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Generic_Cartesian_FFT_pull_svrtk_result_body.xml
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Generic_Cartesian_FFT_pull_svrtk_result_body.xml
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<?xml version="1.0" encoding="utf-8"?>
<gadgetronStreamConfiguration xsi:schemaLocation="http://gadgetron.sf.net/gadgetron gadgetron.xsd"
xmlns="http://gadgetron.sf.net/gadgetron"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<!--
Gadgetron generic recon chain for 2D and 3D cartesian sampling
Triggered by repetition
Recon N is contrast and S is set
Author: Hui Xue
National Heart, Lung and Blood Institute, National Institutes of Health
10 Center Drive, Bethesda, MD 20814, USA
Email: [email protected]
-->
<!-- reader -->
<reader><slot>1008</slot><dll>gadgetron_mricore</dll><classname>GadgetIsmrmrdAcquisitionMessageReader</classname></reader>
<reader><slot>1026</slot><dll>gadgetron_mricore</dll><classname>GadgetIsmrmrdWaveformMessageReader</classname></reader>
<!-- writer -->
<writer><slot>1022</slot><dll>gadgetron_mricore</dll><classname>MRIImageWriter</classname></writer>
<!-- Noise prewhitening -->
<gadget><name>NoiseAdjust</name><dll>gadgetron_mricore</dll><classname>NoiseAdjustGadget</classname></gadget>
<!-- RO asymmetric echo handling -->
<gadget><name>AsymmetricEcho</name><dll>gadgetron_mricore</dll><classname>AsymmetricEchoAdjustROGadget</classname></gadget>
<!-- RO oversampling removal -->
<gadget><name>RemoveROOversampling</name><dll>gadgetron_mricore</dll><classname>RemoveROOversamplingGadget</classname></gadget>
<!-- Data accumulation and trigger gadget -->
<gadget>
<name>AccTrig</name>
<dll>gadgetron_mricore</dll>
<classname>AcquisitionAccumulateTriggerGadget</classname>
<property><name>trigger_dimension</name><value></value></property>
<property><name>sorting_dimension</name><value></value></property>
</gadget>
<gadget>
<name>BucketToBuffer</name>
<dll>gadgetron_mricore</dll>
<classname>BucketToBufferGadget</classname>
<property><name>N_dimension</name><value>contrast</value></property>
<property><name>S_dimension</name><value>average</value></property>
<property><name>split_slices</name><value>false</value></property>
<property><name>ignore_segment</name><value>true</value></property>
<property><name>verbose</name><value>true</value></property>
</gadget>
<!-- Prep ref -->
<gadget>
<name>PrepRef</name>
<dll>gadgetron_mricore</dll>
<classname>GenericReconCartesianReferencePrepGadget</classname>
<!-- parameters for debug and timing -->
<property><name>debug_folder</name><value></value></property>
<property><name>perform_timing</name><value>true</value></property>
<property><name>verbose</name><value>true</value></property>
<!-- averaging across repetition -->
<property><name>average_all_ref_N</name><value>true</value></property>
<!-- every set has its own kernels -->
<property><name>average_all_ref_S</name><value>true</value></property>
<!-- whether always to prepare ref if no acceleration is used -->
<property><name>prepare_ref_always</name><value>true</value></property>
</gadget>
<!-- Coil compression -->
<gadget>
<name>CoilCompression</name>
<dll>gadgetron_mricore</dll>
<classname>GenericReconEigenChannelGadget</classname>
<!-- parameters for debug and timing -->
<property><name>debug_folder</name><value></value></property>
<property><name>perform_timing</name><value>true</value></property>
<property><name>verbose</name><value>true</value></property>
<property><name>average_all_ref_N</name><value>true</value></property>
<property><name>average_all_ref_S</name><value>true</value></property>
<!-- Up stream coil compression -->
<property><name>upstream_coil_compression</name><value>true</value></property>
<property><name>upstream_coil_compression_thres</name><value>0.002</value></property>
<property><name>upstream_coil_compression_num_modesKept</name><value>0</value></property>
</gadget>
<!-- Recon -->
<gadget>
<name>Recon</name>
<dll>gadgetron_mricore</dll>
<classname>GenericReconCartesianFFTGadget</classname>
<!-- image series -->
<property><name>image_series</name><value>0</value></property>
<!-- Coil map estimation, Inati or Inati_Iter -->
<property><name>coil_map_algorithm</name><value>Inati</value></property>
<!-- parameters for debug and timing -->
<property><name>debug_folder</name><value></value></property>
<property><name>perform_timing</name><value>true</value></property>
<property><name>verbose</name><value>true</value></property>
</gadget>
<!-- Partial fourier handling -->
<gadget>
<name>PartialFourierHandling</name>
<dll>gadgetron_mricore</dll>
<classname>GenericReconPartialFourierHandlingFilterGadget</classname>
<!-- parameters for debug and timing -->
<property><name>debug_folder</name><value></value></property>
<property><name>perform_timing</name><value>false</value></property>
<property><name>verbose</name><value>false</value></property>
<!-- if incoming images have this meta field, it will not be processed -->
<property><name>skip_processing_meta_field</name><value>Skip_processing_after_recon</value></property>
<!-- Parfial fourier handling filter parameters -->
<property><name>partial_fourier_filter_RO_width</name><value>0.15</value></property>
<property><name>partial_fourier_filter_E1_width</name><value>0.15</value></property>
<property><name>partial_fourier_filter_E2_width</name><value>0.15</value></property>
<property><name>partial_fourier_filter_densityComp</name><value>false</value></property>
</gadget>
<!-- Kspace filtering -->
<gadget>
<name>KSpaceFilter</name>
<dll>gadgetron_mricore</dll>
<classname>GenericReconKSpaceFilteringGadget</classname>
<!-- parameters for debug and timing -->
<property><name>debug_folder</name><value></value></property>
<property><name>perform_timing</name><value>false</value></property>
<property><name>verbose</name><value>false</value></property>
<!-- if incoming images have this meta field, it will not be processed -->
<property><name>skip_processing_meta_field</name><value>Skip_processing_after_recon</value></property>
<!-- parameters for kspace filtering -->
<property><name>filterRO</name><value>Gaussian</value></property>
<property><name>filterRO_sigma</name><value>1.0</value></property>
<property><name>filterRO_width</name><value>0.15</value></property>
<property><name>filterE1</name><value>Gaussian</value></property>
<property><name>filterE1_sigma</name><value>1.0</value></property>
<property><name>filterE1_width</name><value>0.15</value></property>
<property><name>filterE2</name><value>Gaussian</value></property>
<property><name>filterE2_sigma</name><value>1.0</value></property>
<property><name>filterE2_width</name><value>0.15</value></property>
</gadget>
<!-- FOV Adjustment -->
<gadget>
<name>FOVAdjustment</name>
<dll>gadgetron_mricore</dll>
<classname>GenericReconFieldOfViewAdjustmentGadget</classname>
<!-- parameters for debug and timing -->
<property><name>debug_folder</name><value></value></property>
<property><name>perform_timing</name><value>false</value></property>
<property><name>verbose</name><value>false</value></property>
</gadget>
<!-- Image Array Scaling -->
<gadget>
<name>Scaling</name>
<dll>gadgetron_mricore</dll>
<classname>GenericReconImageArrayScalingGadget</classname>
<!-- parameters for debug and timing -->
<property><name>perform_timing</name><value>false</value></property>
<property><name>verbose</name><value>false</value></property>
<property><name>min_intensity_value</name><value>64</value></property>
<property><name>max_intensity_value</name><value>4095</value></property>
<property><name>scalingFactor</name><value>1.0</value></property>
<property><name>use_constant_scalingFactor</name><value>true</value></property>
<property><name>auto_scaling_only_once</name><value>true</value></property>
<property><name>scalingFactor_dedicated</name><value>100.0</value></property>
</gadget>
<!-- ImageArray to images -->
<gadget>
<name>ImageArraySplit</name>
<dll>gadgetron_mricore</dll>
<classname>ImageArraySplitGadget</classname>
</gadget>
<!-- after recon processing -->
<gadget>
<name>ComplexToFloatAttrib</name>
<dll>gadgetron_mricore</dll>
<classname>ComplexToFloatGadget</classname>
</gadget>
<gadget>
<name>FloatToShortAttrib</name>
<dll>gadgetron_mricore</dll>
<classname>FloatToUShortGadget</classname>
<property><name>max_intensity</name><value>32767</value></property>
<property><name>min_intensity</name><value>0</value></property>
<property><name>intensity_offset</name><value>0</value></property>
</gadget>
<gadget>
<name>ArrayImagePassthroughPython</name>
<dll>gadgetron_python</dll>
<classname>PythonGadget</classname>
<property><name>python_module</name><value>nifti_python_gadgetron_svrtk_result_body</value></property>
<property><name>python_class</name><value>IsmrmrdToNiftiGadget</value></property>
</gadget>
<gadget>
<name>ImageFinish</name>
<dll>gadgetron_mricore</dll>
<classname>ImageFinishGadget</classname>
</gadget>
</gadgetronStreamConfiguration>