scholarly journals TDM: a temporal decomposition method for removing venous effects from task-based fMRI

2019 ◽  
Author(s):  
Kendrick Kay ◽  
Keith W. Jamison ◽  
Ruyuan Zhang ◽  
Kamil Ugurbil
Keyword(s):  
High Resolution ◽  
Spin Echo ◽  
Pulse Sequences ◽  
High Sensitivity ◽  
Blood Oxygenation ◽  
Dimensional Manifold ◽  
Spatial Accuracy ◽  
Gradient Echo ◽  
Spatial Coverage ◽  
Temporal Decomposition

AbstractMost functional magnetic resonance imaging (fMRI) is conducted with gradient-echo pulse sequences. Although this yields high sensitivity to blood oxygenation level dependent (BOLD) signals, gradient-echo acquisitions are heavily influenced by venous effects which limit the ultimate spatial resolution and spatial accuracy of fMRI. While alternative acquisition methods such as spin-echo can be used to mitigate venous effects, these methods lead to serious reductions in signal-to-noise ratio and spatial coverage, and are difficult to implement without leakage of undesirable non-spin-echo effects into the data. Moreover, analysis heuristics such as masking veins or sampling inner cortical depths using high-resolution fMRI may be helpful, but sacrifice information from many parts of the brain. Here, we describe a new analysis method that is compatible with conventional gradient-echo acquisition and provides venous-free response estimates throughout the entire imaged volume. The method involves fitting a low-dimensional manifold characterizing variation in response timecourses observed in a given dataset, and then using identified early and late timecourses as basis functions for decomposing responses into components related to the microvasculature (capillaries and small venules) and the macrovasculature (veins), respectively. We show that this Temporal Decomposition through Manifold Fitting (TDM) method is robust, consistently deriving meaningful timecourses in individual fMRI scan sessions. Moreover, we show that by removing late components, TDM substantially reduces the superficial cortical depth bias present in gradient-echo BOLD responses and eliminates artifacts in cortical activity maps. TDM is general: it can be applied to any task-based fMRI experiment, can be used with standard- or high-resolution fMRI acquisitions, and can even be used to remove residual venous effects from specialized acquisition methods like spin-echo. We suggest that TDM is a powerful method that improves the spatial accuracy of fMRI and provides insight into the origins of the BOLD signal.

scholarly journals A critical assessment of data quality and venous effects in ultra-high-resolution fMRI

2018 ◽  
Author(s):  
Kendrick Kay ◽  
Keith W. Jamison ◽  
Luca Vizioli ◽  
Ruyuan Zhang ◽  
Eshed Margalit ◽  
...  
Keyword(s):  
High Resolution ◽  
Signal To Noise Ratio ◽  
Activity Patterns ◽  
Sampling Rate ◽  
Pulse Sequences ◽  
Blood Oxygenation ◽  
Fine Scale ◽  
Cortical Folding ◽  
Neuroscience Research ◽  
Spatial Coverage

AbstractAdvances in hardware, pulse sequences, and reconstruction techniques have made it possible to perform functional magnetic resonance imaging (fMRI) at sub-millimeter resolution while maintaining high spatial coverage and acceptable signal-to-noise ratio. Here, we examine whether ultra-high-resolution fMRI can be exploited for routine use in neuroscience research. We conducted fMRI in human visual cortex during a simple event-related visual experiment (7T, gradient-echo EPI, 0.8-mm isotropic voxels, 2.2-s sampling rate, 84 slices), and developed analysis and visualization tools to assess the quality of the data. We make three main observations. First, we find that the acquired fMRI images, combined with appropriate surface-based processing, provide reliable and accurate measurements of fine-scale blood oxygenation level dependent (BOLD) activity patterns. Second, we show that the highly folded structure of cortex causes substantial biases on spatial resolution and data visualization. Third, we examine the well-recognized issue of venous contributions to fMRI signals. In a systematic assessment of large sections of cortex measured at a fine scale, we show that time-averaged T2*-weighted EPI intensity is a simple, robust marker of venous effects. These venous effects are unevenly distributed across cortex, are more pronounced in gyri and outer cortical depths, and are, to a certain degree, in consistent locations across subjects relative to cortical folding. Furthermore, we show that these venous effects are strongly correlated with BOLD responses evoked by the experiment. We conclude that ultra-high-resolution fMRI can provide robust information about fine-scale BOLD activity patterns, but special care must be exercised in visualizing and interpreting these patterns, especially with regards to the confounding influence of the brain’s vasculature. To help translate these methodological findings to neuroscience research, we provide practical suggestions for both high-resolution and standard-resolution fMRI studies.

Experimental intracerebral and subarachnoid/intraventricular haemorrhages: MR detectability at 0.5 T and 1.5 T

2002 ◽  
Vol 43 (5) ◽  
pp. 464-473
Author(s):  
M. Alemany Ripoll ◽  
R. Raininko
Keyword(s):  
Cerebrospinal Fluid ◽  
Mr Imaging ◽  
Spin Echo ◽  
Autologous Blood ◽  
Pulse Sequences ◽  
Proton Density ◽  
Gradient Echo ◽  
The Brain ◽  
Formalin Fixed

Purpose: To compare the detectability of small experimental intracranial haemorrhages on MR imaging at 0.5 T and 1.5 T, from hyperacute to subacute stages. Material and Methods: 1 ml of autologous blood was injected into the brain of 15 rabbits to create intraparenchymal haematomas. Since the blood partially escaped into the cerebrospinal fluid (CSF) spaces, detectability of subarachnoid and intraventricular blood was also evaluated. MR imaging at 0.5 T and at 1.5 T was repeated up to 14 days, including T1-, proton density- and T2-weighted (w) spin-echo (SE), FLAIR and T2*-w gradient echo (GE) pulse sequences. The last MR investigation was compared to the formalin-fixed brain sections in 7 animals. Results: The intraparenchymal haematomas were best revealed with T2*-w GE sequences, with 100% of sensitivity at 1.5 T and 90–95% at 0.5 T. Blood in the CSF spaces was significantly ( p < 0.05) better detected at 1.5 T with T2*-w GE sequences and detected best during the first 2 days. The next most sensitive sequence for intracranial blood was FLAIR. SE sequences were rather insensitive. Conclusion: 1.5 T equipment is superior to 0.5 T in the detection of intracranial haemorrhages from acute to subacute stages. T2*-w GE sequences account for this result but other sequences are also needed for a complete examination.

Comparison of High Resolution Gradient Echo, XBONE T1, XBONE T2, Spin Echo T1 and 3D SST1 magnetic resonance imaging sequences for imagining the canine elbow

2014 ◽  
Vol 17 (4) ◽  
pp. 587-591 ◽  
Author(s):  
Y. Zhalniarovich ◽  
Z. Adamiak ◽  
J. Głodek ◽  
P. Przyborowska ◽  
P. Holak
Keyword(s):  
High Resolution ◽  
Biceps Brachii ◽  
Sagittal Plane ◽  
Spin Echo ◽  
Gradient Echo ◽  
Flexor Muscle ◽  
Triceps Brachii ◽  
Joint Surfaces ◽  
Flexor Carpi Ulnaris ◽  
Triceps Brachii Muscle

AbstractTwenty canine elbows were examined by low-field MRI. The objective of this study was to compare five magnetic resonance sequences: High Resolution Gradient Echo in the sagittal plane, XBONE T2 in the sagittal plane, Spin Echo T1 in the sagittal plane, Spin Echo T1 in the dorsal plane and 3D SST1 and XBONE T1 in the transverse plane, and to determine which sequences have the highest diagnostic value in imagining the canine elbow. High Resolution Gradient Echo, XBONE T2 and Spin Echo T1 sequences in the sagittal plane proved to be very useful in evaluations of osseous structures such as the medial coronoid process, the anconeal process of the ulna and joint surfaces. The above sequences facilitate evaluations of radial extensor muscle of the wrist, biceps brachii muscle, triceps brachii muscle and the flexor carpi ulnaris muscle. 3D SST1 and XBONE T1 sequences in the transverse plane produce high-quality images of the medial humeral condyle and surfaces of the elbow joint. Those sequences are also useful for evaluating the surrounding muscles: extensor digitorum communis muscle, extensor carpi radialis muscle, deltoid muscle, biceps brachii muscle, pronator teres muscle and flexor carpi ulnaris muscle. The Spin Echo T1 sequence in the dorsal plane facilitates assessments of joint surfaces, medial humeral condyle, superficial digital flexor muscle, deep digital flexor muscle, triceps brachii muscle and extensor digitorum lateralis muscle. The Spin Echo T1 sequence in the sagittal plane has a short scan time, but it produces images of lower quality than High Resolution Gradient Echo and XBONE T2 sequences in the sagittal plane.

scholarly journals Quantitative Radiomics: Impact of Pulse Sequence Parameter Selection on MRI-Based Textural Features of the Brain

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
John Ford ◽  
Nesrin Dogan ◽  
Lori Young ◽  
Fei Yang
Keyword(s):  
Pulse Sequence ◽  
Spin Echo ◽  
Pulse Sequences ◽  
Parameter Selection ◽  
Inversion Recovery ◽  
Textural Features ◽  
Imaging Data ◽  
Gradient Echo ◽  
The Impact ◽  
The Brain

Objectives. Radiomic features extracted from diverse MRI modalities have been investigated regarding their predictive and/or prognostic value in a variety of cancers. With the aid of a 3D realistic digital MRI phantom of the brain, the aim of this study was to examine the impact of pulse sequence parameter selection on MRI-based textural parameters of the brain. Methods. MR images of the employed digital phantom were realized with SimuBloch, a simulation package made for fast generation of image sequences based on the Bloch equations. Pulse sequences being investigated consisted of spin echo (SE), gradient echo (GRE), spoiled gradient echo (SP-GRE), inversion recovery spin echo (IR-SE), and inversion recovery gradient echo (IR-GRE). Twenty-nine radiomic textural features related, respectively, to gray-level intensity histograms (GLIH), cooccurrence matrices (GLCOM), zone size matrices (GLZSM), and neighborhood difference matrices (GLNDM) were evaluated for the obtained MR realizations, and differences were identified. Results. It was found that radiomic features vary considerably among images generated by the five different T1-weighted pulse sequences, and the deviations from those measured on the T1 map vary among features, from a few percent to over 100%. Radiomic features extracted from T1-weighted spin-echo images with TR varying from 360 ms to 620 ms and TE = 3.4 ms showed coefficients of variation (CV) up to 45%, while up to 70%, for T2-weighted spin-echo images with TE varying over the range 60–120 ms and TR = 6400 ms. Conclusion. Variability of radiologic textural appearance on MR realizations with respect to the choice of pulse sequence and imaging parameters is feature-dependent and can be substantial. It calls for caution in employing MRI-derived radiomic features especially when pooling imaging data from multiple institutions with intention of correlating with clinical endpoints.

scholarly journals Evaluation of Imaging Schemes for Pulsed Arterial Spin Labelling of the Human Kidney Cortex

2018 ◽  
Author(s):  
Charlotte E. Buchanan ◽  
Eleanor F. Cox ◽  
Susan T. Francis
Keyword(s):  
Spin Echo ◽  
Human Kidney ◽  
Echo Planar Imaging ◽  
Arterial Spin Labelling ◽  
Kidney Cortex ◽  
Gradient Echo ◽  
Planar Imaging ◽  
Spatial Coverage ◽  
Echo Planar ◽  
Spin Labelling

Purpose: A number of imaging readout schemes have been proposed for renal arterial spin labelling (ASL) to quantify kidney cortex perfusion, including gradient echo based methods of balanced fast field echo (bFFE) and gradient-echo echo-planar imaging (GE-EPI), or spin echo based schemes of spin-echo echo planar imaging (SE-EPI) and turbo spin-echo (TSE). Here, we compare these imaging schemes to evaluate the optimal imaging scheme for pulsed ASL (PASL) assessment of human kidney cortex perfusion at 3 T. Methods: Ten healthy volunteers with normal renal function were scanned using each 2D multislice imaging scheme, in combination with a respiratory triggered FAIR (flow-sensitive alternating inversion recovery) ASL scheme on a 3 T Philips Achieva scanner. All volunteers returned for a second identical scan session within two weeks of the first scan session. Comparisons were made between the imaging schemes in terms of perfusion weighted image (PWI) signal-to-noise ratio (SNR) and perfusion quantification, temporal SNR (tSNR), spatial coverage, and repeatability. Results: For each imaging scheme, renal cortex perfusion was calculated (bFFE: 276 &plusmn; 29 mL/100 g/min, GE-EPI: 222 &plusmn; 18 mL/100 g/min, SE-EPI: 201 &plusmn; 36 mL/100 g/min, TSE: 200 &plusmn; 20 mL/100 g/min). Perfusion was found to be higher for GE based readouts compared to SE based readouts, with significantly higher measured perfusion for the bFFE readout compared to all other schemes (P &lt; 0.05), attributed to the greater vascular signal present. Despite the PWI-SNR being significantly lower for SE-EPI compared to all other schemes (P &lt; 0.05), the SE-EPI readout gave the highest tSNR and was found to be the most reproducible scheme for the assessment of kidney cortex, with a CoV of 17.2%, whilst minimizing variability of the perfusion weighted signal across slices for whole kidney perfusion assessment. Conclusion: For the assessment of kidney cortex perfusion, SE-EPI provides optimal tSNR, minimal variability across slices and repeatable data acquired in a short scan time with low specific absorption rate.&nbsp;

Basic pulse sequences

2018 ◽  
pp. 17-25
Author(s):  
Sebastian Kozerke ◽  
Redha Boubertakh ◽  
Marc Miquel
Keyword(s):  
Cardiac Imaging ◽  
Spin Echo ◽  
Pulse Sequences ◽  
Image Sequences ◽  
Black Blood ◽  
Time Varying ◽  
Gradient Echo ◽  
Anatomical Imaging ◽  
Blood Imaging ◽  
Bright Blood

Pulse sequences control the timing of radiofrequency pulses and time-varying gradients that are necessary to create an image. Sequences are divided into different types: gradient echo, spin echo, and hybrid echo sequences. In cardiac imaging, ‘black blood’ spin echo images are used for anatomical imaging, while ‘bright blood’ imaging is used to study function and is based on gradient echo or hybrid echo sequences. Some key applications of those sequences, e.g. water–fat imaging or T2*-mapping to detect iron loading, are discussed. Preparation pulses can be used to modify image contrast to, for example, improve black blood images or for quantitative applications, including T1- and T2-mapping. To help the reader navigate through the sea of sequence acronyms, the chapter ends with a quick guide covering the acronyms used by the main scanner manufacturers.

Evaluation of optimised 3D turbo spin echo and gradient echo MR pulse sequences of the knee at 3T and 1.5T

Radiography ◽  
2020 ◽  
Author(s):  
O.M. Abdulaal ◽  
L. Rainford ◽  
P.J. MacMahon ◽  
P. Kenny ◽  
F. Carty ◽  
...  
Keyword(s):  
Spin Echo ◽  
Pulse Sequences ◽  
Turbo Spin Echo ◽  
Gradient Echo ◽  
Turbo Spin ◽  
Mr Pulse Sequences
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