[DOC] Improve help sections

[Remi-Gau]

Is there an existing issue for this?

• [X] I have searched the existing issues

New feature

When typing help foo it could be nice to have a "See also" section at the bottom of the help to create hyperlink to other functions.

Not sure if this works for Octave but this could help with matlab

https://nl.mathworks.com/help/matlab/matlab_prog/add-help-for-your-program.html

Unclear documentation

No response

[Remi-Gau]

To see what functions don't have this

grep -riL "See also" src/ | grep \\.m

src/workflows/preproc/bidsWholeBrainFuncMask.m src/workflows/bidsInverseNormalize.m src/infra/checkToolbox.m src/infra/returnBsmDocURL.m src/infra/getRepoInfo.m src/infra/elapsedTime.m src/infra/returnRepoURL.m src/infra/getEnvInfo.m src/infra/silenceOctaveWarning.m src/infra/checkDependencies.m src/infra/resizeAliMask.m src/infra/returnRootDir.m src/infra/getVersion.m src/infra/returnRtdURL.m src/QA/computeRobustOutliers.m src/QA/anatQA.m src/QA/plotEvents.m src/QA/realignQA.m src/QA/censoring.m src/batches/lesion/setBatchLesionOverlapMap.m src/batches/lesion/setBatchLesionAbnormalitiesDetection.m src/batches/lesion/setBatchLesionSegmentation.m src/batches/setBachRename.m src/batches/stats/setBatchFatorialDesignGlobalCalcAndNorm.m src/batches/stats/setBatchFactorialDesignImplicitMasking.m src/batches/setBatchPrintFigure.m src/batches/setBatchImageCalculation.m src/batches/preproc/setBatchInverseNormalize.m src/batches/preproc/setBatchNormalize.m src/batches/preproc/setBatchComputeVDM.m src/batches/setBatch3Dto4D.m src/bids_model/getContrastsListForFactorialDesign.m src/bids_model/BidsModel.m~ src/bids_model/getContrastsListFromSource.m src/bids_model/checkContrast.m src/bids_model/BidsModel.m src/bids_model/getDummyContrastsList.m src/bids_model/checkGroupBy.m src/bids_model/getContrastsList.m src/bids_model/getInclusiveMask.m src/cli/getOptionsFromCliArgument.m src/stats/results/setNidm.m src/stats/results/returnName.m src/stats/results/convertPvalueToString.m src/stats/results/setMontage.m src/stats/subject_level/reorderCounfounds.m src/stats/subject_level/removeIntercept.m src/stats/subject_level/getSessionForRegressorNb.m src/stats/subject_level/deleteResidualImages.m src/stats/subject_level/selectConfoundsByVarianceExplained.m src/stats/subject_level/getEventsData.m src/stats/subject_level/allRunsHaveSameNbRegressors.m src/stats/group_level/groupLevelGlmType.m src/stats/utils/getRegressorIdx.m src/stats/utils/labelActivations.m src/stats/utils/isTtest.m src/stats/utils/fillInResultStructure.m src/stats/utils/createGlmDirName.m src/defaults/setRenamingConfig.m src/defaults/setDirectories.m src/defaults/mniToIxi.m src/defaults/getOptionsFromModel.m src/defaults/set_spm_2_bids_defaults.m src/defaults/ALI_my_defaults.m src/defaults/MACS_my_defaults.m src/defaults/defaultContrastsStructure.m src/defaults/spm_my_defaults.m src/defaults/defaultResultsStructure.m src/utils/isZipped.m src/utils/renamePng.m src/utils/returnBatchFileName.m src/utils/volumeSplicing.m src/utils/computeTsnr.m src/utils/checkMaskOrUnderlay.m src/utils/deregexify.m src/utils/cleanUpWorkflow.m src/utils/createDataDictionary.m src/utils/regexify.m src/utils/setFields.m src/utils/computeMeanValueInMask.m src/utils/returnDependency.m src/utils/unfoldStruct.m src/bids/addStcToQuery.m src/bids/validate.m src/bids/getROIs.m src/bids/roiGlmOutputName.m src/bids/removeEmptyQueryFields.m src/bids/buildIndividualSpaceRoiFilename.m src/bids/isSkullstripped.m src/bids/isMni.m src/bids/returnNameSkullstripOutput.m src/IO/renameUnwarpParameter.m src/IO/onsetsMatToTsv.m src/IO/unzipAndReturnsFullpathName.m src/IO/cleanCrash.m src/IO/regressorsMatToTsv.m src/IO/overwriteDir.m src/IO/addReadme.m src/IO/saveSpmScript.m src/IO/loadAndCheckOptions.m src/IO/addLicense.m src/IO/renameSegmentParameter.m src/IO/addGitIgnore.m src/messages/pathToPrint.m src/messages/printBatchName.m src/messages/printToScreen.m src/messages/bidspmHelp.m src/messages/bugReport.m src/messages/printProcessingSubject.m src/messages/printCredits.m src/messages/errorHandling.m src/messages/timeStamp.m src/messages/notImplemented.m src/messages/deprecated.m src/messages/printWorkflowName.m src/messages/logger.m src/preproc/fieldmaps/getTotalReadoutTime.m src/preproc/fieldmaps/getBlipDirection.m src/preproc/utils/segmentationAlreadyDone.m src/preproc/utils/getAcquisitionTime.m src/preproc/utils/createPialSurface.m src/preproc/utils/skullstrippingAlreadyDone.m src/preproc/utils/removeDummies.m

[Remi-Gau]

Files with no USAGE section:

grep -riL "USAGE" src/ | grep \\.m

src/workflows/preproc/bidsWholeBrainFuncMask.m src/reports/boilerplate_preprocess.mustache src/reports/partials/computing_environment.mustache src/reports/partials/slice_timing.mustache src/reports/partials/skullstripping.mustache src/reports/partials/remove_dummies.mustache src/reports/partials/credits.mustache src/reports/boilerplate_create_roi.mustache src/reports/boilerplate_stats.mustache src/QA/plotConfounds.m src/QA/computeRobustOutliers.m src/QA/anatQA.m src/QA/computeFDandRMS.m src/QA/plotEvents.m src/QA/censoring.m src/constants/lowLevelActions.m src/constants/supportedAtlases.m src/bids_model/getContrastsListForFactorialDesign.m src/bids_model/getContrastsListFromSource.m src/bids_model/BidsModel.m src/bids_model/checkGroupBy.m src/validators/isTtest.m src/cli/inputParserForSmooth.m src/cli/getBidsFilterFile.m src/cli/cliCopy.m src/cli/inputParserForCreateModel.m src/cli/cliCreateRoi.m src/cli/inputParserForPreprocess.m src/cli/cliPreprocess.m src/cli/cliDefaultModel.m src/cli/inputParserForCopy.m src/cli/inputParserForStats.m src/cli/baseInputParser.m src/cli/inputParserForCreateRoi.m src/cli/cliSmooth.m src/cli/cliStats.m src/stats/results/returnName.m src/stats/results/convertPvalueToString.m src/stats/subject_level/removeIntercept.m src/stats/subject_level/getEventsData.m src/stats/group_level/groupLevelGlmType.m src/defaults/defaultContrastsStructure.m src/defaults/defaultResultsStructure.m src/bids/validate.m src/bids/roiGlmOutputName.m src/bids/removeEmptyQueryFields.m src/bids/returnNameSkullstripOutput.m src/messages/pathToPrint.m src/messages/printBatchName.m src/messages/printCredits.m src/messages/printWorkflowName.m src/preproc/utils/createPialSurface.m