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Ralf Deichmann

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26 papers
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26

YNIMG Journal 2020 Journal Article

How stable is quantitative MRI? – Assessment of intra- and inter-scanner-model reproducibility using identical acquisition sequences and data analysis programs

  • René-Maxime Gracien
  • Michelle Maiworm
  • Nadine Brüche
  • Manoj Shrestha
  • Ulrike Nöth
  • Elke Hattingen
  • Marlies Wagner
  • Ralf Deichmann

Background Quantitative MRI (qMRI) techniques allow assessing cerebral tissue properties. However, previous studies on the accuracy of quantitative T1 and T2 mapping reported a scanner model bias of up to 10% for T1 and up to 23% for T2. Such differences would render multi-centre qMRI studies difficult and raise fundamental questions about the general precision of qMRI. A problem in previous studies was that different methods were used for qMRI parameter mapping or for measuring the transmitted radio frequency field B1 which is critical for qMRI techniques requiring corrections for B1 non-uniformities. Aims The goal was to assess the intra- and inter-scanner reproducibility of qMRI data at 3 ​T, using two different scanner models from the same vendor with exactly the same multiparametric acquisition protocol. Methods Proton density (PD), T1, T2* and T2 mapping was performed on healthy subjects and on a phantom, performing each measurement twice for each of two scanner models. Although the scanners had different hardware and software versions, identical imaging sequences were used for PD, T1 and T2* mapping, adapting the codes of an existing protocol on the older system line by line to match the software version of the newer scanner. For T2-mapping, the respective manufacturer’s sequence was used which depended on the software version. However, system-dependent corrections were carried out in this case. Reproducibility was assessed by average values in regions of interest. Results Mean scan-rescan variations were not exceeding 2. 14%, with average values of 1. 23% and 1. 56% for the new and old system, respectively. Inter-scanner model deviations were not exceeding 5. 21% with average values of about 2. 2–3. 8% for PD, 2. 5–3. 0% for T2*, 1. 6–3. 1% for T1 and 3. 3–5. 2% for T2. Conclusions Provided that identical acquisition sequences are used, discrepancies between qMRI data acquired with different scanner models are low. The level of systematic differences reported in this work may help to interpret multi-centre data.

YNICL Journal 2017 Journal Article

Longitudinal changes of cortical microstructure in Parkinson's disease assessed with T1 relaxometry

  • Lucas Nürnberger
  • René-Maxime Gracien
  • Pavel Hok
  • Stephanie-Michelle Hof
  • Udo Rüb
  • Helmuth Steinmetz
  • Rüdiger Hilker
  • Johannes C. Klein

BACKGROUND: Histological evidence suggests that pathology in Parkinson's disease (PD) goes beyond nigrostriatal degeneration and also affects the cerebral cortex. Quantitative MRI (qMRI) techniques allow the assessment of changes in brain tissue composition. However, the development and pattern of disease-related cortical changes have not yet been demonstrated in PD with qMRI methods. The aim of this study was to investigate longitudinal cortical microstructural changes in PD with quantitative T1 relaxometry. METHODS: 13 patients with mild to moderate PD and 20 matched healthy subjects underwent high resolution T1 mapping at two time points with an interval of 6.4 years (healthy subjects: 6.5 years). Data from two healthy subjects had to be excluded due to MRI artifacts. Surface-based analysis of cortical T1 values was performed with the FreeSurfer toolbox. RESULTS: = 0.007). CONCLUSIONS: In patients with PD, the development of widespread changes in cortical microstructure was observed as reflected by a reduction of cortical T1. The pattern of T1 decrease in PD patients exceeded the normal T1 decrease as found in physiological aging and showed considerable overlap with the pattern of cortical thinning demonstrated in previous PD studies. Therefore, cortical T1 might be a promising additional imaging marker for future longitudinal PD studies. The biological mechanisms underlying cortical T1 reductions remain to be further elucidated.

YNIMG Journal 2017 Journal Article

Quantitative in vivo T2 mapping using fast spin echo techniques – A linear correction procedure

  • Ulrike Nöth
  • Manoj Shrestha
  • Jan-Rüdiger Schüre
  • Ralf Deichmann

A method is presented for correcting the effects of stimulated and indirect echoes on quantitative T2 mapping data acquired with multiple spin echo techniques, such as turbo spin echo. In contrast to similar correction techniques proposed in the literature, the method does not require a priori knowledge of the radio frequency (RF) pulse profiles. In a first step, for the T2 mapping protocol under investigation, signal decay curves S(TE) are simulated for a range of different RF pulse profiles. The actual signal decay S(TE) is then measured on a phantom with known T2, so the approximate RF pulse profiles can be derived via comparison with the simulated decay curves. In a second step, with the RF pulses obtained from step one, signal decay curves S(TE) are simulated for different T2 values and fitted mono-exponentially, thus allowing to deduce the relationship between true T2 and the apparent T2 (T2app) values. Results show that this relationship is approximately linear, allowing for a direct correction of T2app maps. If the amplitude of the transmitted RF field (B1) does not exceed the nominal value by more than 10%, it is shown that a B1-independent correction of T2app maps yields sufficiently accurate results for T2. A B1-dependent version is also presented. The method is tested in vitro on a phantom with different T2 values and in vivo on healthy subjects.

YNIMG Journal 2015 Journal Article

A human post-mortem brain model for the standardization of multi-centre MRI studies

  • Amgad Droby
  • Carsten Lukas
  • Anne Schänzer
  • Isabella Spiwoks-Becker
  • Antonio Giorgio
  • Ralf Gold
  • Nicola De Stefano
  • Harald Kugel

Multi-centre MRI studies of the brain are essential for enrolling large and diverse patient cohorts, as required for the investigation of heterogeneous neurological and psychiatric diseases. However, the multi-site comparison of standard MRI data sets that are weighted with respect to tissue parameters such as the relaxation times (T1, T2) and proton density (PD) may be problematic, as signal intensities and image contrasts depend on site-specific details such as the sequences used, imaging parameters, and sensitivity profiles of the radiofrequency (RF) coils. Water or gel phantoms are frequently used for long-term and/or inter-site quality assessment. However, these phantoms hardly mimic the structure, shape, size or tissue distribution of the human brain. The goals of this study were: (1) to validate the long-term stability of a human post-mortem brain phantom, performing quantitative mapping of T1, T2, and PD, and the magnetization transfer ratio (MTR) over a period of 18months; (2) to acquire and analyse data for this phantom and the brain of a healthy control (HC) in a multi-centre study for MRI protocol standardization in four centres, while conducting a voxel-wise as well as whole brain grey (GM) and white matter (WM) tissue volume comparison. MTR, T2, and the quotient of PD in WM and GM were stable in the post-mortem brain with no significant changes. T1 was found to decrease from 267/236ms (GM/WM) to 234/216ms between 5 and 17weeks post embedment, stabilizing during an 18-month period following the first scan at about 215/190ms. The volumetric measures, based on T1-weighted MP-RAGE images obtained at all participating centres, revealed inter- and intra-centre variations in the evaluated GM and WM volumes that displayed similar trends in both the post-mortem brain as well as the HC. At a confidence level of 95%, brain regions such as the brainstem, deep GM structures as well as boundaries between GM and WM tissues were found to be less reproducible than other brain regions in all participating centres. The results demonstrate that a post-mortem brain phantom may be used as a reliable tool for multi-centre MR studies.

YNIMG Journal 2014 Journal Article

An improved method for retrospective motion correction in quantitative T2* mapping

  • Ulrike Nöth
  • Steffen Volz
  • Elke Hattingen
  • Ralf Deichmann

A new method for motion correction of T2*-weighted data and resulting quantitative T2* maps is presented. For this method, additional data sets with a reduced number of phase encoding steps covering the k-space centre are acquired. Motion correction is based on a 3-step procedure: (1) calculation of improved input data sets with reduced artefact levels from the original data, (2) creation of a target data set free of movement artefacts on the basis of the improved input data sets, and (3) fitting of original data to the target data set, yielding an optimum combination of acquired k-space data which suppresses lines affected by movement. The method was tested on healthy subjects performing pre-trained movement. Motion correction was successful unless the same k-space line was affected by movement in all data sets acquired on a specific subject. The method was applied to patients suffering from subarachnoid haemorrhage (group 1) or tumours (group 2) with accompanying edema in the brain. Motion correction improved the interpretability of T2*-weighted patient data and resulting quantitative T2* maps considerably by allowing a clear delineation between ventricle and edema and a clear localisation of haemorrhage (group 1) or a clear delineation of tumour accompanying edema (group 2) which was not possible in data affected by movement.

YNIMG Journal 2012 Journal Article

Acupuncture — Deep pain with an autonomic dimension?

  • Florian Beissner
  • Ralf Deichmann
  • Christian Henke
  • Karl-Jürgen Bär

Stimulation of acupuncture point Pc6, located above the median nerve, has been shown to be effective in treating nausea and vomiting. It has also frequently been reported to cause a heart rate reduction. The mechanism behind this autonomic reaction has not been clarified, so far. We combined brainstem-sensitive functional magnetic resonance imaging with heart rate recording and time-resolved rating of the needling sensation to measure neuronal correlates of sensations and autonomic reactions during acupuncture. On the cortical level, needling sensation activated typical pain-related areas, of which the ventromedial and dorsolateral prefrontal cortex and perigenual anterior cingulate cortex were further involved in mediating the heart rate response. In the brainstem, needling sensation activated nuclei of the descending pain control system, in which a network of hypothalamus, periaqueductal gray, rostral ventromedial medulla, and ventrolateral medulla was identified as the source of the heart rate changes. Our findings indicate that acupuncture may be a special pain stimulus, whose autonomic concomitants could explain its non-analgesic effects and in some cases even have a therapeutic potential.

YNIMG Journal 2012 Journal Article

Quantitative proton density mapping: correcting the receiver sensitivity bias via pseudo proton densities

  • Steffen Volz
  • Ulrike Nöth
  • Alina Jurcoane
  • Ulf Ziemann
  • Elke Hattingen
  • Ralf Deichmann

Most methods for mapping proton densities (PD) in brain tissue are based on measuring all parameters influencing the signal intensity with subsequent elimination of any weighting not related to PD. This requires knowledge of the receiver coil sensitivity profile (RP), the measurement of which can be problematic. Recently, a method for compensating the influence of RP non-uniformities on PD data at a field strength of 3T was proposed, based on bias field correction of spoiled gradient echo image data to remove the low spatial frequency bias imposed by RP variations from uncorrected PD maps. The purpose of the current study was to present and test an independent method, based on the well-known linear relationship between the longitudinal relaxation rate R1 and 1/PD in brain tissue. For healthy subjects, RP maps obtained with this method and the resulting PD maps are very similar to maps based on bias field correction, and quantitative PD values acquired with the new independent method are in very good agreement with literature values. Furthermore, both methods for PD mapping are compared in the presence of several pathologies (multiple sclerosis, stroke, meningioma, recurrent glioblastoma).

YNIMG Journal 2012 Journal Article

Vascular component analysis of hyperoxic and hypercapnic BOLD contrast

  • Christian Schwarzbauer
  • Ralf Deichmann

Hyperoxia or hypercapnia provides a useful experimental tool to systematically alter the blood oxygenation level dependent (BOLD) contrast. Typical applications include calibrated functional magnetic resonance imaging (fMRI), BOLD sensitivity mapping, vessel size imaging or cerebrovascular reactivity mapping. This article describes a novel biophysical model of hyperoxic and hypercapnic BOLD contrast, which accounts for the magnetic susceptibility effects of molecular oxygen that is dissolved in blood and tissue, in addition to the well-established effects caused by the paramagnetic properties of deoxyhaemoglobin. Furthermore, the concept of vascular component analysis (VCA) is introduced and is shown to provide a computationally efficient tool for investigating the vascular specificity of hyperoxic and hypercapnic BOLD contrast. A theoretical investigation of gradient and spin echo BOLD contrast based on computer simulations was performed to compare three different conditions (hypercapnia induced by breathing 6% CO2, hyperoxia induced by breathing 100% O2, and simultaneous hypercapnia and hyperoxia induced by breathing carbogen, i. e. 5% CO2 in 95% CO2) with baseline (breathing air). Simulations were carried out for different levels of metabolic oxygen extraction fraction (OEF) ranging from 0 to 0. 5. The key findings can be summarised as follows: (i) for hyperoxia the susceptibility of dissolved O2 may lead to a significant arterial BOLD contrast; (ii) under normoxic conditions the susceptibility of dissolved O2 is negligible; (iii) an almost complete loss of BOLD sensitivity may occur at lower OEF values in all parts of the vascular tree, whereas hyperoxic BOLD sensitivity is largely maintained; (iv) under hyperoxic conditions, a transition from positive to negative BOLD contrast occurs with decreasing OEF values. These findings have important implications for experimental applications of hyperoxic and hypercapnic BOLD contrast and may enable new clinical applications in ischemic stroke and other forms of acquired brain injury.

YNIMG Journal 2011 Journal Article

fMRI of the brainstem using dual-echo EPI

  • Florian Beissner
  • Ralf Deichmann
  • Simon Baudrexel

The brainstem is the part of the human brain that plays a pivotal role in the maintenance of many critical body functions. Due to the elevated level of cardiogenic noise, few fMRI studies have investigated the brainstem so far. Cardiac-gated echo-planar imaging with acquisition of two echoes per excitation (dual-echo EPI) is one method that significantly reduces cardiogenic noise and, thus, allows for fMRI measurements of the brainstem. As information on optimal preprocessing approaches for brainstem-fMRI data is still scarce, the goal of this study was to compare different combinations of normalization and smoothing procedures as implemented in standard fMRI software packages and to identify the combinations yielding optimal results for dual-echo EPI. 21 healthy subjects were measured while executing a simple motor paradigm to activate the facial and trigeminal motor nucleus in the brainstem. After motion correction and calculation of T2*-maps the data were preprocessed with 24 combinations of standard normalization (SPM classic, SPM unified, FSL, ABC) and smoothing procedures (pre-/post-smoothing with 3mm-, 4. 5mm- and 6mm-kernel) before undergoing first- and second-level statistical analysis. Activation results were compared for first-level and second-level statistics using two anatomically defined regions of interest. Five methods were found to be sensitive for activation of both nuclei. These included FSL normalization with 3mm and 4. 5mm pre-smoothing as well as 3mm post-smoothing, SPM unified normalization with 3mm pre-smoothing and ABC normalization with 4. 5mm pre-smoothing. All these methods can be recommended for normalization and smoothing when analyzing fMRI data of the brainstem acquired by cardiac-gated dual-echo EPI.

YNIMG Journal 2011 Journal Article

Resting state fMRI reveals increased subthalamic nucleus–motor cortex connectivity in Parkinson's disease

  • Simon Baudrexel
  • Torsten Witte
  • Carola Seifried
  • Frederic von Wegner
  • Florian Beissner
  • Johannes C. Klein
  • Helmuth Steinmetz
  • Ralf Deichmann

Parkinson's disease (PD) is associated with abnormal hypersynchronicity in basal ganglia-thalamo-cortical loops. The clinical effectiveness of subthalamic nucleus (STN) high frequency stimulation indicates a crucial role of this nucleus within the affected motor networks in PD. Here we investigate alterations in the functional connectivity (FC) profile of the STN using resting state BOLD correlations on a voxel-by-voxel basis in functional magnetic resonance imaging (fMRI). We compared early stage PD patients (n=31) during the medication-off state with healthy controls (n=44). The analysis revealed increased FC between the STN and cortical motor areas (BA 4 and 6) in PD patients in accordance with electrophysiological studies. Moreover, FC analysis of the primary motor cortex (M1) hand area revealed that the FC increase was primarily found in the STN area within the basal ganglia. These findings are in good agreement with recent experimental data, suggesting that an increased STN–motor cortex synchronicity mediated via the so called hyperdirect motor cortex–subthalamic pathway might play a fundamental role in the pathophysiology of PD. An additional subgroup analysis was performed according to the presence (n=16) or absence (n=15) of tremor in patients. Compared to healthy controls tremor patients showed increased STN FC specifically in the hand area of M1 and the primary sensory cortex. In non-tremor patients, increased FC values were also found between the STN and midline cortical motor areas including the SMA. Taken together our results underline the importance of the STN as a key node for the modulation of BG-cortical motor network activity in PD patients.

YNIMG Journal 2010 Journal Article

A fast B1-mapping method for the correction and normalization of magnetization transfer ratio maps at 3 T

  • Steffen Volz
  • Ulrike Nöth
  • Anna Rotarska-Jagiela
  • Ralf Deichmann

In neuroimaging, there is increasing interest in magnetization transfer (MT) techniques which yield information about bound water protons. One of the main applications is the investigation of the myelin integrity in the central nervous system (CNS). However, several problems may arise, in particular at high magnetic field strengths: B1 inhomogeneities may yield deviations of the MT saturation angle and thus non-uniformities of the measured MT ratio (MTR). This effect can be corrected for but requires in general additional time consuming B1 mapping. Furthermore, increased values of the specific absorption rate (SAR) may require a reduction of the saturation angle for individual subjects, impairing comparability of results. In this work, a B1 mapping method based on magnetization-prepared FLASH with slice selective preparation and excitation pulses and correction for relaxation effects is presented, yielding B1 maps with whole brain coverage, an in-plane resolution of 4 mm, a slice thickness of 3 mm, and a clinically acceptable duration of 46 s. The method is tested both in vitro and in vivo and applied in a subsequent in vivo study to show that MTR values in human brain tissue depend approximately linearly on the preparation angle, with a slope similar to values reported for 1. 5 T. Calibration data and B1 maps are applied to B1 inhomogeneity corrections of MTR maps. Subsequently, it is shown that B1-corrected MTR maps acquired at reduced preparation angles due to individual SAR restrictions can be normalized, allowing for a direct comparison with maps acquired at the full angle.

YNIMG Journal 2010 Journal Article

Dual echo EPI – The method of choice for fMRI in the presence of magnetic field inhomogeneities?

  • Christian Schwarzbauer
  • Toralf Mildner
  • Wolfgang Heinke
  • Matthew Brett
  • Ralf Deichmann

FMRI studies of the orbitofrontal cortex or the inferior temporal lobes are often compromised by susceptibility artefacts, which may result in signal reduction or loss in gradient echo (GE) EPI. Spin echo (SE) EPI is considerably more robust against susceptibility-related signal loss, but its intrinsic sensitivity to changes in the blood oxygenation level dependent (BOLD) contrast is generally lower. In this study, we performed a direct comparison of GE and SE fMRI using a single-shot dual echo EPI acquisition scheme. Transient hypercapnia, induced by breathing Carbogen (5% CO2, 95% O2), was used as a global physiological stimulus to alter the BOLD contrast. In regions affected by magnetic field inhomogeneities, SE EPI provided significantly higher BOLD sensitivity than GE EPI. Such regions included the orbitofrontal cortex, temporal pole, anterior inferior temporal cortex, as well as parts of the lateral inferior temporal cortex and the lateral cerebellum. Dual echo fMRI benefits from the robustness of SE EPI in these critical regions while utilising the generally higher sensitivity of GE EPI in normal regions. It therefore provides an attractive solution for fMRI studies that require optimum sensitivity in both normal and critical brain regions. Furthermore, a general method is proposed to combine the GE and SE data into a single hybrid data set that provides optimum sensitivity in the whole brain. This method can be applied to any experimental design that can be expressed in terms of a generalised linear model. The feasibility of this approach is demonstrated both theoretically and experimentally.

YNIMG Journal 2010 Journal Article

Dual-echo EPI for non-equilibrium fMRI — Implications of different echo combinations and masking procedures

  • Florian Beissner
  • Simon Baudrexel
  • Steffen Volz
  • Ralf Deichmann

Dual-echo EPI is based on the acquisition of two images with different echo times per excitation, thus allowing for the calculation of purely T2* weighted data. The technique can be used for the measurement of functional activation whenever the prerequisite of constant equilibrium magnetization cannot be fulfilled due to variable inter-volume delays. The latter is the case when image acquisition is triggered by physiological parameters (e. g. cardiac gating) or by the subject's response. Despite its frequent application, there is currently no standardized way of combining the information obtained from the two acquired echoes. The goal of this study was to quantify the implication of different echo combination methods (quotients of echoes and quantification of T 2 *) and calculation modalities, either pre-smoothing data before combination or subjecting unsmoothed combined data to masking (no masking, volume-wise masking, joint masking), on the theoretically predicted signal-to-noise ratio (SNR) of the BOLD response and on activation results of two fMRI experiments using finger tapping and visual stimulation in one group (n =5) and different motor paradigms to activate motor areas in the cortex and the brainstem in another group (n =21). A significant impact of echo combination and masking procedure was found for both SNR and activation results. The recommended choice is a direct calculation of T 2 * values, either using joint masking on unsmoothed data, or pre-smoothing images prior to T 2 * calculation. This method was most beneficial in areas close to the surface of the brain or adjacent to the ventricles and may be especially relevant to brainstem fMRI.

YNIMG Journal 2010 Journal Article

Quantitative mapping of T1 and T2* discloses nigral and brainstem pathology in early Parkinson's disease

  • Simon Baudrexel
  • Lucas Nürnberger
  • Udo Rüb
  • Carola Seifried
  • Johannes C. Klein
  • Thomas Deller
  • Helmuth Steinmetz
  • Ralf Deichmann

Quantitative magnetic resonance imaging is a promising in vivo imaging technique revealing insights into different aspects of brain morphology in neurodegenerative diseases based on the determination of physical tissue parameters. Using combined T1- and T2*-mapping, we investigated changes of local relaxation times in the midbrain and lower brainstem of 20 patients with early Parkinson's disease (PD) compared to 20 healthy controls. Voxelwise statistical parametric mapping disclosed a widespread reduction of midbrain T1 values contralateral to the clinically more severely affected limbs. Within the SN, the T1 decrease matched the known pattern of selective neuronal loss as examined in various post-mortem studies, suggesting that T1 is a marker for PD related tissue pathology. However, the spatial extent of T1 reductions exceeded the SN and reached non-dopaminergic areas in the pontomesencephalic junction potentially involved in early non-motor symptoms of PD. In contrast, T2*-mapping revealed a bilateral decrease of T2* values restricted to the SN, indicating a local increase in total iron content. We conclude that, particularly in longitudinal studies, quantitative T1 may be a valuable marker for the monitoring of progressive neuronal loss in PD, whereas nigral T2* reductions might be more closely associated with an increased general vulnerability for the development of the disorder.

YNIMG Journal 2009 Journal Article

Reduction of susceptibility-induced signal losses in multi-gradient-echo images: Application to improved visualization of the subthalamic nucleus

  • Steffen Volz
  • Elke Hattingen
  • Christine Preibisch
  • Thomas Gasser
  • Ralf Deichmann

T2⁎-weighted gradient echo (GE) images yield good contrast of iron-rich structures like the subthalamic nuclei due to microscopic susceptibility induced field gradients, providing landmarks for the exact placement of deep brain stimulation electrodes in Parkinson's disease treatment. An additional advantage is the low radio frequency (RF) exposure of GE sequences. However, T2⁎-weighted images are also sensitive to macroscopic field inhomogeneities, resulting in signal losses, in particular in orbitofrontal and temporal brain areas, limiting anatomical information from these areas. In this work, an image correction method for multi-echo GE data based on evaluation of phase information for field gradient mapping is presented and tested in vivo on a 3 Tesla whole body MR scanner. In a first step, theoretical signal losses are calculated from the gradient maps and a pixelwise image intensity correction is performed. In a second step, intensity corrected images acquired at different echo times TE are combined using optimized weighting factors: in areas not affected by macroscopic field inhomogeneities, data acquired at long TE are weighted more strongly to achieve the contrast required. For large field gradients, data acquired at short TE are favored to avoid signal losses. When compared to the original data sets acquired at different TE and the respective intensity corrected data sets, the resulting combined data sets feature reduced signal losses in areas with major field gradients, while intensity profiles and a contrast-to-noise (CNR) analysis between subthalamic nucleus, red nucleus and the surrounding white matter demonstrate good contrast in deep brain areas.

YNIMG Journal 2008 Journal Article

Voxel-based cortical thickness measurements in MRI

  • Chloe Hutton
  • Enrico De Vita
  • John Ashburner
  • Ralf Deichmann
  • Robert Turner

The thickness of the cerebral cortex can provide valuable information about normal and abnormal neuroanatomy. High resolution MRI together with powerful image processing techniques has made it possible to perform these measurements automatically over the whole brain. Here we present a method for automatically generating voxel-based cortical thickness (VBCT) maps. This technique results in maps where each voxel in the grey matter is assigned a thickness value. Sub-voxel measurements of thickness are possible using sub-sampling and interpolation of the image information. The method is applied to repeated MRI scans of a single subject from two MRI scanners to demonstrate its robustness and reproducibility. A simulated data set is used to show that small focal differences in thickness between two groups of subjects can be detected. We propose that the analysis of VBCT maps can provide results that are complementary to other anatomical analyses such as voxel-based morphometry.

YNIMG Journal 2006 Journal Article

Improvement of the image quality of T1-weighted anatomical brain scans

  • Clare Howarth
  • Chloe Hutton
  • Ralf Deichmann

T1-weighted anatomical brain scans are routinely used in neuroimaging studies, for example, as anatomical reference for functional data and in brain morphometry studies. Subject motion can degrade the quality of these images. An additional problem is the occurrence of signal dropouts in the case of long echo times and low receiver bandwidths. These problems are addressed in two different studies. In the first study, it is shown that the high scalp signal, which results from the low T1 value of fat, may cause a typical ringing artefact in the presence of head motion. This problem may be enhanced if phased array coils are used for signal reception due to their increased sensitivity in the peripheral head regions. It is shown that this artefact can be avoided by combining certain fat suppression techniques that reduce the scalp signal. In the second study, it is shown that signal dropout affects mainly the orbitofrontal cortex and the temporal lobes, and that a bandwidth of 100 Hz/pixel should be chosen for the investigation of these areas to avoid signal losses while maintaining an acceptable signal-to-noise ratio. Experimental results are based on the MDEFT sequence but can be applied to other T1-weighted sequences like FLASH and MP-RAGE. Furthermore, the presented methods for improving the image quality can be combined with other artefact reduction techniques.

YNIMG Journal 2006 Journal Article

Optimal EPI parameters for reduction of susceptibility-induced BOLD sensitivity losses: A whole-brain analysis at 3 T and 1.5 T

  • Nikolaus Weiskopf
  • Chloe Hutton
  • Oliver Josephs
  • Ralf Deichmann

Most functional magnetic resonance imaging (fMRI) studies record the blood oxygen level-dependent (BOLD) signal using fast gradient-echo echo-planar imaging (GE EPI). However, GE EPI can suffer from substantial signal dropout caused by inhomogeneities in the static magnetic field. These field inhomogeneities occur near air/tissue interfaces, because they are generated by variations in magnetic susceptibilities. Thus, fMRI studies are often limited by a reduced BOLD sensitivity (BS) in inferior brain regions. Recently, a method has been developed which allows for optimizing the BS in dropout regions by specifically adjusting the slice tilt, the direction of the phase-encoding (PE), and the z-shim moment. However, optimal imaging parameters were only reported for the orbitofrontal cortex (OFC) and inferior temporal lobes. The present study determines the optimal slice tilt, PE direction, and z-shim moment at 3 T and 1. 5 T, otherwise using standard fMRI acquisition parameters. Results are reported for all brain regions, yielding a whole-brain atlas of optimal parameters. At both field strengths, optimal parameters increase the BS by more than 60% in many voxels in the OFC and by at least 30% in the other dropout regions. BS gains are shown to be more widespread at 3 T, suggesting an increased benefit from the dropout compensation at higher fields. Even the mean BS of a large brain region, e. g. , encompassing the medial OFC, can be increased by more than 15%. The maps of optimal parameters allow for assessing the feasibility and improving fMRI of brain regions affected by susceptibility-induced BS losses.

YNIMG Journal 2002 Journal Article

Echo Time Dependence of BOLD Contrast and Susceptibility Artifacts

  • Maria Luisa Gorno-Tempini
  • Chloe Hutton
  • Oliver Josephs
  • Ralf Deichmann
  • Cathy Price
  • Robert Turner

Echo-planar imaging with gradient echo allows whole-brain images to be rapidly acquired. However, its main limitation is that magnetic field inhomogeneities in regions of the brain close to bone and air-filled sinuses result in reduced signal-to-noise ratio and signal loss. In particular this is a problem for imaging the temporal lobes, and can therefore affect the results of some language-related studies. Decreasing the echo time (TE) increases the signal-to-noise ratio and reduces the amount of signal loss in susceptible regions. In this study we investigate the TE dependence of BOLD (blood oxygenation level-dependent) contrast and, in particular, how it is influenced in regions with susceptibility artifacts. We use a dual echo-time sequence to compare brain activations measured with two different TEs, TE = 40 ms and TE = 27 ms. The paradigm involves comparing famous faces to scrambled faces, a low-level control condition. It was chosen because famous faces have been repeatedly shown to activate the fusiform gyri and anterior temporal lobes in both PET and fMRI. Our results show that it is possible to detect robust activations at a lower TE in brain regions not affected by susceptibility artifacts (i. e. , fusiform gyri), allowing for faster scanning times. However, although the amount of signal loss is reduced at the lower TE, this does not appear to be sufficient to recover the BOLD signal in regions affected by susceptibility artifacts (i. e. , anterior temporal lobes).

YNIMG Journal 2002 Journal Article

Image Distortion Correction in fMRI: A Quantitative Evaluation

  • Chloe Hutton
  • Andreas Bork
  • Oliver Josephs
  • Ralf Deichmann
  • John Ashburner
  • Robert Turner

A well-recognized problem with the echo-planar imaging (EPI) technique most commonly used for functional magnetic resonance imaging (fMRI) studies is geometric distortion caused by magnetic field inhomogeneity. This makes it difficult to achieve an accurate registration between a functional activation map calculated from an EPI time series and an undistorted, high resolution anatomical image. A correction method based on mapping the spatial distribution of field inhomogeneities can be used to reduce these distortions. This approach is attractive in its simplicity but requires postprocessing to improve the robustness of the acquired field map and reduce any secondary artifacts. Furthermore, the distribution of the internal magnetic field throughout the head is position dependent resulting in an interaction between distortion and head motion. Therefore, a single field map may not be sufficient to correct for the distortions throughout a whole fMRI time series. In this paper we present a quantitative evaluation of image distortion correction for fMRI at 2T. We assess (i) methods for the acquisition and calculation of field maps, (ii) the effect of image distortion correction on the coregistration between anatomical and functional images, and (iii) the interaction between distortion and head motion, assessing the feasibility of using field maps to reduce this effect. We propose that field maps with acceptable noise levels can be generated easily using a dual echo-time EPI sequence and demonstrate the importance of distortion correction for anatomical coregistration, even for small distortions. Using a dual echo-time series to generate a unique field map at each time point, we characterize the interaction between head motion and geometric distortion. However, we suggest that the variance between successively measured field maps introduces additional unwanted variance in the voxel time-series and is therefore not adequate to correct for time-varying distortions.

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