diff --git a/clpipe/data/RegressionOptions.json b/clpipe/data/RegressionOptions.json deleted file mode 100644 index 3c7781f7..00000000 --- a/clpipe/data/RegressionOptions.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "MotionParams": ["trans_x","trans_y" ,"trans_z","rot_x","rot_z","rot_y"], - "WhiteMatter": "white_matter", - "CSF": "csf", - "FDLabel": "framewise_displacement", - "GlobalSignal": "global_signal", - "RegressionOptions": [ - - { - "Name": "QuadLagged", - "Quadratic": true, - "Lagged": true - }, - { - "Name": "Quad", - "Quadratic": true, - "Lagged": false - - }, - { - "Name": "Lagged", - "Quadratic": false, - "Lagged": true - }, - { - "Name": "Regress", - "Quadratic": false, - "Lagged": false - } - - - - - ] - - - -} \ No newline at end of file diff --git a/clpipe/data/defaultConfig.json b/clpipe/data/defaultConfig.json deleted file mode 100644 index a8cdf8ee..00000000 --- a/clpipe/data/defaultConfig.json +++ /dev/null @@ -1,193 +0,0 @@ -{ - "ProjectTitle": "A Neuroimaging Project", - "Authors/Contributors": "SET AUTHOR", - "ProjectDirectory": "", - "EmailAddress": "SET EMAIL ADDRESS", - "SourceOptions": { - "SourceURL": "fw://", - "DropoffDirectory": "", - "TempDirectory": "", - "CommandLineOpts": "-y", - "TimeUsage": "1:0:0", - "MemUsage": "10G", - "CoreUsage": "1" - }, - "DICOMToBIDSOptions": { - "DICOMDirectory": "", - "BIDSDirectory": "", - "ConversionConfig": "", - "DICOMFormatString": "", - "TimeUsage": "1:0:0", - "MemUsage": "5000", - "CoreUsage": "2", - "LogDirectory": "" - }, - "BIDSValidationOptions": { - "BIDSValidatorImage": "/proj/hng/singularity_imgs/validator.simg", - "LogDirectory": "" - }, - "FMRIPrepOptions": { - "BIDSDirectory": "", - "WorkingDirectory": "SET WORKING DIRECTORY", - "OutputDirectory": "", - "FMRIPrepPath": "/proj/hng/singularity_imgs/fmriprep_22.1.1.sif", - "FreesurferLicensePath": "/proj/hng/singularity_imgs/license.txt", - "UseAROMA": false, - "CommandLineOpts": "", - "TemplateFlowToggle": true, - "TemplateFlowPath": "/proj/hng/singularity_imgs/template_flow", - "TemplateFlowTemplates": [ - "MNI152NLin2009cAsym", - "MNI152NLin6Asym", - "OASIS30ANTs", - "MNIPediatricAsym", - "MNIInfant" - ], - "FMapCleanupROIs": 3, - "FMRIPrepMemoryUsage": "50G", - "FMRIPrepTimeUsage": "16:0:0", - "NThreads": "12", - "LogDirectory": "", - "DockerToggle": false, - "DockerFMRIPrepVersion": "" - }, - "PostProcessingOptions": { - "WorkingDirectory": "", - "WriteProcessGraph": true, - "TargetDirectory": "", - "TargetImageSpace": "MNI152NLin2009cAsym", - "TargetTasks": [], - "TargetAcquisitions": [], - "OutputDirectory": "", - "ProcessingSteps": [ - "SpatialSmoothing", - "TemporalFiltering", - "IntensityNormalization", - "ApplyMask" - ], - "ProcessingStepOptions": { - "TemporalFiltering": { - "Implementation": "fslmaths", - "FilteringHighPass": 0.008, - "FilteringLowPass": -1, - "FilteringOrder": 2 - }, - "IntensityNormalization": { - "Implementation": "10000_GlobalMedian" - }, - "SpatialSmoothing": { - "Implementation": "SUSAN", - "FWHM": 6 - }, - "AROMARegression": { - "Implementation": "fsl_regfilt" - }, - "ScrubTimepoints": { - "InsertNA": true, - "Columns": [ - { - "TargetVariable": "cosine*", - "Threshold": 100, - "ScrubAhead": 0, - "ScrubBehind": 0, - "ScrubContiguous": 0 - }, - { - "TargetVariable": "framewise_displacement", - "Threshold": 0.2, - "ScrubAhead": 1, - "ScrubBehind": 0, - "ScrubContiguous": 0 - } - ] - }, - "Resample": { - "ReferenceImage": "SET REFERENCE IMAGE" - }, - "TrimTimepoints": { - "FromEnd": 0, - "FromBeginning": 0 - }, - "ConfoundRegression": { - "Implementation": "afni_3dTproject" - } - }, - "ConfoundOptions": { - "Columns": [ - "csf", - "csf_derivative1", - "white_matter", - "white_matter_derivative1" - ], - "MotionOutliers": { - "Include": true, - "ScrubVar": "framewise_displacement", - "Threshold": 0.9, - "ScrubAhead": 0, - "ScrubBehind": 0, - "ScrubContiguous": 0 - } - }, - "BatchOptions": { - "MemoryUsage": "20000", - "TimeUsage": "2:0:0", - "NThreads": "1" - } - }, - "ProcessingStreams": [ - { - "ProcessingStream": "smooth_aroma-regress_filter_normalize", - "PostProcessingOptions": { - "ProcessingSteps": [ - "SpatialSmoothing", - "AROMARegression", - "TemporalFiltering", - "IntensityNormalization" - ] - } - }, - { - "ProcessingStream": "filter_confound-regress", - "PostProcessingOptions": { - "ProcessingSteps": [ - "TemporalFiltering", - "ConfoundRegression" - ] - } - }, - { - "ProcessingStream": "smooth_aroma-regress_filter_normalize_fwhm-8", - "PostProcessingOptions": { - "ProcessingSteps": [ - "SpatialSmoothing", - "AROMARegression", - "TemporalFiltering", - "IntensityNormalization" - ], - "ProcessingStepOptions": { - "SpatialSmoothing": { - "FWHM": 8 - } - } - } - } - ], - "ROIExtractionOptions": { - "TargetDirectory": "", - "TargetSuffix": "", - "OutputDirectory": "", - "Atlases": [ - "power" - ], - "RequireMask": true, - "PropVoxels": 0.5, - "OverlapOk": false, - "MemoryUsage": "20G", - "TimeUsage": "2:0:0", - "NThreads": "1", - "LogDirectory": "" - }, - "RunLog": [], - "StatusCache": "", - "BatchConfig": "slurmUNCConfig.json" -} \ No newline at end of file diff --git a/clpipe/data/configSchema.json b/tests/data/legacy_config_schema.json similarity index 100% rename from clpipe/data/configSchema.json rename to tests/data/legacy_config_schema.json