search for indications of subtle pathologies. Moreover, the MP2RAGE sequence can also be used for the qualitative assessment of myelinated structures.

High-resolution multi-T1 -weighted contrast and T1 mapping with low B 1 >+ sensitivity using the fluid and white matter suppression (FLAWS) sequence at 7T

PURPOSE

To demonstrate that fluid and white matter suppression (FLAWS) imaging can be used for high-resolution T₁ mapping with low transmitted bias field ( B 1 + ) sensitivity at 7T.

METHODS

The FLAWS sequence was optimized for 0.8-mm isotropic resolution imaging. The theoretical accuracy and precision of the FLAWS T₁ mapping was compared with the one of the magnetization-prepared two rapid gradient echoes (MP2RAGE) sequence optimized for low B 1 + sensitivity. FLAWS images were acquired at 7T on six healthy volunteers (21 to 48 years old; two women). MP2RAGE and saturation-prepared with two rapid gradient echoes (SA2RAGE) datasets were also acquired to obtain T₁ mapping references and B 1 + maps. The contrast-to-noise ratio (CNR) between brain tissues was measured in the FLAWS-hco and MP2RAGE-uni images. The Pearson correlation was measured between the MP2RAGE and FLAWS T₁ maps. The effect of B 1 + on FLAWS T₁ mapping was assessed using the Pearson correlation.

RESULTS

The FLAWS-hco images were characterized by a higher brain tissue CNR ( CNR WM / GM = 5.5 , CNR WM / CSF = 14.7 , CNR GM / CSF = 10.3 ) than the MP2RAGE-uni images ( CNR WM / GM = 4.9 , CNR WM / CSF = 6.6 , CNR GM / CSF = 3.7 ). The theoretical accuracy and precision of the FLAWS T₁ mapping ( acc = 91.9 % ; prec = 90.2 % ) were in agreement with those provided by the MP2RAGE T₁ mapping ( acc = 90.0 % ; prec = 86.8 % ). A good agreement was found between in vivo T₁ values measured with the MP2RAGE and FLAWS sequences (r = 0.91). A weak correlation was found between the FLAWS T₁ map and the B 1 + map within cortical gray matter and white matter segmentations ( r WM = - 0.026 ; r GM = 0.081 ).

CONCLUSION

The results from this study suggest that FLAWS is a good candidate for high-resolution T₁ -weighted imaging and T₁ mapping at the field strength of 7T.

Cerebral artery segmentation based on magnetization-prepared two rapid acquisition gradient echo multi-contrast images in 7 Tesla magnetic resonance imaging

Cerebral artery segmentation plays an important role in the direct visualization of the human brain to obtain vascular system information. On ultra-high field magnetic resonance imaging, cerebral arteries appearing hyperintense on T1 weighted (T1w) images could be segmented from brain tissues such as gray and white matter. In this study, we propose an automated method to segment the cerebral arteries using multi-contrast images including T1w images of a magnetization-prepared two rapid acquisition gradient echo (MP2RAGE) sequence at 7 T. The proposed method, termed MP2rase-CA (MP2rage based RApid SEgmentation Cerebral Artery), employed a seed-based region-growing strategy and Frangi filtering as well as our brain tissue segmentation (MP2rase Brain Tissue). Time-of-flight (TOF) magnetic resonance angiography (MRA) images were obtained as a reference to evaluate the MP2rase-CA. We successfully performed vessel segmentations, from T1w MP2RAGE images, which mostly overlapped with the segmentations of large cerebral arteries from the TOF-MRA. We also investigated the effect of the large cerebral arteries on spatial transformation of anatomical images to standard coordinate space using vessel segmentation by MP2rase-CA. As a result, the T1w image without the cerebral arteries by MP2rase-CA showed better agreement with the standard atlas compared with the T1w image containing the arteries. In addition, voxel-based morphology showed significant differences between T1w images with and without cerebral arteries in brain areas nearby large arteries. Thus, because MP2rase-CA using MP2RAGE images can obtain brain tissue anatomical information as well as relatively large cerebral artery information without need for additional structure acquisition, it is useful and time saving for functional and structural studies.

Image Guidance in Deep Brain Stimulation Surgery to Treat Parkinson's Disease: A Comprehensive Review

Deep brain stimulation (DBS) is an effective therapy as an alternative to pharmaceutical treatments for Parkinson's disease (PD). Aside from factors such as instrumentation, treatment plans, and surgical protocols, the success of the procedure depends heavily on the accurate placement of the electrode within the optimal therapeutic targets while avoiding vital structures that can cause surgical complications and adverse neurologic effects. Although specific surgical techniques for DBS can vary, interventional guidance with medical imaging has greatly contributed to the development, outcomes, and safety of the procedure. With rapid development in novel imaging techniques, computational methods, and surgical navigation software, as well as growing insights into the disease and mechanism of action of DBS, modern image guidance is expected to further enhance the capacity and efficacy of the procedure in treating PD. This article surveys the state-of-the-art techniques in image-guided DBS surgery to treat PD, and discusses their benefits and drawbacks, as well as future directions on the topic.

Use of Multiplied, Added, Subtracted and/or FiTted Inversion Recovery (MASTIR) pulse sequences

The group of Multiplied, Added, Subtracted and/or fiTted Inversion Recovery (MASTIR) pulse sequences in which usually two or more inversion recovery (IR) images of different types are combined is described, and uses for this type of sequence are outlined. IR sequences of different types can be multiplied, added, subtracted, and/or fitted together to produce variants of the MASTIR sequence. The sequences provide a range of options for increasing image contrast, demonstrating specific tissues and fluids of interest, and suppressing unwanted signals. A formalism using the concept of pulse sequences as tissue property filters is used to explain the signal, contrast and weighting of the pulse sequences with both univariate and multivariate filter models. Subtraction of one magnitude reconstructed IR image from another with a shorter TI can produce very high T₁ dependent positive contrast from small increases in T₁. The reverse subtracted IR sequence can provide high positive contrast enhancement with gadolinium chelates and iron deposition which decrease T₁. Additional contrast to that arising from increases in T₁ can be produced by supplementing this with contrast arising from concurrent increases in ρ_m and T₂, as well as increases or decreases in diffusion using subtraction IR with echo subtraction and/or diffusion subtraction. Phase images may show 180º differences as a result of rotating into the transverse plane both positive and negative longitudinal magnetization. Phase images with contrast arising in this way, or other ways, can be multiplied by magnitude IR images to increase the contrast of the latter. Magnetization Transfer (MT) and susceptibility can be used with IR sequences to improve contrast. Selective images of white and brown adipose tissue lipid and water components can be produced using different TIs and in and out-of-phase TEs. Selective images of ultrashort and short T₂ tissue components can be produced by nulling long T₂ tissue components with an inversion pulse and subtraction of images with longer TEs from images with ultrashort TEs. The Double Echo Sliding IR (DESIRE) sequence provides images with a wide range of TIs from which it is possible to choose values of TI to achieve particular types of tissue and/or fluid contrast (e.g., for subtraction with different TIs, as described above, and for long T₂ tissue signal nulling with UTE sequences). Unwanted tissue and fluid signals can be suppressed by addition and subtraction of phase-sensitive (ps) and magnitude reconstructed images. The sequence also offers options for synergistic use of the changes in blood and tissue ρ_m, T₁, T₂/T₂*, D* and perfusion that can be seen with fMRI of the brain. In-vivo and ex-vivo illustrative examples of normal brain, cartilage, multiple sclerosis, Alzheimer's disease, and peripheral nerve imaged with different forms of the MASTIR sequence are included.

Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways

BACKGROUND AND PURPOSE

The brain stem is a complex configuration of small nuclei and pathways for motor, sensory, and autonomic control that are essential for life, yet internal brain stem anatomy is difficult to characterize in living subjects. We hypothesized that the 3D fast gray matter acquisition T1 inversion recovery sequence, which uses a short inversion time to suppress signal from white matter, could improve contrast resolution of brain stem pathways and nuclei with 3T MR imaging.

MATERIALS AND METHODS

After preliminary optimization for contrast resolution, the fast gray matter acquisition T1 inversion recovery sequence was performed in 10 healthy subjects (5 women; mean age, 28.8 ± 4.8 years) with the following parameters: TR/TE/TI = 3000/2.55/410 ms, flip angle = 4°, isotropic resolution = 0.8 mm, with 4 averages (acquired separately and averaged outside k-space to reduce motion; total scan time = 58 minutes). One subject returned for an additional 5-average study that was combined with a previous session to create a highest quality atlas for anatomic assignments. A 1-mm isotropic resolution, 12-minute version, proved successful in a patient with a prior infarct.

RESULTS

The fast gray matter acquisition T1 inversion recovery sequence generated excellent contrast resolution of small brain stem pathways in all 3 planes for all 10 subjects. Several nuclei could be resolved directly by image contrast alone or indirectly located due to bordering visualized structures (eg, locus coeruleus and pedunculopontine nucleus).

CONCLUSIONS

The fast gray matter acquisition T1 inversion recovery sequence has the potential to provide imaging correlates to clinical conditions that affect the brain stem, improve neurosurgical navigation, validate diffusion tractography of the brain stem, and generate a 3D atlas for automatic parcellation of specific brain stem structures.

Test-retest variability of brain morphometry analysis: an investigation of sequence and coil effects

Background

Precise and reliable brain morphometry analysis is critical for clinical and research purposes. The magnetization-prepared rapid gradient echo (MPRAGE), multi-echo MPRAGE (MEMPRAGE) and magnetization-prepared 2 rapid acquisition gradient echo (MP2RAGE) sequences have all been used to acquire brain structural images, but it is unclear which of these sequences is the most suitable for brain morphometry and whether the number of coil channels (20 or 32) affects scan precision. This study aimed to assess the impact of T1-weighted image acquisition variables (sequence and head coil) on the repeatability of resultant automated volumetric measurements.

Methods

Twenty-four healthy volunteers underwent back-to-back scanning protocols with three sequences and two different coils (i.e., six scanning conditions in total) presented in a randomized order in a single session. MorphoBox prototype and FreeSurfer were used for brain segmentation. Brain structures were divided into cortical and subcortical regions for more precise analysis. The acquired volume and thickness values were used to calculate test-retest variability (TRV) values. TRV values from the six different combinations were compared for total brain structures, total cortical structures, total subcortical structures, and every single structure.

Results

The median TRV value for all brain regions was 1.23% with MorphoBox and 3.14% with FreeSurfer. When using FreeSurfer results to compare the six combinations, for total brain structures volume and total cortical structures volume and thickness, the MEMPRAGE-32 channel combination showed significantly lower TRV values than the others (P<0.01). Similar results were observed with MorphoBox. For total subcortical structures, the MP2RAGE-32 channel combination showed the lowest TRV values with both MorphoBox (lower about 0.01% to 0.17%) and FreeSurfer analyses (lower about 0.02% to 0.37%).

Conclusions

TRV values were generally low, indicating generally high reliability for every region. The MEMPRAGE sequence was the most reliable of the three sequences for total brain structures and cortical structures. However, MP2RAGE was the most reliable for subcortical structures. The 32-channel coil showed better repeatability results than the 20-channel coil.

Regional T1 mapping of the whole cervical spinal cord using an optimized MP2RAGE sequence

The recently-proposed MP2RAGE sequence was purposely optimized for cervical spinal cord imaging at 3T. Sequence parameters were chosen to optimize gray/white matter T₁ contrast with sub-millimetric resolution and scan-time < 10 min while preserving reliable T₁ determination with minimal B₁⁺ variation effects within a range of values compatible with pathologies and surrounding structures. Results showed good agreements with IR-based measurements, high MP2RAGE-based T₁ reproducibility and preliminary evidences of age- and tract-related T₁ variations in the healthy spinal cord.

Multi T1-weighted contrast MRI with fluid and white matter suppression at 1.5 T

INTRODUCTION

The fluid and white matter suppression sequence (FLAWS) provides two T1-weighted co-registered datasets: a white matter (WM) suppressed contrast (FLAWS1) and a cerebrospinal fluid (CSF) suppressed contrast (FLAWS2). FLAWS has the potential to improve the contrast of the subcortical brain regions that are important for Deep Brain Stimulation surgery planning. However, to date FLAWS has not been optimized for 1.5 T. In this study, the FLAWS sequence was optimized for use at 1.5 T. In addition, the contrast-enhancement properties of FLAWS image combinations were investigated using two voxel-wise FLAWS combined images: the division (FLAWS-div) and the high contrast (FLAWS-hc) image.

METHODS

FLAWS sequence parameters were optimized for 1.5 T imaging using an approach based on the use of a profit function under constraints for brain tissue signal and contrast maximization. MR experiments were performed on eleven healthy volunteers (age 18-30). Contrast (CN) and contrast to noise ratio (CNR) between brain tissues were measured in each volunteer. Furthermore, a qualitative assessment was performed to ensure that the separation between the internal globus pallidus (GPi) and the external globus pallidus (GPe) is identifiable in FLAWS1.

RESULTS

The optimized set of sequence parameters for FLAWS at 1.5 T provided contrasts similar to those obtained in a previous study at 3 T. The separation between the GPi and the GPe was clearly identified in FLAWS1. The CN of FLAWS-hc was higher than that of FLAWS1 and FLAWS2, but was not different from the CN of FLAWS-div. The CNR of FLAWS-hc was higher than that of FLAWS-div.

CONCLUSION

Both qualitative and quantitative assessments validated the optimization of the FLAWS sequence at 1.5 T. Quantitative assessments also showed that FLAWS-hc provides an enhanced contrast compared to FLAWS1 and FLAWS2, with a higher CNR than FLAWS-div.

Advantages of fluid and white matter suppression (FLAWS) with MP2RAGE compared with double inversion recovery turbo spin echo (DIR-TSE) at 7T

Cerebrospinal fluid (CSF) and white matter (WM) signal suppression techniques allow better visualization of both WM and gray matter (GM) lesions in such disorders as multiple sclerosis and epilepsy. Recently, a technique, FLuid And White matter Suppression "FLAWS", has been proposed at 3 T based on the magnetization-prepared with two rapid gradient echoes (MP2RAGE) sequence. In this study, the FLAWS-MP2RAGE pulse sequence was compared with a double inversion recovery turbo spin echo (DIR-TSE) sequence at 7 T. Twenty-two healthy volunteers were examined. Isotropic spatial resolution of 1 mm and a scan time of approximately 6 min were chosen due to a restricted clinical schedule. Homogeneity of CSF and WM signal suppression was compared with GM signal as an intensity reference. Volumes of GM visualization and specific absorption rates (SARs) were compared using Wilcoxon-rank sum tests with Bonferroni-Holm correction for multiple comparisons. WM-to-GM signal ratios in FLAWS-MP2RAGE images were significantly lower than DIR-TSE (median: 24.5% vs 59.0%, P <  0.0001), whereas CSF-to-GM signal ratios in FLAWS-MP2RAGE were significantly higher than DIR-TSE (57.1% vs 38.3%, P =  0.0001). Ranges of the signal ratios between 20 and 80 percentiles were lower in FLAWS-MP2RAGE than DIR-TSE for WM (24.1% vs 37.2%, P <  0.0001) but were higher in FLAWS-MP2RAGE compared with DIR-TSE for CSF (80.8% vs 63.0%, P =  0.0001). Pixels of low GM signal (< 20% of the median) were mainly distributed at the skull base, and these low signal GM volume ratios were lower in FLAWS-MP2RAGE than DIR-TSE (2.27% vs 6.18%, P <  0.0001). Median SAR in sixteen subjects was 2.5 times higher in DIR-TSE than in FLAWS-MP2RAGE. FLAWS-MP2RAGE showed superior and more homogenous WM signal suppression, better GM visualization at the skull base and lower SAR compared with DIR-TSE, suggesting superiority of FLAWS-MP2RAGE at 7 T.

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

We proposed a method for segmentation of brain tissues-gray matter, white matter, and cerebrospinal fluid-using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FSL, FreeSurfer, and SPM12. The processing time of the proposed method (28 ± 0 s) was significantly shorter than those of FSL and SPM12 (444 ± 4 s and 159 ± 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained using FSL than with those obtained using SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and white matter in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.

Lateral geniculate nucleus volumetry at 3T and 7T: Four different optimized magnetic-resonance-imaging sequences evaluated against a 7T reference acquisition

PURPOSE

The lateral geniculate nucleus (LGN) is an essential nucleus of the visual pathway, occupying a small volume (60-160 mm³) among the other thalamic nuclei. The reported LGN volumes vary greatly across studies due to technical limitations and due to methodological differences of volume assessment. Yet, structural and anatomical alterations in ophthalmologic and neurodegenerative pathologies can only be revealed by a precise and reliable LGN representation. To improve LGN volume assessment, we first implemented a reference acquisition for LGN volume determination with optimized Contrast to Noise Ratio (CNR) and high spatial resolution. Next, we compared CNR efficiency and rating reliability of 3D Magnetization Prepared Rapid Gradient Echo (MPRAGE) images using white matter nulled (WMn) and grey matter nulled (GMn) sequences and its subtraction (WMn-GMn) relative to the clinical standard Proton Density Turbo Spin Echo (PD 2D TSE) and the reference acquisition. We hypothesized that 3D MPRAGE should provide a higher CNR and volume determination accuracy than the currently used 2D sequences.

MATERIALS AND METHODS

In 31 healthy subjects, we obtained at 3 and 7 T the following MR sequences: PD-TSE, MPRAGE with white/grey matter signal nulled (WMn/GMn), and a motion-corrected segmented MPRAGE sequence with a resolution of 0.4 × 0.4 × 0.4 mm³ (reference acquisition). To increase CNR, GMn were subtracted from WMn (WMn-GMn). Four investigators manually segmented the LGN independently.

RESULTS

The reference acquisition provided a very sharp depiction of the LGN and an estimated mean LGN volume of 124 ± 3.3 mm³. WMn-GMn had the highest CNR and gave the most reproducible LGN volume estimations between field strengths. Even with the highest CNR efficiency, PD-TSE gave inconsistent LGN volumes with the weakest reference acquisition correlation. The LGN WM rim induced a significant difference between LGN volumes estimated from WMn and GMn. WMn and GMn LGN volume estimations explained most of the reference acquisition volumes' variance. For all sequences, the volume rating reliability were good. On the other hand, the best CNR rating reliability, LGN volume and CNR correlations with the reference acquisition were obtained with GMn at 7 T.

CONCLUSION

WMn and GMn MPRAGE allow reliable LGN volume determination at both field strengths. The precise location and identification of the LGN (volume) can help to optimize neuroanatomical and neurophysiological studies, which involve the LGN structure. Our optimized imaging protocol may be used for clinical applications aiming at small nuclei volumetric and CNR quantification.

Individualized tractography-based parcellation of the globus pallidus pars interna using 7T MRI in movement disorder patients prior to DBS surgery

The success of deep brain stimulation (DBS) surgeries for the treatment of movement disorders relies on the accurate placement of an electrode within the motor portion of subcortical brain targets. However, the high number of electrodes requiring relocation indicates that today's methods do not ensure sufficient accuracy for all patients. Here, with the goal of aiding DBS targeting, we use 7 Tesla (T) MRI data to identify the functional territories and parcellate the globus pallidus pars interna (GPi) into motor, associative and limbic regions in individual subjects. 7 T MRI scans were performed in seventeen patients (prior to DBS surgery) and one healthy control. Tractography-based parcellation of each patient's GPi was performed. The cortex was divided into four masks representing motor, limbic, associative and "other" regions. Given that no direct connections between the GPi and the cortex have been shown to exist, the parcellation was carried out in two steps: 1) The thalamus was parcellated based on the cortical targets, 2) The GPi was parcellated using the thalamus parcels derived from step 1. Reproducibility, via repeated scans of a healthy subject, and validity of the findings, using different anatomical pathways for parcellation, were assessed. Lastly, post-operative imaging data was used to validate and determine the clinical relevance of the parcellation. The organization of the functional territories of the GPi observed in our individual patient population agrees with that previously reported in the literature: the motor territory was located posterolaterally, followed anteriorly by the associative region, and further antero-ventrally by the limbic territory. While this organizational pattern was observed across patients, there was considerable variability among patients. The organization of the functional territories of the GPi was remarkably reproducible in intra-subject scans. Furthermore, the organizational pattern was observed consistently by performing the parcellation of the GPi via the thalamus and via a different pathway, going through the striatum. Finally, the active therapeutic contact of the DBS electrode, identified with a combination of post-operative imaging and post-surgery DBS programming, overlapped with the high-probability "motor" region of the GPi as defined by imaging-based methods. The consistency, validity, and clinical relevance of our findings have the potential for improving DBS targeting, by increasing patient-specific knowledge of subregions of the GPi to be targeted or avoided, at the stage of surgical planning, and later, at the stage when stimulation is adjusted.

Gray-matter-specific MR imaging improves the detection of epileptogenic zones in focal cortical dysplasia: A new sequence called fluid and white matter suppression (FLAWS)

Objectives

To evaluate the diagnostic value and characteristic features of FCD epileptogenic zones using a novel sequence called fluid and white matter suppression (FLAWS).

Materials and methods

Thirty-nine patients with pathologically confirmed FCD and good surgery outcomes (class I or II, according to the Engel Epilepsy Surgery Outcome Scale) were retrospectively included in the study. All the patients underwent a preoperative whole-brain MRI examination that included conventional sequences (T2WI, T1WI, two-dimensional (2D) axial, coronal fluid-attenuated inversion recovery [FLAIR]) and FLAWS. An additional 3D-FLAIR MRI sequence was performed in 17 patients. To evaluate the sensitivity and specificity of FLAWS and investigate the cause of false-positives, 36 healthy volunteers were recruited as normal controls. Two radiologists evaluated all the image data. The detection rates of the FCD epileptogenic zone on different sequences were compared based on five criteria: abnormal cortical morphology (thickening, thinning, or abnormally deep sulcus); abnormal cortical signal intensity; blurred gray-white matter junction; abnormal signal intensity of the subcortical white matter, and the transmantle sign. The sensitivity and specificity of FLAWS for detecting the FCD lesions were calculated with the reviewers blinded to all the clinical information, i.e. to the patient identity and the location of the resected regions. To explore how many features were sufficient for the diagnosis of the epileptogenic zones, the frequency of each criterion in the resected regions and their combinations were assessed on FLAWS, according to the results of the assessment when the reviewers were aware of the location of the resected regions. Based on the findings of the 17 patients with an additional 3D-FLAIR scan when the reviewers were aware of the location of the resected regions, quantitative analysis of the regions of interest was used to compare the tissue contrast among 2D-axial FLAIR, 3D-FLAIR, and the FLAWS sequence. Visualization score analysis was used to evaluate the visualization of the five features on conventional, 3D-FLAIR, and FLAWS images. Finally, to explore the reason for false-positive results, a further evaluation of the whole brain FLAWS images was conducted for all the subjects.

Results

The sensitivity and specificity for detecting the FCD lesions on the FLAWS sequence were 71.9% and 71.1%, respectively. When the reviewers were blinded to the location of the resected regions, the detection rate of the FLAWS sequence was significantly higher than that of the conventional sequences (P = 0.00). In the 17 patients who underwent an additional 3D FLAIR scan, no statistically significant difference was found between the FLAWS and the 3D-FLAIR (P = 0.25). All the patients had at least two imaging features, one of which was “the blurred junction of the gray-white matter.” The transmantle sign, which is widely believed to be a specific feature of FCD type II, could also be observed in type I on the FLAWS sequence. The relative tissue contrast of FLAWS was higher than that of the 2D-FLAIR with respect to lesion/white matter (WM), deep gray matter (GM)/WM, and cortex/WM (P = 0.00 for all three measures) and higher than that of the 3D-FLAIR with respect to the lesion/WM (P = 0.01). The visualization score analysis showed that the visualization of FLAWS was more enhanced than that of the conventional and 3D-FLAIR images with respect to the blurred junction (P = 0.00 for both comparisons) and the abnormal signal intensity of the subcortical white matter (P = 0.01 for both comparisons). The thin-threadlike signal and individual FCD features outside the epileptogenic regions were considered the primary cause of the false-positive results of FLAWS.

Conclusions

FLAWS can help in the detection of FCD epileptogenic zones. It is recommended that epileptogenic zone on FLAWS be diagnosed based on a combination of two features, one of which should be the “blurred junction of the gray-white matter” in types I and II. In type III, the combination of “the blurred junction of the gray-white matter” with “abnormal signal intensity of subcortical white matter” is recommended.

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FLAWS can help in the detection of FCD epileptogenic zones.

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Diagnosis of FCD lesions should be based on a combination of two features.

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The transmantle sign is not specific for FCD type II on FLAWS.

Brain iron chelation by deferiprone in a phase 2 randomised double-blinded placebo controlled clinical trial in Parkinson's disease

Parkinson's disease (PD) is associated with increased iron levels in the substantia nigra (SNc). This study evaluated whether the iron chelator, deferiprone, is well tolerated, able to chelate iron from various brain regions and improve PD symptomology. In a randomised double-blind, placebo controlled trial, 22 early onset PD patients, were administered deferiprone, 10 or 15 mg/kg BID or placebo, for 6 months. Patients were evaluated for PD severity, cognitive function, depression rating and quality of life. Iron concentrations were assessed in the substantia nigra (SNc), dentate and caudate nucleus, red nucleus, putamen and globus pallidus by T2* MRI at baseline and after 3 and 6 months of treatment. Deferiprone therapy was well tolerated and was associated with a reduced dentate and caudate nucleus iron content compared to placebo. Reductions in iron content of the SNc occurred in only 3 patients, with no changes being detected in the putamen or globus pallidus. Although 30 mg/kg deferiprone treated patients showed a trend for improvement in motor-UPDRS scores and quality of life, this did not reach significance. Cognitive function and mood were not adversely affected by deferiprone therapy. Such data supports more extensive clinical trials into the potential benefits of iron chelation in PD.

Convection-enhanced delivery improves MRI visualization of basal ganglia for stereotactic surgery

OBJECTIVE Stereotactic deep brain stimulation surgery is most commonly performed while patients are awake. This allows for intraoperative clinical assessment and electrophysiological target verification, thereby promoting favorable outcomes with few side effects. Intraoperative CT and MRI have challenged this concept of clinical treatment validation. Image-guided surgery is capable of delivering electrodes precisely to a planned, stereotactic target; however, these methods can be limited by low anatomical resolution even with sophisticated MRI modalities. The authors are developing a novel method using convection-enhanced delivery to safely manipulate the extracellular space surrounding common anatomical targets for surgery. By altering the extracellular content of deep subcortical structures and their associated white matter tracts, the MRI visualization of the basal ganglia can be improved to better define the anatomy. This technique could greatly improve the accuracy and success of stereotactic surgery, potentially eliminating the reliance on awake surgery. METHODS Observations were made in the clinical setting where vasogenic and cytotoxic edema improved the MRI visualization of the basal ganglia. These findings were replicated in the experimental setting using an FDA-approved intracerebral catheter that was stereotactically inserted into the thalamus or basal ganglia of 7 swine. Five swine were infused with normal saline, and 2 were infused with autologous CSF. Flow rates varied between 1 μl/min to 6 μl/min to achieve convective distributions. Concurrent MRI was performed at 15-minute intervals to monitor the volume of infusion and observe the imaging changes of the deep subcortical structures. The animals were then clinically observed, and necropsy was performed within 48 hours, 1 week, or 1 month for histological analysis. RESULTS In all animals, the white matter tracts became hyperintense on T2-weighted imaging as compared with basal ganglia nuclei, enabling better definition of the deep brain anatomy. The volume of distribution and infusion (Vd/Vi ratio) ranged from 2.5 to 4.5. There were no observed clinical effects from the infusions. Histological analysis demonstrated mild neuronal effects from saline infusions but no effects from CSF infusions. CONCLUSIONS This work provides the initial foundation for a novel approach to improve the visualization of deep brain anatomy during MRI-guided, stereotactic procedures. Convective infusions of CSF alter the extracellular fluid content of the brain for improved MRI without evidence of clinical or toxic effects.

Altered PDE10A expression detectable early before symptomatic onset in Huntington's disease

There is an urgent need for early biomarkers and novel disease-modifying therapies in Huntington's disease. Huntington's disease pathology involves the toxic effect of mutant huntingtin primarily in striatal medium spiny neurons, which highly express phosphodiesterase 10A (PDE10A). PDE10A hydrolyses cAMP/cGMP signalling cascades, thus having a key role in the regulation of striatal output, and in promoting neuronal survival. PDE10A could be a key therapeutic target in Huntington's disease. Here, we used combined positron emission tomography (PET) and multimodal magnetic resonance imaging to assess PDE10A expression in vivo in a unique cohort of 12 early premanifest Huntington's disease gene carriers with a mean estimated 90% probability of 25 years before the predicted onset of clinical symptoms. We show bidirectional changes in PDE10A expression in premanifest Huntington's disease gene carriers, which are associated with the probability of symptomatic onset. PDE10A expression in early premanifest Huntington's disease was decreased in striatum and pallidum and increased in motor thalamic nuclei, compared to a group of matched healthy controls. Connectivity-based analysis revealed prominent PDE10A decreases confined in the sensorimotor-striatum and in striatonigral and striatopallidal projecting segments. The ratio between higher PDE10A expression in motor thalamic nuclei and lower PDE10A expression in striatopallidal projecting striatum was the strongest correlate with higher probability of symptomatic conversion in early premanifest Huntington's disease gene carriers. Our findings demonstrate in vivo, a novel and earliest pathophysiological mechanism underlying Huntington's disease with direct implications for the development of new pharmacological treatments, which can promote neuronal survival and improve outcome in Huntington's disease gene carriers.

Loss of phosphodiesterase 10A expression is associated with progression and severity in Parkinson's disease

The mechanisms underlying neurodegeneration and loss of dopaminergic signalling in Parkinson's disease are still only partially understood. Phosphodiesterase 10A (PDE10A) is a basal ganglia expressed dual substrate enzyme, which regulates cAMP and cGMP signalling cascades, thus having a key role in the regulation of dopaminergic signalling in striatal pathways, and in promoting neuronal survival. This study aimed to assess in vivo the availability of PDE10A in patients with Parkinson's disease using positron emission tomography molecular imaging with (11)C-IMA107, a highly selective PDE10A radioligand. We studied 24 patients with levodopa-treated, moderate to advanced Parkinson's disease. Their positron emission tomography imaging data were compared to those from a group of 12 healthy controls. Parametric images of (11)C-IMA107 binding potential relative to non-displaceable binding (BPND) were generated from the dynamic (11)C-IMA107 scans using the simplified reference tissue model with the cerebellum as the reference tissue. Corresponding region of interest analysis showed lower mean (11)C-IMA107 BPND in the caudate (P < 0.001), putamen (P < 0.001) and globus pallidus (P = 0.025) in patients with Parkinson's disease compared to healthy controls, which was confirmed with voxel-based analysis. Longer Parkinson's duration correlated with lower (11)C-IMA107 BPND in the caudate (r = -0.65; P = 0.005), putamen (r = -0.51; P = 0.025), and globus pallidus (r = -0.47; P = 0.030). Higher Unified Parkinson's Disease Rating Scale part-III motor scores correlated with lower (11)C-IMA107 BPND in the caudate (r = -0.54; P = 0.011), putamen (r = -0.48; P = 0.022), and globus pallidus (r = -0.70; P < 0.001). Higher Unified Dyskinesia Rating Scale scores in those Parkinson's disease with levodopa-induced dyskinesias (n = 12), correlated with lower (11)C-IMA107 BPND in the caudate (r = -0.73; P = 0.031) and putamen (r = -0.74; P = 0.031). Our findings demonstrate striatal and pallidal loss of PDE10A expression, which is associated with Parkinson's duration and severity of motor symptoms and complications. PDE10A is an enzyme that could be targeted with novel pharmacotherapy, and this may help improve dopaminergic signalling and striatal output, and therefore alleviate symptoms and complications of Parkinson's disease.

State-of-the-art MRI techniques in neuroradiology: principles, pitfalls, and clinical applications

This article reviews the most relevant state-of-the-art magnetic resonance (MR) techniques, which are clinically available to investigate brain diseases. MR acquisition techniques addressed include notably diffusion imaging (diffusion-weighted imaging (DWI), diffusion tensor imaging (DTI), and diffusion kurtosis imaging (DKI)) as well as perfusion imaging (dynamic susceptibility contrast (DSC), arterial spin labeling (ASL), and dynamic contrast enhanced (DCE)). The underlying models used to process these images are described, as well as the theoretic underpinnings of quantitative diffusion and perfusion MR imaging-based methods. The technical requirements and how they may help to understand, classify, or follow-up neurological pathologies are briefly summarized. Techniques, principles, advantages but also intrinsic limitations, typical artifacts, and alternative solutions developed to overcome them are discussed. In this article, we also review routinely available three-dimensional (3D) techniques in neuro MRI, including state-of-the-art and emerging angiography sequences, and briefly introduce more recently proposed 3D quantitative neuro-anatomy sequences, and new technology, such as multi-slice and multi-transmit imaging.

Contrast enhancement by combining T1- and T2-weighted structural brain MR Images

PURPOSE

In order to more precisely differentiate cerebral structures in neuroimaging studies, a novel technique for enhancing the tissue contrast based on a combination of T1-weighted (T1w) and T2-weighted (T2w) MRI images was developed.

METHODS

The combined image (CI) was calculated as CI = (T1w - sT2w)/(T1w + sT2w), where sT2w is the scaled T2-weighted image. The scaling factor was calculated to adjust the gray- matter (GM) voxel intensities in the T2w image so that their median value equaled that of the GM voxel intensities in the T1w image. The image intensity homogeneity within a tissue and the discriminability between tissues in the CI versus the separate T1w and T2w images were evaluated using the segmentation by the FMRIB Software Library (FSL) and FreeSurfer (Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital, Boston, MA) software.

RESULTS

The combined image significantly improved homogeneity in the white matter (WM) and GM compared to the T1w images alone. The discriminability between WM and GM also improved significantly by applying the CI approach. Significant enhancements to the homogeneity and discriminability also were achieved in most subcortical nuclei tested, with the exception of the amygdala and the thalamus.

CONCLUSION

The tissue discriminability enhancement offered by the CI potentially enables more accurate neuromorphometric analyses of brain structures.

In vivo imaging of cerebral dopamine D3 receptors in alcoholism

Animal studies support the role of the dopamine D3 receptor (DRD3) in alcohol reinforcement or liking. Sustained voluntary alcohol drinking in rats has been associated with an upregulation of striatal DRD3 gene expression and selective blockade of DRD3 reduces ethanol preference, consumption, and cue-induced reinstatement. In vivo measurement of DRD3 in the living human brain has not been possible until recently owing to a lack of suitable tools. In this study, DRD3 status was assessed for the first time in human alcohol addiction. Brain DRD3 availability was compared between 16 male abstinent alcohol-dependent patients and 13 healthy non-dependent age-matched males using the DRD3-preferring agonist positron emission tomography (PET) radioligand [(11)C]PHNO with and without blockade with a selective DRD3 antagonist (GSK598809 60 mg p.o.). In striatal regions of interest, where the [(11)C]PHNO PET signal represents primarily DRD2 binding, no differences were seen in [(11)C]PHNO binding between the groups at baseline. However, baseline [(11)C]PHNO binding was higher in alcohol-dependent patients in hypothalamus (VT: 16.5 ± 4 vs 13.7 ± 2.9, p = 0.040), a region in which the [(11)C]PHNO signal almost entirely reflects DRD3 availability. The reductions in regional receptor binding (VT) following a single oral dose of GSK598809 (60 mg) were consistent with those observed in previous studies across all regions. There were no differences in regional changes in VT following DRD3 blockade between the two groups, indicating that the regional fractions of DRD3 are similar in the two groups, and the increased [(11)C]PHNO binding in the hypothalamus in alcohol-dependent patients is explained by elevated DRD3 in this group. Although we found no difference between alcohol-dependent patients and controls in striatal DRD3 levels, increased DRD3 binding in the hypothalamus of alcohol-dependent patients was observed. This may be relevant to the development of future therapeutic strategies to treat alcohol abuse.

Quantitative comparison of cortical surface reconstructions from MP2RAGE and multi-echo MPRAGE data at 3 and 7 T

The Magnetization-Prepared 2 Rapid Acquisition Gradient Echo (MP2RAGE) method achieves spatially uniform contrast across the entire brain between gray matter and surrounding white matter tissue and cerebrospinal fluid by rapidly acquiring data at two points during an inversion recovery, and then combining the two volumes so as to cancel out sources of intensity and contrast bias, making it useful for neuroimaging studies at ultrahigh field strengths (≥7T). To quantify the effectiveness of the MP2RAGE method for quantitative morphometric neuroimaging, we performed tissue segmentation and cerebral cortical surface reconstruction of the MP2RAGE data and compared the results with those generated from conventional multi-echo MPRAGE (MEMPRAGE) data across a group of healthy subjects. To do so, we developed a preprocessing scheme for the MP2RAGE image data to allow for automatic cortical segmentation and surface reconstruction using FreeSurfer and analysis methods to compare the positioning of the surface meshes. Using image volumes with 1mm isotropic voxels we found a scan-rescan reproducibility of cortical thickness estimates to be 0.15 mm (or 6%) for the MEMPRAGE data and a slightly lower reproducibility of 0.19 mm (or 8%) for the MP2RAGE data. We also found that the thickness estimates were systematically smaller in the MP2RAGE data, and that both the interior and exterior cortical boundaries estimated from the MP2RAGE data were consistently positioned within the corresponding boundaries estimated from the MEMPRAGE data. Therefore several measureable differences exist in the appearance of cortical gray matter and its effect on automatic segmentation methods that must be considered when choosing an acquisition or segmentation method for studies requiring cortical surface reconstructions. We propose potential extensions to the MP2RAGE method that may help to reduce or eliminate these discrepancies.

Visualization of intra-thalamic nuclei with optimized white-matter-nulled MPRAGE at 7T

Novel MR image acquisition strategies have been investigated to elicit contrast within the thalamus, but direct visualization of individual thalamic nuclei remains a challenge because of their small size and the low intrinsic contrast between adjacent nuclei. We present a step-by-step specific optimization of the 3D MPRAGE pulse sequence at 7T to visualize the intra-thalamic nuclei. We first measured T1 values within different sub-regions of the thalamus at 7T in 5 individuals. We used these to perform simulations and sequential experimental measurements (n=17) to tune the parameters of the MPRAGE sequence. The optimal set of parameters was used to collect high-quality data in 6 additional volunteers. Delineation of thalamic nuclei was performed twice by one rater and MR-defined nuclei were compared to the classic Morel histological atlas. T1 values within the thalamus ranged from 1400ms to 1800ms for adjacent nuclei. Using these values for theoretical evaluations combined with in vivo measurements, we showed that a short inversion time (TI) close to the white matter null regime (TI=670ms) enhanced the contrast between the thalamus and the surrounding tissues, and best revealed intra-thalamic contrast. At this particular nulling regime, lengthening the time between successive inversion pulses (TS=6000ms) increased the thalamic signal and contrast and lengthening the α pulse train time (N*TR) further increased the thalamic signal. Finally, a low flip angle during the gradient echo acquisition (α=4°) was observed to mitigate the blur induced by the evolution of the magnetization along the α pulse train. This optimized set of parameters enabled the 3D delineation of 15 substructures in all 6 individuals; these substructures corresponded well with the known anatomical structures of the thalamus based on the classic Morel atlas. The mean Euclidean distance between the centers of mass of MR- and Morel atlas-defined nuclei was 2.67mm (±1.02mm). The reproducibility of the MR-defined nuclei was excellent with intraclass correlation coefficient measured at 0.997 and a mean Euclidean distance between corresponding centers of mass found at first versus second readings of 0.69mm (±0.38mm). This 7T strategy paves the way to better identification of thalamic nuclei for neurosurgical planning and investigation of regional changes in neurological disorders.

New developments and applications of the MP2RAGE sequence--focusing the contrast and high spatial resolution R1 mapping

MR structural T1-weighted imaging using high field systems (>3T) is severely hampered by the existing large transmit field inhomogeneities. New sequences have been developed to better cope with such nuisances. In this work we show the potential of a recently proposed sequence, the MP2RAGE, to obtain improved grey white matter contrast with respect to conventional T1-w protocols, allowing for a better visualization of thalamic nuclei and different white matter bundles in the brain stem. Furthermore, the possibility to obtain high spatial resolution (0.65 mm isotropic) R₁ maps fully independent of the transmit field inhomogeneities in clinical acceptable time is demonstrated. In this high resolution R₁ maps it was possible to clearly observe varying properties of cortical grey matter throughout the cortex and observe different hippocampus fields with variations of intensity that correlate with known myelin concentration variations.