Index A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | U | V A addConfoundsToDesignMatrix() (BidsModel method) addGitIgnore() (built-in function) addLicense() (built-in function) addReadme() (built-in function) addStcToQuery() (built-in function) ALI_my_defaults() (built-in function) allRunsHaveSameNbRegressors() (built-in function) anatQA() (built-in function) appendContrast() (built-in function) B baseInputParser() (built-in function) bidsAppsActions() (built-in function) bidsChangeSuffix() (built-in function) bidsCheckVoxelSize() (built-in function) bidsConcatBetaTmaps() (built-in function) bidsCopyInputFolder() (built-in function) bidsCreateROI() (built-in function) bidsCreateVDM() (built-in function) bidsFFX() (built-in function) bidsGenerateT1map() (built-in function) bidsInverseNormalize() (built-in function) bidsLesionAbnormalitiesDetection() (built-in function) bidsLesionOverlapMap() (built-in function) bidsLesionSegmentation() (built-in function) BidsModel (built-in class) bidsModelSelection() (built-in function) bidspmHelp() (built-in function), [1] bidsQA() (built-in function) bidsQAbidspm() (built-in function) bidsQAmriqc() (built-in function) bidsQApreproc() (built-in function) bidsRealignReslice() (built-in function) bidsRealignUnwarp() (built-in function) bidsRemoveDummies() (built-in function) bidsRename() (built-in function) bidsReport() (built-in function) bidsResliceTpmToFunc() (built-in function) bidsResults() (built-in function) bidsRFX() (built-in function) bidsRoiBasedGLM() (built-in function) bidsSegmentSkullStrip() (built-in function) bidsSmoothContrasts() (built-in function) bidsSmoothing() (built-in function) bidsSpatialPrepro() (built-in function) bidsSTC() (built-in function) bidsWholeBrainFuncMask() (built-in function) boilerplate() (built-in function) bugReport() (built-in function) buildIndividualSpaceRoiFilename() (built-in function) C censoring() (built-in function) checkContrast() (built-in function) checkDependencies() (built-in function) checkFmriprep() (built-in function) checkMaskOrUnderlay() (built-in function) checkOptions() (built-in function) checkRegressorName() (built-in function) checkSpmMat() (built-in function) checkToolbox() (built-in function) cleanCrash() (built-in function) cleanUpWorkflow() (built-in function) cliBayesModel() (built-in function) cliCopy() (built-in function) cliCreateRoi() (built-in function) cliDefaultModel() (built-in function) cliPreprocess() (built-in function) cliSmooth() (built-in function) cliStats() (built-in function) collectSrcMetadata() (built-in function) compileScrubbingStats() (built-in function) computeCumulativeFwhm() (built-in function) computeDesignEfficiency() (built-in function) computeFDandRMS() (built-in function) computeMeanValueInMask() (built-in function) computeRobustOutliers() (built-in function) computeTsnr() (built-in function) concatenateConfounds() (built-in function) concatenateImages() (built-in function) concatenateOnsets() (built-in function) concatenateRuns() (built-in function) constructContrastNameFromBidsEntity() (built-in function) convertOnsetTsvToMat() (built-in function) convertPvalueToString() (built-in function) convertRealignParamToTsv() (built-in function) copyFigures() (built-in function) copyGraphWindownOutput() (built-in function) createAndReturnCounfoundMatFile() (built-in function) createAndReturnOnsetFile() (built-in function) createConfounds() (built-in function) createDataDictionary() (built-in function) createDefaultStatsModel() (built-in function) createDerivativeDir() (built-in function) createDesignMatrix() (built-in function) createGlmDirName() (built-in function) createModelFamilies() (built-in function) createPialSurface() (built-in function) D defaultContrastsStructure() (built-in function) defaultResultsStructure() (built-in function) deleteResidualImages() (built-in function) demos.bayes (module) demos.face_repetition (module) demos.MoAE (module) demos.openneuro (module) deprecated() (built-in function) deregexify() (built-in function) designMatrixFigureName() (built-in function) displayArguments() (built-in function) E elapsedTime() (built-in function) endsWithRunNumber() (built-in function) errorHandling() (built-in function) F fileFilterForBold() (built-in function) fillInResultStructure() (built-in function) findSubjectConImage() (built-in function) G generatedBy() (built-in function) getAcquisitionTime() (built-in function) getAnatFilename() (built-in function) getAndCheckRepetitionTime() (built-in function) getAndCheckSliceOrder() (built-in function) getAvailableGroups() (built-in function) getBidsFilterFile() (built-in function) getBlipDirection() (built-in function) getBoldFilename() (built-in function) getBoldFilenameForFFX() (built-in function) getConfoundsRegressorFilename() (built-in function) getContrastNb() (built-in function) getContrastsFromParentNode() (built-in function) getContrastsList() (built-in function) getContrastsListForFactorialDesign() (built-in function) getData() (built-in function) getDist2surf() (built-in function) getDummyContrastFromParentNode() (built-in function) getDummyContrastsList() (built-in function) getEnvInfo() (built-in function) getEventsData() (built-in function) getEventSpecificationRoiGlm() (built-in function) getFFXdir() (built-in function) getFuncVoxelDims() (built-in function) getHRFderivatives() (BidsModel method) getInclusiveMask() (built-in function) getInclusiveMaskThreshold() (BidsModel method) getInfo() (built-in function) getMeanFuncFilename() (built-in function) getMetadataFromIntendedForFunc() (built-in function) getModelMask() (BidsModel method) getOptionsFromCliArgument() (built-in function) getOptionsFromModel() (built-in function) getRegressorIdx() (built-in function) getRepoInfo() (built-in function) getRFXdir() (built-in function) getROIs() (built-in function) getSerialCorrelationCorrection() (BidsModel method) getSessionForRegressorNb() (built-in function) getSubjectList() (built-in function) getTotalReadoutTime() (built-in function) getTpmFilename() (built-in function) getVdmFile() (built-in function) getVersion() (built-in function) groupLevelGlmType() (BidsModel method) I initBids() (built-in function) inputParserForBayesModel() (built-in function) inputParserForCopy() (built-in function) inputParserForCreateModel() (built-in function) inputParserForCreateRoi() (built-in function) inputParserForPreprocess() (built-in function) inputParserForSmooth() (built-in function) inputParserForStats() (built-in function) isMni() (built-in function) isSkullstripped() (built-in function) isTtest() (built-in function) isZipped() (built-in function) L labelActivations() (built-in function) labelSpmSessWithBidsSesAndRun() (built-in function) lib.mancoreg (module) loadAndCheckOptions() (built-in function) logger() (built-in function) lowLevelActions() (built-in function) M MACS_my_defaults() (built-in function) mancoreg() (built-in function) mancoregCallbacks() (built-in function) mniToIxi() (built-in function) N newContrast() (built-in function) noRoiFound() (built-in function) notImplemented() (built-in function) O onsetsMatToTsv() (built-in function) orderAndPadCounfoundMatFile() (built-in function) overwriteDir() (built-in function) P plotConfounds() (built-in function) plotEvents() (built-in function) plotRoiTimeCourse() (built-in function) printAvailableContrasts() (built-in function) printBatchName() (built-in function) printCredits() (built-in function) printProcessingSubject() (built-in function) printToScreen() (built-in function) printWorkflowName() (built-in function) R realignQA() (built-in function) regexify() (built-in function) regressorsMatToTsv() (built-in function) removeDummies() (built-in function) removeEmptyQueryFields() (built-in function) removeIntercept() (built-in function) renameNidm() (built-in function) renameOutputResults() (built-in function) renamePng() (built-in function) renamePngCsvResults() (built-in function) renameSegmentParameter() (built-in function) renameSpmT() (built-in function) renameUnwarpParameter() (built-in function) reorderCounfounds() (built-in function) resizeAliMask() (built-in function) returnBatchFileName() (built-in function) returnBsmDocURL() (built-in function) returnContrastImageFile() (built-in function) returnDependency() (built-in function) returnHomeDir() (built-in function) returnName() (built-in function) returnNameSkullstripOutput() (built-in function) returnNumberScrubbedTimePoints() (built-in function) returnRepoURL() (built-in function) returnResultNameSpec() (built-in function) returnRootDir() (built-in function) returnRtdURL() (built-in function) returnVolumeList() (built-in function) roiGlmOutputName() (built-in function) S sanitizeConfounds() (built-in function) saveAndRunWorkflow() (built-in function) saveMatlabBatch() (built-in function) saveOptions() (built-in function) saveRoiGlmSummaryTable() (built-in function) saveSpmScript() (built-in function) segmentationAlreadyDone() (built-in function) selectConfoundsByVarianceExplained() (built-in function) set_spm_2_bids_defaults() (built-in function) setBachRename() (built-in function) setBatch3Dto4D() (built-in function) setBatchComputeVDM() (built-in function) setBatchContrasts() (built-in function) setBatchCoregistration() (built-in function) setBatchCoregistrationFmap() (built-in function) setBatchCoregistrationFuncToAnat() (built-in function) setBatchCreateVDMs() (built-in function) setBatchEstimateModel() (built-in function) setBatchFactorialDesign() (built-in function) setBatchFactorialDesignGlobalCalcAndNorm() (built-in function) setBatchFactorialDesignImplicitMasking() (built-in function) setBatchGenerateT1map() (built-in function) setBatchGoodnessOfFit() (built-in function) setBatchGroupLevelContrasts() (built-in function) setBatchGroupLevelResults() (built-in function) setBatchImageCalculation() (built-in function) setBatchInformationCriteria() (built-in function) setBatchInverseNormalize() (built-in function) setBatchLesionAbnormalitiesDetection() (built-in function) setBatchLesionOverlapMap() (built-in function) setBatchLesionSegmentation() (built-in function) setBatchMeanAnatAndMask() (built-in function) setBatchNormalizationSpatialPrepro() (built-in function) setBatchNormalize() (built-in function) setBatchPrintFigure() (built-in function) setBatchRealign() (built-in function) setBatchRenameSegmentParameter() (built-in function) setBatchReorient() (built-in function) setBatchReslice() (built-in function) setBatchResults() (built-in function) setBatchSaveCoregistrationMatrix() (built-in function) setBatchSegmentation() (built-in function) setBatchSelectAnat() (built-in function) setBatchSkullStripping() (built-in function) setBatchSmoothConImages() (built-in function) setBatchSmoothing() (built-in function) setBatchSmoothingAnat() (built-in function) setBatchSmoothingFunc() (built-in function) setBatchSTC() (built-in function) setBatchSubjectLevelContrasts() (built-in function) setBatchSubjectLevelGLMSpec() (built-in function) setBatchSubjectLevelResults() (built-in function) setDirectories() (built-in function) setFields() (built-in function) setGraphicWindow() (built-in function) setMontage() (built-in function) setNidm() (built-in function) setRenamingConfig() (built-in function) setUpWorkflow() (built-in function) silenceOctaveWarning() (built-in function) skullstrippingAlreadyDone() (built-in function) specifyContrasts() (built-in function) specifyDummyContrasts() (built-in function) specifySessionLvlContrasts() (built-in function) specifySubLvlContrasts() (built-in function) SPM (BidsModel attribute) spm_my_defaults() (built-in function) src.messages (module) T tempName() (built-in function) timeStamp() (built-in function) transferMetadataFromJson() (built-in function) U unfoldStruct() (built-in function) unzipAndReturnsFullpathName() (built-in function) V validate() (built-in function) validateConstrasts() (BidsModel method) validateContrasts() (built-in function) validateGroupBy() (BidsModel method) validateResultsStructure() (built-in function) validationInputFile() (built-in function) volumeSplicing() (built-in function)
