mia_processes.bricks.preprocess package

Each package corresponds to a software encapsulated in mia_processes.

Contains:

Packages:

• afni: bricks from afni

• ants: bricks from ants

• dipy: bricks from dipy

• freesurfer: bricks from freesurfer

• fsl: bricks from fsl

• matlab_wrap: bricks that wrap MATLAB scripts using Nipype

• mrtrix: bricks from mrtrix3

• others: bricks from other sources (usually homemade bricks)

• spm: bricks from spm

• volbrain: bricks from volbrain

Subpackages

• mia_processes.bricks.preprocess.afni package
  • Submodules
  • mia_processes.bricks.preprocess.afni.processes module
    • Automask
      • Automask.__init__()
      • Automask.list_outputs()
      • Automask.run_process_mia()
    • Calc
      • Calc.__init__()
      • Calc.list_outputs()
      • Calc.run_process_mia()
    • CalcDropTRs
      • CalcDropTRs.__init__()
      • CalcDropTRs.list_outputs()
      • CalcDropTRs.run_process_mia()
    • Despike
      • Despike.__init__()
      • Despike.list_outputs()
      • Despike.run_process_mia()
    • FWHMx
      • FWHMx.__init__()
      • FWHMx.list_outputs()
      • FWHMx.run_process_mia()
    • GCOR
      • GCOR.__init__()
      • GCOR.list_outputs()
      • GCOR.run_process_mia()
    • OutlierCount
      • OutlierCount.__init__()
      • OutlierCount.list_outputs()
      • OutlierCount.run_process_mia()
    • QualityIndex
      • QualityIndex.__init__()
      • QualityIndex.list_outputs()
      • QualityIndex.run_process_mia()
    • RefitDeoblique
      • RefitDeoblique.__init__()
      • RefitDeoblique.list_outputs()
      • RefitDeoblique.run_process_mia()
    • SkullStrip
      • SkullStrip.__init__()
      • SkullStrip.list_outputs()
      • SkullStrip.run_process_mia()
    • TShift
      • TShift.__init__()
      • TShift.list_outputs()
      • TShift.run_process_mia()
    • TStatMean
      • TStatMean.__init__()
      • TStatMean.list_outputs()
      • TStatMean.run_process_mia()
    • Volreg
      • Volreg.__init__()
      • Volreg.list_outputs()
      • Volreg.run_process_mia()
• mia_processes.bricks.preprocess.ants package
  • Submodules
  • mia_processes.bricks.preprocess.ants.processes module
    • AffineInitializer
      • AffineInitializer.__init__()
      • AffineInitializer.list_outputs()
      • AffineInitializer.run_process_mia()
    • ApplyTransforms
      • ApplyTransforms.__init__()
      • ApplyTransforms.list_outputs()
      • ApplyTransforms.run_process_mia()
    • N4BiasFieldCorrection
      • N4BiasFieldCorrection.__init__()
      • N4BiasFieldCorrection.list_outputs()
      • N4BiasFieldCorrection.run_process_mia()
    • Registration
      • Registration.__init__()
      • Registration.list_outputs()
      • Registration.run_process_mia()
• mia_processes.bricks.preprocess.dipy package
  • Submodules
  • mia_processes.bricks.preprocess.dipy.processes module
    • ComputeDKI
      • ComputeDKI.__init__()
      • ComputeDKI.list_outputs()
      • ComputeDKI.run_process_mia()
    • Denoise
      • Denoise.__init__()
      • Denoise.list_outputs()
      • Denoise.run_process_mia()
• mia_processes.bricks.preprocess.freesurfer package
  • Submodules
  • mia_processes.bricks.preprocess.freesurfer.processes module
    • Binarize
      • Binarize.__init__()
      • Binarize.list_outputs()
      • Binarize.run_process_mia()
    • SynthStrip
      • SynthStrip.__init__()
      • SynthStrip.list_outputs()
      • SynthStrip.run_process_mia()
    • SynthStripMriqc
      • SynthStripMriqc.ConvBlock
      • SynthStripMriqc.StripModel
      • SynthStripMriqc.__init__()
      • SynthStripMriqc.conform()
      • SynthStripMriqc.list_outputs()
      • SynthStripMriqc.resample_like()
      • SynthStripMriqc.run_process_mia()
• mia_processes.bricks.preprocess.fsl package
  • Submodules
  • mia_processes.bricks.preprocess.fsl.processes module
    • Bet
      • Bet.__init__()
      • Bet.list_outputs()
      • Bet.run_process_mia()
    • BetSurfacesExtraction
      • BetSurfacesExtraction.__init__()
      • BetSurfacesExtraction.list_outputs()
      • BetSurfacesExtraction.run_process_mia()
    • ConvertXFM
      • ConvertXFM.__init__()
      • ConvertXFM.list_outputs()
      • ConvertXFM.run_process_mia()
    • EpiReg
      • EpiReg.__init__()
      • EpiReg.list_outputs()
      • EpiReg.run_process_mia()
    • ExtractROI
      • ExtractROI.__init__()
      • ExtractROI.list_outputs()
      • ExtractROI.run_process_mia()
    • FastSegment
      • FastSegment.__init__()
      • FastSegment.list_outputs()
      • FastSegment.run_process_mia()
    • Flirt
      • Flirt.__init__()
      • Flirt.list_outputs()
      • Flirt.run_process_mia()
    • Smooth
      • Smooth.__init__()
      • Smooth.list_outputs()
      • Smooth.run_process_mia()
• mia_processes.bricks.preprocess.mrtrix package
  • Submodules
  • mia_processes.bricks.preprocess.mrtrix.processes module
    • ConstrainedSphericalDeconvolution
      • ConstrainedSphericalDeconvolution.__init__()
      • ConstrainedSphericalDeconvolution.list_outputs()
      • ConstrainedSphericalDeconvolution.run_process_mia()
    • DWIBiasCorrect
      • DWIBiasCorrect.__init__()
      • DWIBiasCorrect.list_outputs()
      • DWIBiasCorrect.run_process_mia()
    • DWIBrainMask
      • DWIBrainMask.__init__()
      • DWIBrainMask.list_outputs()
      • DWIBrainMask.run_process_mia()
    • DWICat
      • DWICat.__init__()
      • DWICat.list_outputs()
      • DWICat.run_process_mia()
    • DWIDenoise
      • DWIDenoise.__init__()
      • DWIDenoise.list_outputs()
      • DWIDenoise.run_process_mia()
    • DWIExtract
      • DWIExtract.__init__()
      • DWIExtract.list_outputs()
      • DWIExtract.run_process_mia()
    • DWIPreproc
      • DWIPreproc.__init__()
      • DWIPreproc.list_outputs()
      • DWIPreproc.run_process_mia()
    • EditingTrack
      • EditingTrack.__init__()
      • EditingTrack.list_outputs()
      • EditingTrack.run_process_mia()
    • FilteringTrack
      • FilteringTrack.__init__()
      • FilteringTrack.list_outputs()
      • FilteringTrack.run_process_mia()
    • FitTensor
      • FitTensor.__init__()
      • FitTensor.list_outputs()
      • FitTensor.run_process_mia()
    • Generate5tt2gmwmi
      • Generate5tt2gmwmi.__init__()
      • Generate5tt2gmwmi.list_outputs()
      • Generate5tt2gmwmi.run_process_mia()
    • Generate5ttfsl
      • Generate5ttfsl.__init__()
      • Generate5ttfsl.list_outputs()
      • Generate5ttfsl.run_process_mia()
    • MRCat
      • MRCat.__init__()
      • MRCat.list_outputs()
      • MRCat.run_process_mia()
    • MRConvert
      • MRConvert.__init__()
      • MRConvert.list_outputs()
      • MRConvert.run_process_mia()
    • MRDeGibbs
      • MRDeGibbs.__init__()
      • MRDeGibbs.list_outputs()
      • MRDeGibbs.run_process_mia()
    • MRGridRegrid
      • MRGridRegrid.__init__()
      • MRGridRegrid.list_outputs()
      • MRGridRegrid.run_process_mia()
    • MRMath
      • MRMath.__init__()
      • MRMath.list_outputs()
      • MRMath.run_process_mia()
    • MRTransform
      • MRTransform.__init__()
      • MRTransform.list_outputs()
      • MRTransform.run_process_mia()
    • MTNormalise
      • MTNormalise.__init__()
      • MTNormalise.list_outputs()
      • MTNormalise.run_process_mia()
    • ResponseSDDhollander
      • ResponseSDDhollander.__init__()
      • ResponseSDDhollander.list_outputs()
      • ResponseSDDhollander.run_process_mia()
    • ResponseSDTournier
      • ResponseSDTournier.__init__()
      • ResponseSDTournier.list_outputs()
      • ResponseSDTournier.run_process_mia()
    • SphericalHarmonicExtraction
      • SphericalHarmonicExtraction.__init__()
      • SphericalHarmonicExtraction.list_outputs()
      • SphericalHarmonicExtraction.run_process_mia()
    • TensorMetrics
      • TensorMetrics.__init__()
      • TensorMetrics.list_outputs()
      • TensorMetrics.run_process_mia()
    • Tractography
      • Tractography.__init__()
      • Tractography.list_outputs()
      • Tractography.run_process_mia()
    • TransformFSLConvert
      • TransformFSLConvert.__init__()
      • TransformFSLConvert.list_outputs()
      • TransformFSLConvert.run_process_mia()
• mia_processes.bricks.preprocess.others package
  • Submodules
  • mia_processes.bricks.preprocess.others.processing module
    • ApplyBiasCorrection
      • ApplyBiasCorrection.__init__()
      • ApplyBiasCorrection.list_outputs()
      • ApplyBiasCorrection.run_process_mia()
    • ArtifactMask
      • ArtifactMask.__init__()
      • ArtifactMask.list_outputs()
      • ArtifactMask.run_process_mia()
    • Binarize
      • Binarize.__init__()
      • Binarize.list_outputs()
      • Binarize.run_process_mia()
    • ConformImage
      • ConformImage.__init__()
      • ConformImage.list_outputs()
      • ConformImage.run_process_mia()
    • ConvROI
      • ConvROI.__init__()
      • ConvROI.list_outputs()
      • ConvROI.run_process_mia()
    • Enhance
      • Enhance.__init__()
      • Enhance.list_outputs()
      • Enhance.run_process_mia()
    • EstimateSNR
      • EstimateSNR.__init__()
      • EstimateSNR.list_outputs()
      • EstimateSNR.run_process_mia()
    • ExtractROIbyLabel
      • ExtractROIbyLabel.__init__()
      • ExtractROIbyLabel.list_outputs()
      • ExtractROIbyLabel.run_process_mia()
    • ExtractSignalROI
      • ExtractSignalROI.__init__()
      • ExtractSignalROI.list_outputs()
      • ExtractSignalROI.run_process_mia()
    • GradientThreshold
      • GradientThreshold.__init__()
      • GradientThreshold.list_outputs()
      • GradientThreshold.run_process_mia()
    • Harmonize
      • Harmonize.__init__()
      • Harmonize.list_outputs()
      • Harmonize.run_process_mia()
    • IntensityClip
      • IntensityClip.__init__()
      • IntensityClip.list_outputs()
      • IntensityClip.run_process_mia()
    • Mask
      • Mask.__init__()
      • Mask.list_outputs()
      • Mask.run_process_mia()
    • NonSteadyStateDetector
      • NonSteadyStateDetector.__init__()
      • NonSteadyStateDetector.list_outputs()
      • NonSteadyStateDetector.run_process_mia()
    • Resample1
      • Resample1.__init__()
      • Resample1.list_outputs()
      • Resample1.run_process_mia()
    • Resample2
      • Resample2.__init__()
      • Resample2.list_outputs()
      • Resample2.run_process_mia()
    • RotationMask
      • RotationMask.__init__()
      • RotationMask.list_outputs()
      • RotationMask.run_process_mia()
    • Sanitize
      • Sanitize.__init__()
      • Sanitize.list_outputs()
      • Sanitize.run_process_mia()
    • TSNR
      • TSNR.__init__()
      • TSNR.list_outputs()
      • TSNR.run_process_mia()
    • TemplateFromTemplateFlow
      • TemplateFromTemplateFlow.__init__()
      • TemplateFromTemplateFlow.list_outputs()
      • TemplateFromTemplateFlow.run_process_mia()
    • Threshold
      • Threshold.__init__()
      • Threshold.list_outputs()
      • Threshold.run_process_mia()
    • artifact_mask()
    • is_outlier()
    • threshold()
• mia_processes.bricks.preprocess.spm package
  • Submodules
  • mia_processes.bricks.preprocess.spm.spatial_preprocessing module
    • Coregister
      • Coregister.__init__()
      • Coregister.list_outputs()
      • Coregister.run_process_mia()
    • GM_WM_Normalize
      • GM_WM_Normalize.__init__()
      • GM_WM_Normalize.list_outputs()
      • GM_WM_Normalize.run_process_mia()
    • NewSegment
      • NewSegment.__init__()
      • NewSegment.list_outputs()
      • NewSegment.run_process_mia()
    • Normalize12
      • Normalize12.__init__()
      • Normalize12.list_outputs()
      • Normalize12.run_process_mia()
    • Realign
      • Realign.__init__()
      • Realign.list_outputs()
      • Realign.run_process_mia()
    • SliceTiming
      • SliceTiming.__init__()
      • SliceTiming.list_outputs()
      • SliceTiming.run_process_mia()
    • Smooth
      • Smooth.__init__()
      • Smooth.list_outputs()
      • Smooth.run_process_mia()