searchindex.js

Search.setIndex({"docnames": ["asl", "asl_multiPLD_ASLtbx", "asl_multiPLD_BASIL", "asl_multiPLD_ExploreASL", "asl_singlePLD_BASIL", "bmp", "dwi", "hcp", "index", "io", "misc", "rsfmri", "svdd", "usage"], "filenames": ["asl.rst", "asl_multiPLD_ASLtbx.rst", "asl_multiPLD_BASIL.rst", "asl_multiPLD_ExploreASL.rst", "asl_singlePLD_BASIL.rst", "bmp.rst", "dwi.rst", "hcp.rst", "index.rst", "io.rst", "misc.rst", "rsfmri.rst", "svdd.rst", "usage.rst"], "titles": ["Arterial spin labelling (ASL)", "<no title>", "Processing multi PLD ASL data from VCI and MAS2 studies using BASIL GUI", "Processing multi PLD ASL data from VCI and MAS2 studies using ExploreASL", "Processing single PLD ASL data from OATS 4 Sydney and SCS using BASIL GUI", "Brain MRI pipelines", "Diffusion-weighted imaging (DWI)", "HCP data processing", "My pipelines", "Input/output module", "Miscellaneous tips", "Resting-state BOLD imaging", "Cerebral Small Vessel Disease Lesion Detectors", "Usage"], "terms": {"choos": [0, 2, 4], 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values": [[2, "analysis-initial-parameter-values"]], "Analysis - Analysis Options": [[2, "analysis-analysis-options"]], "Analysis - White paper mode": [[2, "analysis-white-paper-mode"]], "Command line": [[2, "command-line"], [4, "command-line"]], "Further work": [[2, "further-work"]], "Processing multi PLD ASL data from VCI and MAS2 studies using ExploreASL": [[3, "processing-multi-pld-asl-data-from-vci-and-mas2-studies-using-exploreasl"]], "Processing single PLD ASL data from OATS 4 Sydney and SCS using BASIL GUI": [[4, "processing-single-pld-asl-data-from-oats-4-sydney-and-scs-using-basil-gui"]], "Before we go to BASIL GUI": [[4, "before-we-go-to-basil-gui"]], "\u201cInput Data\u201d tab": [[4, "input-data-tab"]], "\u201cData contents\u201d section": [[4, "data-contents-section"]], "\u201cData order\u201d section": [[4, "data-order-section"]], "\u201cAcquisition parameters\u201d section": [[4, "acquisition-parameters-section"]], "\u201cStructure\u201d tab": [[4, "structure-tab"]], "\u201cStructure\u201d section": [[4, "structure-section"]], "\u201cRegistration\u201d section": [[4, "registration-section"]], "\u201cCalibration\u201d tab": [[4, "calibration-tab"]], "\u201cEnable Calibration\u201d section": [[4, "enable-calibration-section"]], "\u201cReference tissue\u201d section": [[4, "reference-tissue-section"]], "\u201cDistortion Correction\u201d tab": [[4, "distortion-correction-tab"]], "\u201cAnalysis\u201d tab": [[4, "analysis-tab"]], "\u201cBasic analysis options\u201d section": [[4, "basic-analysis-options-section"]], "\u201cInitial parameter values\u201d section": [[4, "initial-parameter-values-section"]], "\u201cAnalysis options\u201d section": [[4, "analysis-options-section"]], "\u201cWhite paper mode\u201d section": [[4, "white-paper-mode-section"]], "Expected outputs": [[4, "expected-outputs"]], "Quality control": [[4, "quality-control"]], "ASL parameters": [[4, "asl-parameters"]], "Future work": [[4, "future-work"]], "Known issues": [[4, "known-issues"]], "References": [[4, "references"]], "Diffusion-weighted imaging (DWI)": [[6, "diffusion-weighted-imaging-dwi"]], "Multi-shell diffusion-weighted imaging data with MRtrix3 and FSL": [[6, "multi-shell-diffusion-weighted-imaging-data-with-mrtrix3-and-fsl"]], "Description of dMRI data acquired for VCI and MAS2": [[6, "description-of-dmri-data-acquired-for-vci-and-mas2"]], "Brief overview of MRtrix method": [[6, "brief-overview-of-mrtrix-method"]], "Detailed processing steps": [[6, "detailed-processing-steps"]], "[DISCARD] Processing AP/PA separately": [[6, "discard-processing-ap-pa-separately"]], "Convert DICOM data": [[6, "convert-dicom-data"]], "Denoising": [[6, "denoising"]], "Unringing": [[6, "unringing"]], "Motion and distortion correction": [[6, "motion-and-distortion-correction"]], "[USE THIS] Combining data of all PE\u2019s and process in one go": [[6, "use-this-combining-data-of-all-pe-s-and-process-in-one-go"]], "[OPTION 1] Preprocessing - Convert DICOM data": [[6, "option-1-preprocessing-convert-dicom-data"]], "[OPTION 2] Preprocessing - Convert DICOM data": [[6, "option-2-preprocessing-convert-dicom-data"]], "Preprocessing - Denoising": [[6, "preprocessing-denoising"]], "Preprocessing - Unringing": [[6, "preprocessing-unringing"]], "Preprocessing - Motion and distortion correction": [[6, "preprocessing-motion-and-distortion-correction"]], "Preprocessing - Bias field correction": [[6, "preprocessing-bias-field-correction"]], "Preprocessing - Brain mask estimation": [[6, "preprocessing-brain-mask-estimation"]], "FOD - Response function estimation": [[6, "fod-response-function-estimation"]], "Troubleshooting": [[6, "troubleshooting"]], "To-do list": [[6, "to-do-list"]], "References and further readings": [[6, "references-and-further-readings"]], "Appendices": [[6, "appendices"]], "acqparam.txt and total readout time": [[6, "acqparam-txt-and-total-readout-time"]], "HCP data processing": [[7, "hcp-data-processing"]], "Software installation": [[7, "software-installation"]], "R packages for FSL FIX": [[7, "r-packages-for-fsl-fix"]], "Setting environment variables": [[7, "setting-environment-variables"]], "TO-DO list": [[7, "to-do-list"]], "My pipelines": [[8, "my-pipelines"]], "Input/output module": [[9, "input-output-module"]], "Converting DICOM to BIDS with dcm2bids": [[9, "converting-dicom-to-bids-with-dcm2bids"]], "Install dcm2bids": [[9, "install-dcm2bids"]], "Tutorial go-through": [[9, "tutorial-go-through"]], "Running dcm2bids in VCI/MAS2": [[9, "running-dcm2bids-in-vci-mas2"]], "Miscellaneous tips": [[10, "miscellaneous-tips"]], "CUDA for FSL": [[10, "cuda-for-fsl"]], "Katana on-demand": [[10, "katana-on-demand"]], "Resting-state BOLD imaging": [[11, "resting-state-bold-imaging"]], "Data preparation": [[11, "data-preparation"]], "Visual inspection of image quality": [[11, "visual-inspection-of-image-quality"]], "Generate lists": [[11, "generate-lists"]], "Extract anat brain": [[11, "extract-anat-brain"]], "[OPTIONAL] Despike rsfMRI data": [[11, "optional-despike-rsfmri-data"]], "Remove existing func.feat, func+.feat, etc., if any": [[11, "remove-existing-func-feat-func-feat-etc-if-any"]], "Brain MRI pipelines": [[5, "brain-mri-pipelines"]], "Modules": [[5, "modules"]], "Cerebral Small Vessel Disease Lesion Detectors": [[12, "cerebral-small-vessel-disease-lesion-detectors"]], "Usage": [[13, "usage"]], "Installation": [[13, "installation"]], "Creating recipes": [[13, "creating-recipes"]]}, "indexentries": {}})