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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.

This data are organized in BIDS format. To import the data into MIA using MRI File Manager, click on the “BIDS” button. Note that, the name of the data will be modified between BIDS format and MIA database (name and time of the sequence added), for example:

• BIDS format: “sub-001_ses-01_T1w.nii.gz”

• MIA database: “sub-001_ses-01–2-CS_3DT1DEG-T1TFE-153355_910000.nii.gz”

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