Functional MRI (fMRI) BOLD

Upon completion of this Web Based Training the customer will be able to: • Define the terms Functional MRI (fMRI) and Blood Oxygen Level Dependent (BOLD) • List the fMRI and BOLD advantages and applications • Define the terms Hemoglobin, Oxyhemoglobin and Deoxyhemoglobin • Define the Hemodynamic Response Function (HRF) • Define a paradigm and the various BOLD Stimuli that can be performed • List the Motor Cortexs and their locations in the Brain • Identify the BOLD Parameter card and know how to modify parameters Functional MRI (fMRI) BOLD (Blood Oxygenation Level Dependent) fMRI – Functional MRI • Study of function of specific neural regions or activities of a structure • Measures brain activity by detecting changes   – Blood flow and oxygen levels in response to neural activity   – Active areas of the brain consume more oxygen due to increased blood flow, areas display activation   BOLD – Blood Oxygen Level Dependent • Term used in fMRI • Deoxyhemoglobin – introduces inhomogeneity into the magnetic field, where oxyhemoglobin doesn‘t.   – Increased deoxyhemoglobin concentration – decrease in image intensity   – Decreased deoxyhemoglobin concentration – increase in image intensity   Reference: http://psychcentral.com/lib/what-is-functional-magnetic-resonance-imaging-fmri; http://medical-dictionary.thefreedictionary.com/blood+oxygen+level+dependent Advantages • Non-invasive   – No radioactive tracer   – No Contrast • Define duration of BOLD experiment++ • Multiple measurements   Applications • Pre-surgical planning • Pre and post-operative comparison • Displays active neural regions when a stimulus is performed   – Motor, Sensory, and Cognitive Stimulation and, More • Analyze cerebral organization of functional systems • Display changes in activity due to local brain lesions • Identify functional important areas prior to brain surgery • Intracranial tumors, epileptic foci, vascular malformations Hemoglobin – protein molecule in red blood cells, carries oxygen from lungs to body’s tissues and returns carbon dioxide from tissues back to the lungs2   • 4 protein molecules connected together • 2 alpha-globulin chains • 2 Beta-globulin chains • Heme group center contains an iron atom (Fe)    Reference: 1https://wikidiff.com/oxyhaemoglobin/deoxyhaemoglobin; 2https://www.medicinenet.com/hemoglobin/article.htm Deoxygenated Blood ________________________________________► Signal Loss Oxyhemoglobin – • Hemoglobin loosely combined with oxygen • Present in arterial and capillary blood3 • Bright red in color • Diamagnetic • No T2* shortening and no increased dephasing or protons Deoxyhemoglobin – • Form of hemoglobin that has released oxygen • Predominant protein in red blood cells3 • Purple blue in color • Paramagnetic • Shortens T2 and T2* relaxation times of brain decreases Reference: 3https://wikidiff.com/oxyhemoglobin/deoxyhemoglobin; http://mriquestions.com/bold-contrast.html • Functional MRI provides information about brain activity. • Oxyhemoglobin has a different magnetic resonance signal than deoxyhemoglobin or the surrounding brain tissue. • Brain areas activated by a specific task utilize more oxygen - decreasing the levels of oxyhemoglobin and increases the levels of deoxyhemoglobin.   Oxyhemoglobin is diamagnetic and doesn’t affect the magnetic field. • Deoxyhemoglobin is paramagnetic, and changes in the total amount of deoxyhemoglobin will affect the MR signal. BOLD Effect video BOLD Effect video   Reference:Animation from: http://www.sinauer.com/neuroscience4e/animations1.1.html • Curve represents the brains response and resulting MR Signal changes. • Response to performing a stimulus (Activity). Reference: http://mriquestions.com/does-boldbrain-activity • Exercise or sequence of events carried out by a patient.   – Designed to increase neuronal activity in a specific area or region of the brain. • Tasks performed are followed by a period of rest.   – Active – task performed (paradigm)   – Rest – rest phase (or) alternate task performed (e.g., left and right finger tapping) • Paradigm is repeated multiple measurements to increase the BOLD signal.   • Stimulation is performed during a fixed number of active measurements, followed by rest measurements (or) an alternate type of stimulus. • Same block paradigm is repeated multiple times. • Example     • Active (Finger Tapping) – 10 measurements     • Rest – 10 measurements Motor Stimulus • Finger tapping, ankle flexing, tongue flexing, etc. • Pre-surgical planning to assess effects of lesion proximity to motor strip.     Sensory Stimulus • Auditory   – Rhyming or word generation.   – Assess and visualize lesions proximity and effect on Broca’s area. • Visual Stimulus   – Focus on specific images or projections.   – Assess visual cortex, assist surgeon with minimizing negative surgical effects on vision.       Cognitive Stimulus • Thought and reasoning (or) pain and fear. • Assess anatomic areas associated with processes e.g., learning and repeating pairs of words, memory and decision making Cerebral Cortex1 • Largest region of the cerebrum. • Plays a key role in memory, attention, perception, cognition, awareness, thought, language, and consciousness. • Divided into functional areas that serve various motor, sensory, and cognitive functions. Motor Cortex2 • Responsible for planning, control and execution of voluntary movements.  • Divided into three main areas - the primary motor cortex, the pre-motor cortex, and the supplementary motor cortex.   – Primary motor cortex2 - Controls voluntary movements   – Pre-motor cortex2 - evaluates and accurately determines the group of muscles that are used to carry out movement.   – Supplementary Motor Area (SMA)2 - coordinates and executes bi-lateral movements that need to be accomplished simultaneously to perform a task or action.  Primary Somatosensory Cortex3   • Receives all sensory input from the body Posterior Parietal Cortex4   • Plays an important role in spatial reasoning, attention and planned movements. Broca’s Area5   • Controls motor functions involved with speech production and language comprehension. Wernicke’s Area6   • One of the main areas of the cerebral cortex responsible for language comprehension. Primary Auditory Cortex7   • Significant part of the hearing process.  Processes sound, volume and pitch. Primary Visual Cortex8   • Essential to the conscious processing of visual stimuli. Reference: 1 https://en.wikipedia.org/wiki/Cerebral_cortex; Ihttps://en.wikipedia.org/wiki/Motor_cortex; 2https://bodytomy.com/motor-cortex-location-structure-function,   Reference Images: 3 https://study.com/academy/lesson/somatosensory-cortex-definition-location-function.html, 4https://en.wikipedia.org/wiki/Posterior_parietal_cortex Reference Images: http://mybrainnotes.com/memory-language-brain.html; 5https://www.thoughtco.com/brocas-area-anatomy-373215; 6https://www.thoughtco.com/wernickes-area-anatomy-373231 7https://www.knowyourbody.net/primary-auditory-cortex.html; 8https://www.neuroscientificallychallenged.com/blog/know-your-brain-primary-visual-cortex • Pictorial representation of the human body based on a neurological map • Displays areas within the brain that perform various processing functions in the body   – Sensory functions   – Motor functions Reference: https://www.google.com/search?q=homunculus+brain+pictures&tbm=isch&tbo=u&source=univ&sa=X&ved=2ahUKEwiv1tebw7jcAhVO0FkKHajeDmcQ7Al6BAgFEBs&biw=987&bih=716#imgrc=8SOgyE2DGUMEKM; 9https://en.wikipedia.org/wiki/Cortical_homunculus Dot Cockpit > Programs   • Head > programs > bold imaging • Data sets acquired   – Localizer       - AAhead_scout   – Anatomical Data       - t1_mprage_sag_p2   – Field Map       - gre_field_map (Gradient Echo) • BOLD Experiment   – ep2d_bold_moco_p2 Dot Cockpit > Library   • head > library > bold imaging Alternative BOLD Sequences   • gre_field_mapping • ep2d_bold_moco_p2 • ep2d_bold_pace_p2 • ep2d_pace_moco_dynt_p2 • ep2d_pace_moc_filter_p2 • SMS-BOLD   – ep2d_bold_moco_p2_s2   – ep2d_bold_moco_p2_s2_1.5mm BOLD Imaging is based on an EPI technique t-maps can be distorted SOLUTION – Field Map   • Includes a measurement of the main magnetic field (B0 field) • Field Map identifies areas with distortion or signal nulling   – Activation in these areas may not be accurate • Check Field Map overlay on anatomical images Field Map overlaid on 3D Anatomical data • Functional Area – shown in color • Field Map – shown in violet Reference: Siemens Verio_BOLD_Imaging_B15_Quickguide.pdf ep2d_fid – Pulse Sequence   • ep 2D Single Shot • Free Induction Decay (FID) Reference: Siemens Magnets, Spines, and Resonances BOLD Paradigm – Instruction   • Review the paradigm/stimulus the patient • Patient repeats or performs the stimulus • Review commands (Go, Stop, video displayed with commands) • Discuss the importance of holding the head still during exam BOLD Measurement   • AAhead_scout – Localizer • t1_mprage_sag_p2 – 3D Sequence – anatomy (e.g., MPRAGE) • gre_field_mapping – Field Map • ep2d_bold_moco_p2 – BOLD sequence   – Define BOLD parameters     Select GO – starts sequence     • Alternate rest and activation commands   Exam Task Card  Data Acquisition • Comprehensive statistical analysis of fMRI data. • Measurement data is modeled using a variety of functions (e.g., hemodynamic response function)   – ON – data is acquired with the General Linear Model and the t-maps are calculated   – OFF – images are saved without evaluation GLM Evaluation   • t-test is integrated into GLM   – t-map     • Shows evaluated measurement data (functional information)       - Negative correlates → dark pixels       - Positive correlates  → bright pixels Finger Tapping: Threshold 4 T-map without threshold (Saved under EvaSeries_GLM) • ON – t-maps are stored during the measurement   – Required for an inline evaluation   – Real time operation in the Neuro 3D Task Card   – StartMRI series created in the Patient Browser       • OFF – t-maps are not stored during the measurement Note: real time, inline evaluation in the Neuro 3D (MR) Task Card is available on Numaris 4 systems only GLM uses a design matrix to display data analysis   • (1) Displays all measurements used for evaluation   – White = used measurements   – Black = unused measurements • (2) Paradigm – Active/Baseline • (3) Paradigm folded with HRF (Hemodynamic Response Function) • (4) Offset component • (5) Evolution of paradigm over time • (6) Model function for modeling oscillations over time • Ignore Meas. at Start   – Number of initial measurements are not used for evaluation   – Avoids start-up artifacts • Ignore after transition   – Number of measurements are ignored after changing the stimulation.   – Example     • Ignore after transition = 2     • First change in paradigm for measurement 11     • Measurements, 1, 2, 11 and 12 are ignored • ON –  hemodynamic response function is included in the computation.     • OFF – hemodynamic response function is not included in the computation. • ON – high pass filter is applied   – Low frequency oscillations over time are eliminated via the high pass filter   – Number of components of the high pass filter is automatically determined       • OFF – high pass filter is not applied • Value for pixel intensity “threshold” to calculate overlaid images   – Changing value - Can "reduce or increase" amount of activation seen in the activation map   – Determines if a pixel from the t-test images have enough intensity to be used for reconstructing the image overlay       • Threshold doesn't apply for reconstructing pure t-test images • Can "reduce or increase" the amount of activation see in the activation map • Number of measurements per paradigm (e.g., Paradigm size = 20; Rest = 10; Active = 10)     • Paradigm Table   – Setting for all measurements within a paradigm   – Each measurement has a separate line in the table     • Active – measurement performed with stimulation     • Baseline – measurement performed without stimulation • Reduces relative motion artifacts between data sets • Correction performed through interpolation • Rigid body model motion correction • Also referred to as ART – Advanced Retrospective Technique • Interpolation methods:     • Linear interpolation       - Fastest method of real-time post-processing.     • 3D k-Space Interpolation       - Performed in Fourier space.       - Provides good quality real-time post-processing.       - Typically the default selection for BOLD examination. Datasets are acquired and retrospectively realigned in 3D using k-space interpolation. Figure 1 – displays patient movement Figure 2 – 3D Motion Correction • ON – activates a low pass filter for smoothing images   – Signal-to-Noise Ratio (SNR)   –  Spatial Resolution (Image sharpness is reduced)   – High filter values → strong filtration   – Applied in image domain       • OFF – low pass filter is not applied Filter Width   • (1) No Filter • (2) Weak = 2.0 • (3) Average = 1.0 • (4) Strong = 0.5 • Determines total amount of measurements for the BOLD experiment   – Paradigm size – number of repetitions • Delay time between two subsequent measurements     • Idea is to allow a quiet period to give commands to the patient     • Played out for each measurement (not only in the transitions) in order to always have the same time-sequence   – e.g.,  delay time set for all measurements     • Maximum Delay in TR – depends on the TR of the protocol • Each Measurement    – ON – separate series are generated for each measurement   – OFF – all measurements are saved in the same series 3D PACE – Prospective Motion CorrEction   Advanced Motion Correction is performed during BOLD acquisition   Tracks head and corrects motion Translation Rotation   Motion is detected and position is updated in real-time before the next acquisition   Improves accuracy of overlay of fMRI and anatomic data   Can combine with ART 3D PACE – Hard-coded in the ep2D_pace sequence BOLD (epi sequences) Regional Saturation Band Shape > Asymmetric Place sharp edge next to anatomical region Patients with dental implants and retainers No Sat Band Asymmetric Sat Band Paradigm – Left Finger Tapping All slices for a single measurement are displayed together e.g., 36 slices   Minimizes storage space   Transfer large data sets   Note – this feature requires the Inline BOLD, or 3D PACE license syngo Classic   Neuro 3D (MR) Task Card Anatomy, Field Map, and BOLD data fused Clip Planes Color and threshold can be modified MR Neuro 3D Tools to evaluate clinical fMRI Advanced features for research orientated applications Multi contrast evaluation of up to 4 fMRI contrasts Datasets automatically selected and registered across multiple sessions Benefits Supports Pre-surgical Planning MR Neuro 3D – fMRI Step   (1) MPR image segments (displays fused statistical maps) (2) VRT segment (3) Blend slider (4) Slider to adjust color saturation (5) Selection list for color LUTs for non-active and       active areas (6) Buttons for color settings (7) List of BOLD acquisitions