diff --git a/vfa_t1/CartesianReadout3D.spv b/vfa_t1/CartesianReadout3D.spv new file mode 100644 index 0000000..ab0ac6f --- /dev/null +++ b/vfa_t1/CartesianReadout3D.spv @@ -0,0 +1,541 @@ + + + + + VariablePlugins + + + axisSBKey.keyPath + frequency + center + 0.0 + editableName + Frequency (Hz) + orderedIndex + 0 + pluginClass + SBVariableAxis + pluginName + Variable Axis + pluginVersion + 1 + range + 400 + res + 65 + selectionStart + 0.0 + + + editableName + Minimize TR + enabled + 1 + pluginClass + SBMinimizeTRPlugin + pluginName + Minimize TR + pluginURL + http://www.SpinBench.com/ + pluginVersion + 1 + + + Waveforms + + PulsePlugins + + + anchor + + activeAnchor + start + anchorType + 1 + anchoredToSBKey + startOfTR + position + 0.0 + + editableName + Cartesian Readout + fov + 24 + hasPhaseEncoding + 1 + hasRewinder + 1 + kxCoverage + 1 + kyCoverage + 1 + netArea + 0.0 + pluginClass + SBCartesianReadout + pluginName + Cartesian Readout + pluginVersion + 1 + samplingRate + 250 + x0Component + 1 + x1Component + 0.0 + xPostReadoutOverlap + 1 + xPreReadoutOverlap + 1 + xReadoutOverlap + 0.0 + xRes + 256 + y0Component + 0.0 + y1Component + 0.0 + yPostReadoutOverlap + 1 + yPreReadoutOverlap + 1 + yReadoutOverlap + 0.0 + yRes + 256 + z0Component + 0.0 + z1Component + 1 + zPostReadoutOverlap + 1 + zPreReadoutOverlap + 1 + zReadoutOverlap + 0.0 + + + anchor + + activeAnchor + end + anchorType + 1 + anchoredToSBKey + <Cartesian Readout>.readoutStart + position + 1.0399999618530273 + + editableName + Phase Encode Gradient + fov + 24 + pluginClass + SBPhaseEncodeGradient + pluginName + Phase Encode Gradient + pluginVersion + 1 + res + 5 + x0Component + 0.0 + xDurationOverlap + 1 + y0Component + 1 + yDurationOverlap + 1 + z0Component + 0.0 + zDurationOverlap + 1 + + + anchor + + activeAnchor + start + anchorType + 1 + anchoredToSBKey + <Cartesian Readout>.readoutEnd + position + 2.0639998912811279 + + editableName + Phase Encode Gradient 1 + fov + 24 + pluginClass + SBPhaseEncodeGradient + pluginName + Phase Encode Gradient + pluginVersion + 1 + res + 5 + x0Component + 0.0 + xDurationOverlap + 1 + y0Component + -1 + yDurationOverlap + 1 + z0Component + 0.0 + zDurationOverlap + 1 + + + SequencePlugins + + + editableName + Repeat + pluginClass + SBRepeatPlugin + pluginName + Repeat + pluginVersion + 1 + repetitions + 256 + + + editableName + Draw Pulses + maskType + 0 + pluginClass + SBDrawPulsesPlugin + pluginName + Draw Pulses + pluginNames + + Phase Encode Gradient + Phase Encode Gradient 1 + + pluginVersion + 1 + + + duration + 1.5440000295639038 + editableName + New TR + pluginClass + SBNewTRPlugin + pluginName + New TR + pluginVersion + 1 + useGlobal + 1 + + + editableName + Repeat 1 + pluginClass + SBRepeatPlugin + pluginName + Repeat + pluginVersion + 1 + repetitions + 5 + + + editableName + Draw Pulses 1 + maskType + 1 + pluginClass + SBDrawPulsesPlugin + pluginName + Draw Pulses + pluginNames + + Phase Encode Gradient + Phase Encode Gradient 1 + + pluginVersion + 1 + + + editableName + Overlay Combinations + numInputs + 2 + pluginClass + SBOverlayAllCombinationsPlugin + pluginName + Overlay Combinations + pluginVersion + 1 + + + numGradAxes + 3 + numOtherAxes + 0 + + absoluteTime + 798.7198486328125 + activeInspector + 4 + appVersion + 2.5.1 + beginAtSS + 0 + chronaxie + 0.35999999999999999 + dFrequency + 0.0 + editingMode + 0 + fieldStrength + 3 + freelyRotatable + 1 + frequency + 0.0 + gamma + 4258 + gradCoilHeatingGain + 63 + gradLimit + 4 + gradLimitXScale + 1 + gradLimitYScale + 1 + gradLimitZScale + 1 + inspectorWidth + 310 + magnification + 5.3433389663696289 + mainWindowFrame + + height + 674 + width + 1162 + x + 66 + y + 82 + + maxReadoutRate + 500 + nominalGradLimitScale + 1 + numRfRxChannels + 4 + numRfTxChannels + 1 + outputPlugins + + + displayStyle + Magnitude / Phase + editableName + Profile + magnification + 1 + pluginClass + SBProfileViewPlugin + pluginName + Profile + pluginURL + [ Not Specified ] + pluginVersion + 1 + showYValues + 0 + viewBottom + 342 + viewHeight + 253 + viewLeft + 25 + viewWidth + 292 + + + editableName + Waveforms + gradDisplayStyle + XYZ Separate Plots + pluginClass + SBWaveformViewPlugin + pluginName + Waveforms + pluginURL + [ Not Specified ] + pluginVersion + 1 + rfDisplayStyle + XY Combined Plot + showReadoutWindows + 0 + showValues + 0 + viewBottom + 118 + viewHeight + 214 + viewLeft + 25 + viewWidth + 292 + + + editableName + Time Controller + pluginClass + SBTimeControlPlugin + pluginName + Time Controller + pluginURL + [ Not Specified ] + pluginVersion + 1 + viewBottom + 70 + viewHeight + 48 + viewLeft + 1 + viewWidth + 340 + + + editableName + View Scaling Controller + pluginClass + SBViewScalingPlugin + pluginName + View Scaling Controller + pluginURL + [ Not Specified ] + pluginVersion + 1 + viewBottom + 447 + viewHeight + 153 + viewLeft + 0.0 + viewWidth + 23 + + + editableName + Sequencing View + pluginClass + SBSequencingViewPlugin + pluginName + Sequencing View + pluginURL + [ Not Specified ] + pluginVersion + 1 + viewBottom + 375.5 + viewHeight + 234.5 + viewLeft + 349.16015625 + viewWidth + 426.06640625 + + + editableName + k-Space Trajectory + magnification + 1 + pluginClass + SBTrajectoryViewPlugin + pluginName + k-Space Trajectory + pluginURL + [ Not Specified ] + pluginVersion + 1 + showAllTrs + 1 + showReadoutKSpace + 1 + showValues + 1 + viewBottom + 36.5 + viewHeight + 328 + viewLeft + 367.01953125 + viewWidth + 337.21875 + xWaveform + kx + yWaveform + ky + + + protonDensity + 1 + readoutSampleDivisor + 2 + receiverPhase + 0.0 + rfLimit + 0.10000000000000001 + slewMagLimitXScale + 0.0 + slewMagLimitYScale + 0.0 + slewMagLimitZScale + 0.0 + slewRateLimit + 15 + slewRateLimitXScale + 1 + slewRateLimitXSlope + 0.0 + slewRateLimitYScale + 1 + slewRateLimitYSlope + 0.0 + slewRateLimitZScale + 1 + slewRateLimitZSlope + 0.0 + t1 + 800 + t2 + 150 + timeWithinTr + 3.1198486328124999 + tr + 3.1040000915527344 + trNum + 255 + waveSamplingRate + 50 + xPosition + 0.0 + xVelocity + 0.0 + yPosition + 0.0 + yVelocity + 0.0 + zPosition + 0.0 + zVelocity + 0.0 + + diff --git a/vfa_t1/README.md b/vfa_t1/README.md index e69de29..8494e17 100644 --- a/vfa_t1/README.md +++ b/vfa_t1/README.md @@ -0,0 +1,32 @@ +## Intro + +The variable flip angle (VFA) implementation of [qMRLab](https://qmrlab.org) takes following as input: +* Data + * `VFAData`: [vol X N] image data where N is # of FAs. + * `B1map`: [vol] b1 transmit field map + * `Mask`: [vol] binary ROI mask +* Parameters + * `FA`: [1 X N] array + * `TR`: [1 X N] array + +For details you can see the interactive [`vfa_t1`](https://qmrlab.readthedocs.io/en/master/vfa_t1_batch.html) tutorial [executable online](https://qmrlab.org/jekyll/2018/12/11/T1-mapping-variable-flip-angle.html). + +For creating B1map, double angle method is also available in qMRLab: [`b1_dam`](https://qmrlab.readthedocs.io/en/master/b1_dam_batch.html). + +*** + +## Pulse sequence implementation + +### Sequence components + +### Scan control + +### Reconstruction + + +*** + + + + + diff --git a/vfa_t1/SlabSelect.spv b/vfa_t1/SlabSelect.spv new file mode 100644 index 0000000..a315f04 --- /dev/null +++ b/vfa_t1/SlabSelect.spv @@ -0,0 +1,376 @@ + + + + + VariablePlugins + + + axisSBKey.keyPath + yPosition + center + 0.0 + editableName + YPosition (mm) + orderedIndex + 0 + pluginClass + SBVariableAxis + pluginName + Variable Axis + pluginVersion + 1 + range + 60 + res + 65 + selectionStart + 0.0 + + + editableName + Minimize TR + enabled + 1 + pluginClass + SBMinimizeTRPlugin + pluginName + Minimize TR + pluginURL + http://www.SpinBench.com/ + pluginVersion + 1 + + + Waveforms + + PulsePlugins + + + anchor + + activeAnchor + peak + anchorType + 1 + anchoredToSBKey + <Slice Select Gradient>.plateauRefocusPoint + position + 0.96694701910018921 + + duration + 1.5 + editableName + Sinc RF + enforceRFLimit + 1 + pluginClass + SBSincRF + pluginName + Sinc RF + pluginVersion + 1 + rfGain_0_0 + 1 + rfPhase_0_0 + 0.0 + timeBandwidth + 4 + tip + 20 + window + 1 + + + anchor + + activeAnchor + start + anchorType + 1 + anchoredToSBKey + startOfTR + position + 0.0 + + editableName + Slice Select Gradient + hasPrewinder + 0 + hasRewinder + 1 + netArea + 2.2892627716064453 + plateauDuration + 1.5 + plateauRefocusOffset + 0.75 + pluginClass + SBSliceSelectGradient + pluginName + Slice Select Gradient + pluginVersion + 1 + prewindFirstMoment + 0 + rewindFirstMoment + 0 + rfPulse + Sinc RF + tbw + 4 + thickness + 5 + x0Component + 0.0 + xPlateauOverlap + 0.0 + xPostPlateauOverlap + 1 + xPrePlateauOverlap + 1 + y0Component + 1 + yPlateauOverlap + 0.0 + yPostPlateauOverlap + 1 + yPrePlateauOverlap + 1 + z0Component + 0.0 + zPlateauOverlap + 0.0 + zPostPlateauOverlap + 1 + zPrePlateauOverlap + 1 + + + SequencePlugins + + + editableName + Draw Pulses + maskType + 0 + pluginClass + SBDrawPulsesPlugin + pluginName + Draw Pulses + pluginNames + + pluginVersion + 1 + + + numGradAxes + 3 + numOtherAxes + 0 + + absoluteTime + 2.822756290435791 + activeInspector + 2 + appVersion + 2.5.1 + beginAtSS + 0 + chronaxie + 0.35999999999999999 + dFrequency + 0.0 + editingMode + 0 + fieldStrength + 3 + freelyRotatable + 1 + frequency + 0.0 + gamma + 4258 + gradCoilHeatingGain + 63 + gradLimit + 2.2000000000000002 + gradLimitXScale + 1 + gradLimitYScale + 1 + gradLimitZScale + 1 + inspectorWidth + 222 + magnification + 1.25 + mainWindowFrame + + height + 662 + width + 727 + x + 264 + y + 91 + + maxReadoutRate + 500 + nominalGradLimitScale + 1 + numRfRxChannels + 4 + numRfTxChannels + 1 + outputPlugins + + + displayStyle + Magnitude / Phase + editableName + Profile + magnification + 1 + pluginClass + SBProfileViewPlugin + pluginName + Profile + pluginURL + [ Not Specified ] + pluginVersion + 1 + showYValues + 0 + viewBottom + 335 + viewHeight + 253 + viewLeft + 75.57421875 + viewWidth + 292 + + + editableName + Waveforms + gradDisplayStyle + XYZ Separate Plots + pluginClass + SBWaveformViewPlugin + pluginName + Waveforms + pluginURL + [ Not Specified ] + pluginVersion + 1 + rfDisplayStyle + XY Combined Plot + showReadoutWindows + 0 + showValues + 0 + viewBottom + 106 + viewHeight + 214 + viewLeft + 25 + viewWidth + 292 + + + editableName + Time Controller + pluginClass + SBTimeControlPlugin + pluginName + Time Controller + pluginURL + [ Not Specified ] + pluginVersion + 1 + viewBottom + 58 + viewHeight + 48 + viewLeft + 1 + viewWidth + 340 + + + editableName + View Scaling Controller + pluginClass + SBViewScalingPlugin + pluginName + View Scaling Controller + pluginURL + [ Not Specified ] + pluginVersion + 1 + viewBottom + 435 + viewHeight + 153 + viewLeft + 0.0 + viewWidth + 23 + + + protonDensity + 1 + readoutSampleDivisor + 2 + receiverPhase + 0.0 + rfLimit + 0.10000000000000001 + slewMagLimitXScale + 0.0 + slewMagLimitYScale + 0.0 + slewMagLimitZScale + 0.0 + slewRateLimit + 10 + slewRateLimitXScale + 1 + slewRateLimitXSlope + 0.17000000000000001 + slewRateLimitYScale + 1 + slewRateLimitYSlope + 0.17000000000000001 + slewRateLimitZScale + 1 + slewRateLimitZSlope + 0.17000000000000001 + t1 + 800 + t2 + 150 + timeWithinTr + 2.822756290435791 + tr + 3.0004544258117676 + trNum + 0 + waveSamplingRate + 100 + xPosition + 0.0 + xVelocity + 0.0 + yPosition + 0.0 + yVelocity + 0.0 + zPosition + -2.7808995246887207 + zVelocity + 0.0 + + diff --git a/vfa_t1/SpoilerGradient.spv b/vfa_t1/SpoilerGradient.spv new file mode 100644 index 0000000..44baad1 --- /dev/null +++ b/vfa_t1/SpoilerGradient.spv @@ -0,0 +1,323 @@ + + + + + VariablePlugins + + + axisSBKey.keyPath + frequency + center + 0.0 + editableName + Frequency (Hz) + orderedIndex + 0 + pluginClass + SBVariableAxis + pluginName + Variable Axis + pluginVersion + 1 + range + 400 + res + 65 + selectionStart + 0.0 + + + editableName + Minimize TR + enabled + 1 + pluginClass + SBMinimizeTRPlugin + pluginName + Minimize TR + pluginURL + http://www.SpinBench.com/ + pluginVersion + 1 + + + Waveforms + + PulsePlugins + + + anchor + + activeAnchor + start + anchorType + 1 + anchoredToSBKey + startOfTR + position + 0.0 + + area + 10 + editableName + Area Trapezoid + pluginClass + SBAreaTrapezoid + pluginName + Area Trapezoid + pluginVersion + 1 + x0Component + 0.0 + xFallOverlap + 1 + xPlateauOverlap + 1 + xRiseOverlap + 1 + y0Component + 0.0 + yFallOverlap + 1 + yPlateauOverlap + 1 + yRiseOverlap + 1 + z0Component + 1 + zFallOverlap + 1 + zPlateauOverlap + 1 + zRiseOverlap + 1 + + + SequencePlugins + + + editableName + Draw Pulses + maskType + 0 + pluginClass + SBDrawPulsesPlugin + pluginName + Draw Pulses + pluginNames + + pluginVersion + 1 + + + numGradAxes + 3 + numOtherAxes + 0 + + absoluteTime + 2.7999999999999998 + activeInspector + 4 + appVersion + 1.3.2 + beginAtSS + 0 + chronaxie + 0.35999999999999999 + dFrequency + 0.0 + editingMode + 0 + fieldStrength + 1.5 + freelyRotatable + 1 + frequency + 0.0 + gamma + 4258 + gradCoilHeatingGain + 63 + gradLimit + 4 + gradLimitXScale + 1 + gradLimitYScale + 1 + gradLimitZScale + 1 + inspectorWidth + 222 + magnification + 1.25 + mainWindowFrame + + height + 662 + width + 727 + x + 238 + y + 115 + + maxReadoutRate + 500 + nominalGradLimitScale + 1 + numRfRxChannels + 4 + numRfTxChannels + 1 + outputPlugins + + + displayStyle + Magnitude / Phase + editableName + Profile + magnification + 1 + pluginClass + SBProfileViewPlugin + pluginName + Profile + pluginURL + [ Not Specified ] + pluginVersion + 1 + showYValues + 0 + viewBottom + 330 + viewHeight + 253 + viewLeft + 25 + viewWidth + 292 + + + editableName + Waveforms + gradDisplayStyle + XYZ Separate Plots + pluginClass + SBWaveformViewPlugin + pluginName + Waveforms + pluginURL + [ Not Specified ] + pluginVersion + 1 + rfDisplayStyle + XY Combined Plot + showReadoutWindows + 0 + showValues + 0 + viewBottom + 106 + viewHeight + 214 + viewLeft + 25 + viewWidth + 292 + + + editableName + Time Controller + pluginClass + SBTimeControlPlugin + pluginName + Time Controller + pluginURL + [ Not Specified ] + pluginVersion + 1 + viewBottom + 58 + viewHeight + 48 + viewLeft + 1 + viewWidth + 340 + + + editableName + View Scaling Controller + pluginClass + SBViewScalingPlugin + pluginName + View Scaling Controller + pluginURL + [ Not Specified ] + pluginVersion + 1 + viewBottom + 435 + viewHeight + 153 + viewLeft + 0.0 + viewWidth + 23 + + + protonDensity + 1 + readoutSampleDivisor + 2 + receiverPhase + 0.0 + rfLimit + 0.10000000000000001 + slewMagLimitXScale + 0.0 + slewMagLimitYScale + 0.0 + slewMagLimitZScale + 0.0 + slewRateLimit + 15 + slewRateLimitXScale + 1 + slewRateLimitXSlope + 0.0 + slewRateLimitYScale + 1 + slewRateLimitYSlope + 0.0 + slewRateLimitZScale + 1 + slewRateLimitZSlope + 0.0 + t1 + 800 + t2 + 150 + timeWithinTr + 2.7999999999999998 + tr + 1.2836059331893921 + trNum + 0 + waveSamplingRate + 50 + xPosition + 0.0 + xVelocity + 0.0 + yPosition + 0.0 + yVelocity + 0.0 + zPosition + 0.0 + zVelocity + 0.0 + + diff --git a/vfa_t1/application.apd b/vfa_t1/application.apd new file mode 100644 index 0000000..3c9d9d8 --- /dev/null +++ b/vfa_t1/application.apd @@ -0,0 +1,36 @@ +[Application] +defaultName = VFA T1 +interface = lib:threeplane.ui +continuous = 1 +sharedSlot = Real-Time +calibrations = RealTimeShimming, Adjustments, CFtuning +controlScript = control.js +reconScript = recon.js +singleJSEngine = false +continuous = 0 +exclusiveRuns = 2 + +[excitation] +type = waveform +file = SlabSelect.spv +quadraticPhaseIncrement = 117 + +[echodelay] +type = delay +duration = 3000 + +[readout] +type = waveform +file = CartesianReadout3D.spv +loopIndex = 0 +associatedRF = excitation + +[spoiler] +type = waveform +file = SpoilerGradient.spv + +[tiploop] +type = loop +maximumIndex = 2 +loopIndex = 1 + diff --git a/vfa_t1/control.js b/vfa_t1/control.js new file mode 100644 index 0000000..9ddd4a9 --- /dev/null +++ b/vfa_t1/control.js @@ -0,0 +1,228 @@ +/* +================== qMRLab vfa_t1 pulse sequence = +This is the controller script which is responsible for +passing the variables between the GUI (control.ui) and +RTHawk's sequencing engine. + +Waveforms exported by SpinBench and described by application.apd +determine the initial state of the sequence. For this +application, initial parameters are fetched from: + +- [excitation] SincRF + Z (SlabSelect.spv) +- [echodelay] in us, to be exposed to GUI. (Not linked to a file) +- [readout] 3D Cartesian Readout (CartesianReadout3D.spv) +- [spoiler] Area Trapezoid (SpoilerGradient.spv) + +Author: Agah Karakuzu agahkarakuzu@gmail.com +Created: October, 2019. +// ================================================= +*/ + +// Get sequence ID +var sequenceId = rth.sequenceId(); + +// Fetch initial parameters described in CartesianReadout3D.spv +var xRes = SB.readout[".xRes"]; +var yRes = SB.readout[".yRes"]; +var zRes = SB.readout[".res"]; + +rth.addCommand(new RthUpdateChangeReconstructionParameterCommand(sequenceId, "xSize", xRes)); +rth.addCommand(new RthUpdateChangeReconstructionParameterCommand(sequenceId, "ySize", yRes)); +rth.addCommand(new RthUpdateChangeReconstructionParameterCommand(sequenceId, "zSize", zRes)); + +// Get minimum TR +var scannerTR = new RthUpdateGetTRCommand(sequenceId, [], []); +rth.addCommand(scannerTR); +var minTR = scannerTR.tr(); +var startingTR = minTR; + +// Starting FOV also depends on CartesianReadout3D.spv +// In SpinBench, FOV is defined in cm. +var startingFOV = SB.readout[".fov"]; // cm + +// Slice thickness depends on SlabSelect.spv +// In SpinBench, SliceThickness is defined in mm. +var startingThickness = SB.excitation[".thickness"]; // mm + +rth.informationInsert(sequenceId,"mri.SliceThickness",startingThickness); +var startingResolution = startingFOV/SB.readout[".xRes"] * 10; // mm +var startingZResolution = startingThickness/zRes * 10; // At the beginning zFOV equaled to slice thickness of SS + +var startingTE = 3; //ms +// Start of TE is anchored to the tip of sinc RF. +var peakLocation = SB.excitation[".peak"]; +rth.informationInsert(sequenceId,"mri.EchoTime",startingTE + peakLocation); + +// Assume FA from SB as the smaller. +var startingFA2 = SB.excitation[".tip"]; //20 +// FA should be in decreasing order (FA1 > FA2) +var startingFA1 = startingFA2 - 17; + + +var sliceThickness = startingThickness; +var fieldOfView = startingFOV; + +//FIXME: This is temporary. Fix the order +var flipAngle1 = startingFA2; +var flipAngle2 = startingFA1; + +var echoTime = startingTE; +var repetitionTime = startingTR; + +// Import display tool + +rth.importJS("lib:RthDisplayThreePlaneTools.js"); +var displayTools = new RthDisplayThreePlaneTools(); + +// Change functions + +function changeFOV(fov){ + if (fov + + Form + + + + 0 + 0 + 695 + 581 + + + + Form + + + + + + + + + + + + FOV [cm] + + + + + + + + + + + + + Slice Thickness [mm] + + + + + + + + + + + + + Flip Angle 1 [deg] + + + + + + + + + + + + + Flip Angle 2 [deg] + + + + + + + + + + + + + TR [ms] + + + + + + + + + + + + + TE [ms] + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + RthParameterInputWidget + QWidget +
RthParameterInputWidget.h
+ 1 + + + + + diff --git a/vfa_t1/recon.js b/vfa_t1/recon.js new file mode 100644 index 0000000..f9236d1 --- /dev/null +++ b/vfa_t1/recon.js @@ -0,0 +1,91 @@ +/* +================== qMRLab vfa_t1 pulse sequence = +This script is responsible for collecting raw data +and reconstructing images. + +Waveforms exported by SpinBench and described by application.apd +determine the initial state of the sequence. For this +application, initial parameters are fetched from: + +- [excitation] SincRF + Z (SlabSelect.spv) +- [echodelay] in us, to be exposed to GUI. (Not linked to a file) +- [readout] 3D Cartesian Readout (CartesianReadout3D.spv) +- [spoiler] Area Trapezoid (SpoilerGradient.spv) + +For now, base resolution components are hardcoded to be +256X256mm (inplane) and 5mm (slab thickness) for the +3D readout. + +TODO: These parameters are to be fetched from controller. + +Author: Agah Karakuzu agahkarakuzu@gmail.com +Created: October, 2019. +// ================================================= +*/ + +var sequenceId = rth.sequenceId(); +var instanceName = rth.instanceName(); + +var observer = new RthReconRawObserver(); +observer.setSequenceId(sequenceId); +observer.observeValueForKey("acquisition.samples", "samples"); + + +function reconBlock(input) { + + this.sort = new RthReconRawToImageSort(); + + this.sort.setPhaseEncodes(256); + this.sort.setSamples(256); + this.sort.setSliceEncodes(5); + + this.sort.setAccumulate(256*5); + + this.sort.setInput(input); + + this.fft = new RthReconImageFFT(); + this.fft.setInput(this.sort.output()); + + this.output = function() { + return this.fft.output(); + }; +} + +// For each `coil we need sort and FFT. + +var sos = new RthReconImageSumOfSquares(); +var block = []; + +function connectCoils(coils){ + block = []; + for (var i = 0; i