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How to test bricks and pipeline ?

Data are available to use and test Mia: mia_data_users.

The participants.tsv file specifies which pipelines or bricks can be tested with each data.

Bricks and pipelines documentation

To use certain mia_processes bricks (atomic processes), third-party software used in these bricks must be installed.

• bricks

  • preprocess

    • afni

      • Automask

      • Calc

      • CalcDropTRs

      • Despike

      • FWHMx

      • GCOR

      • OutliersCount

      • QualityIndex

      • RefitDeoblique

      • SkullStrip

      • TShift

      • TStatMean

      • Volreg

    • ants

      • AffineInitializer

      • ApplyTransform

      • N4BiasFieldCorrection

      • Registration

    • dipy

      • ComputeDKI

      • Denoise

    • freesurfer

      • Binarize

      • SynthStrip

      • SynthStripMriqc

    • fsl

      • Bet

      • BetSurfacesExtraction

      • ConvertXFM

      • EpiReg

      • ExtractROI

      • FastSegment

      • Flirt

      • Smooth

    • matlab_wrap

      • ComputeBrainVolume

    • mrtrix

      • ConstrainedSphericalDeconvolution

      • DWIBiasCorrect

      • DWIBrainMask

      • DWICat

      • DWIDenoise

      • DWIExtract

      • DWIPreproc

      • EditingTrack

      • FilteringTrack

      • FitTensor

      • Generate5tt2gmwmi

      • Generate5ttfsl

      • MRCat

      • MRConvert

      • MRDeGibbs

      • MRGridRegrid

      • MRMath

      • MRTransform

      • MTNormalise

      • ResponseSDDhollander

      • ResponseSDTournier

      • SphericalHarmonicExtraction

      • TensorMetrics

      • Tractography

      • TransformFSLConvert

    • others

      • ApplyBiasCorrection

      • ArtifactMask

      • Binarize

      • ConformImage

      • ConvROI

      • Enhance

      • EstimateSNR

      • ExtractROIbyLabel

      • ExtractSignalROI

      • GradientThreshold

      • Harmonize

      • IntensityClip

      • Mask

      • NonSteadyDetector

      • Resample1

      • Resample2

      • RotationMask

      • Sanitize

      • TSNR

      • TemplateFromTemplateFlow

      • Threshold

    • spm

      • Coregister

      • GM_WM_Normalize

      • NewSegment

      • Normalize12

      • Realign

      • SliceTiming

      • Smooth

    • volbrain

      • AssemblyNetDocker

      • GetLabels

      • LabelsCorrespondence

  • reports

    • AnatIQMs

    • BoldIQMs

    • BoldIQMsPlot

    • CarpetParcellation

    • ComputeDVARS

    • FramewiseDisplacement

    • LateralizationIndexCurve

    • Mean_stdDev_calc

    • PlotSignalROI

    • ReportAnatMriqc

    • ReportCO2inhalCvr

    • ReportFuncMriqc

    • ReportGE2REC

    • ReportGroupMriqc

    • ReportPerfDsc

    • Result_collector

    • Spikes

  • stats

    • spm

      • EstimateContrast

      • EstimateModel

      • Level1Design

      • MultipleRegressionDesign

      • OneSampleTTestDesign

      • PairedTTestDesign

      • TwoSampleTTestDesign

  • tools

    • Concat_to_list

    • Concat_to_list_of_list

    • Deconv_from_aif

    • Delete_Data

    • Files_To_List

    • Filter_Files_List

    • Find_In_List

    • Get_Conditions_From_BIDS_tsv

    • Get_Conditions_From_csv

    • Get_Eprime_info_GE2REC

    • Get_Patient_Name

    • Get_Regressors_From_csv

    • Import_Data

    • Input_Filter

    • List_Duplicate

    • List_Of_List_To_List

    • List_To_File

    • Make_AIF

    • Make_A_List

    • Make_CVR_reg_physio

• pipelines

  • CerebVascularReact

    • CO2_inhalation

  • DWITractography

    • Dwi_whole_brain_tractograpy

  • FunctionalLangageMemory

    • GE2REC

    • GE2REC without behavioural data

  • Perfusion

    • Perfdsc

  • Preprocess

    • Anat_airmask

    • Anat_headmask

    • Anat_mni_tpms

    • Anat_skullstrip

    • Anat_skullstrip_synthstrip

    • Anat_spatial_norm

    • Bold_hmc

    • Bold_mni_align

    • Bold_spatial_preprocessing1

    • Bold_spatial_preprocessing2

    • Bold_spatial_preprocessing3

    • Dwi_fod_msmt_csd

    • Dwi_preprocessing

    • Dwi_tissue_boundaries

    • Spatial_mask

  • QualityControl

    • Anat_mriqc

    • Bold_mri_qc

    • Bold_signals_roi

  • Reports

    • Bold_iqms

    • Extract_roi_param

  • Stat

    • Bold_stat_cvr