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Generated mrtrix tasks from print-pydra-dev
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‎.gitignore‎

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@@ -140,4 +140,3 @@ _version.py
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# Mac Garbage
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.DS_Store
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/pydra/tasks/mrtrix3/v3_0

‎generate‎

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#!/usr/bin/env bash
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set -e
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PKG_DIR=$(dirname $0)
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CURRENT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
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AUTO_CONV_SUFFIX="-auto-gen"
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REBASED_SUFFIX="-rebased-on-auto-gen"
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if ! git diff-index --quiet HEAD --; then
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echo "Current branch '$CURRENT_BRANCH' has uncommitted changes. Please commit or stash them before proceeding."
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exit 1
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fi
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echo "Automatically converting Nipype tasks to Pydra tasks..."
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echo "Create '$CURRENT_BRANCH$REBASED_SUFFIX' and '$CURRENT_BRANCH$AUTO_CONV_SUFFIX' branches if not present and switch to $CURRENT_BRANCH$AUTO_CONV_SUFFIX"
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echo "NB: $CURRENT_BRANCH$AUTO_CONV_SUFFIX will contain the conversion specs from '$CURRENT_BRANCH' and the auto-generted tasks,"
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echo "wherease '$CURRENT_BRANCH$REBASED_SUFFIX' will be the changes in the current branch rebased on that"
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if [ "$CURRENT_BRANCH" == "*$REBASED_SUFFIX"]; then
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BASE_BRANCH=${CURRENT_BRANCH%"$REBASED_SUFFIX"}$AUTO_CONV_SUFFIX
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REBASE_BRANCH=$CURRENT_BRANCH
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git checkout $BASE_BRANCH
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else
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REBASE_BRANCH=${CURRENT_BRANCH}$REBASED_SUFFIX
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BASE_BRANCH=${CURRENT_BRANCH}$AUTO_CONV_SUFFIX
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git checkout -b $REBASE_BRANCH
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git checkout -b $BASE_BRANCH
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fi
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echo "Running auto-generation of MRtrix3 tasks..."
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CMD_DIR=$(dirname $(which mrconvert))
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python3 $PKG_DIR/generate.py $CMD_DIR $PKG_DIR 3.1.0
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echo "Committing converted tasks to ${CURRENT_BRANCH}$AUTO_CONV_SUFFIX..."
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git add pydra/tasks/mrtrix3
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git commit -m "auto-generated MRtrix3 Pydra tasks" || echo true
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echo "Rebasing '$REBASE_BRANCH' to apply changes..."
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git checkout $REBASE_BRANCH
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git rebase $BASE_BRANCH
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echo "Successfully converted Nipype tasks to Pydra tasks and rebased manual edits over the top of them in '$REBASE_BRANCH'

‎generate.py‎

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@@ -234,7 +234,7 @@ def auto_gen_cmd(
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base_cmd = str(cmd_dir / cmd[0])
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cmd = [base_cmd] + cmd[1:]
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try:
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code_str = sp.check_output(cmd + ["__print_usage_pydra__"]).decode("utf-8")
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code_str = sp.check_output(cmd + ["__print_pydra_code__"]).decode("utf-8")
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except sp.CalledProcessError:
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if log_errors:
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logger.error("Could not generate interface for '%s'", cmd_name)

‎pydra/tasks/mrtrix3/v3_1/__init__.py‎

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# Auto-generated, do not edit
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from .fivett2gmwmi import Fivett2Gmwmi
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from .fivett2vis import Fivett2Vis
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from .fivettcheck import FivettCheck
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from .fivettedit import FivettEdit
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from .fivettgen_deep_atropos import FivettGen_Deep_atropos
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from .fivettgen_freesurfer import FivettGen_Freesurfer
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from .fivettgen_fsl import FivettGen_Fsl
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from .fivettgen_gif import FivettGen_Gif
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from .fivettgen_hsvs import FivettGen_Hsvs
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from .afdconnectivity import AfdConnectivity
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from .amp2response import Amp2Response
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from .amp2sh import Amp2Sh
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from .connectome2tck import Connectome2Tck
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from .connectomeedit import ConnectomeEdit
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from .connectomestats import ConnectomeStats
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from .dcmedit import DcmEdit
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from .dcminfo import DcmInfo
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from .dirflip import DirFlip
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from .dirgen import DirGen
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from .dirmerge import DirMerge
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from .dirorder import DirOrder
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from .dirrotate import DirRotate
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from .dirsplit import DirSplit
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from .dirstat import DirStat
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from .dwi2adc import Dwi2Adc
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from .dwi2fod import Dwi2Fod
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from .dwi2mask_3dautomask import Dwi2Mask_3dautomask
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from .dwi2mask_ants import Dwi2Mask_Ants
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from .dwi2mask_b02template import Dwi2Mask_B02template
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from .dwi2mask_consensus import Dwi2Mask_Consensus
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from .dwi2mask_fslbet import Dwi2Mask_Fslbet
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from .dwi2mask_hdbet import Dwi2Mask_Hdbet
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from .dwi2mask_legacy import Dwi2Mask_Legacy
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from .dwi2mask_mean import Dwi2Mask_Mean
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from .dwi2mask_mtnorm import Dwi2Mask_Mtnorm
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from .dwi2mask_synthstrip import Dwi2Mask_Synthstrip
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from .dwi2mask_trace import Dwi2Mask_Trace
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from .dwi2response_dhollander import Dwi2Response_Dhollander
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from .dwi2response_fa import Dwi2Response_Fa
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from .dwi2response_manual import Dwi2Response_Manual
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from .dwi2response_msmt_5tt import Dwi2Response_Msmt_5tt
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from .dwi2response_tax import Dwi2Response_Tax
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from .dwi2response_tournier import Dwi2Response_Tournier
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from .dwi2tensor import Dwi2Tensor
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from .dwibiascorrect_ants import DwiBiascorrect_Ants
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from .dwibiascorrect_fsl import DwiBiascorrect_Fsl
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from .dwibiascorrect_mtnorm import DwiBiascorrect_Mtnorm
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from .dwibiasnormmask import DwiBiasnormmask
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from .dwicat import DwiCat
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from .dwidenoise import DwiDenoise
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from .dwiextract import DwiExtract
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from .dwifslpreproc import DwiFslpreproc
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from .dwigradcheck import DwiGradcheck
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from .dwinormalise_group import DwiNormalise_Group
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from .dwinormalise_manual import DwiNormalise_Manual
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from .dwinormalise_mtnorm import DwiNormalise_Mtnorm
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from .dwishellmath import DwiShellmath
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from .fixel2peaks import Fixel2Peaks
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from .fixel2sh import Fixel2Sh
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from .fixel2tsf import Fixel2Tsf
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from .fixel2voxel import Fixel2Voxel
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from .fixelcfestats import FixelCfestats
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from .fixelconnectivity import FixelConnectivity
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from .fixelconvert import FixelConvert
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from .fixelcorrespondence import FixelCorrespondence
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from .fixelcrop import FixelCrop
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from .fixelfilter import FixelFilter
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from .fixelreorient import FixelReorient
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from .fod2dec import Fod2Dec
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from .fod2fixel import Fod2Fixel
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from .label2colour import Label2Colour
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from .label2mesh import Label2Mesh
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from .labelconvert import LabelConvert
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from .labelsgmfirst import LabelSgmfirst
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from .labelstats import LabelStats
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from .mask2glass import Mask2Glass
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from .maskdump import MaskDump
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from .maskfilter import MaskFilter
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from .mesh2voxel import Mesh2Voxel
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from .meshconvert import MeshConvert
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from .meshfilter import MeshFilter
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from .mraverageheader import MrAverageheader
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from .mrcat import MrCat
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from .mrcentroid import MrCentroid
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from .mrcheckerboardmask import MrCheckerboardmask
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from .mrclusterstats import MrClusterstats
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from .mrcolour import MrColour
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from .mrconvert import MrConvert
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from .mrdegibbs import MrDegibbs
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from .mrdump import MrDump
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from .mredit import MrEdit
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from .mrfilter import MrFilter
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from .mrgrid import MrGrid
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from .mrhistmatch import MrHistmatch
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from .mrhistogram import MrHistogram
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from .mrinfo import MrInfo
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from .mrmath import MrMath
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from .mrmetric import MrMetric
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from .mrregister import MrRegister
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from .mrstats import MrStats
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from .mrthreshold import MrThreshold
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from .mrtransform import MrTransform
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from .mrtrix_cleanup import MrTrix_Cleanup
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from .mtnormalise import MtNormalise
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from .peaks2amp import Peaks2Amp
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from .peaks2fixel import Peaks2Fixel
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from .population_template import PopulationTemplate
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from .responsemean import ResponseMean
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from .sh2amp import Sh2Amp
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from .sh2peaks import Sh2Peaks
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from .sh2power import Sh2Power
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from .sh2response import Sh2Response
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from .shbasis import ShBasis
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from .shconv import ShConv
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from .tck2connectome import Tck2Connectome
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from .tck2fixel import Tck2Fixel
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from .tckconvert import TckConvert
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from .tckdfc import TckDfc
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from .tckedit import TckEdit
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from .tckgen import TckGen
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from .tckglobal import TckGlobal
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from .tckinfo import TckInfo
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from .tckmap import TckMap
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from .tckresample import TckResample
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from .tcksample import TckSample
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from .tcksift import TckSift
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from .tcksift2 import TckSift2
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from .tckstats import TckStats
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from .tcktransform import TckTransform
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from .tensor2metric import Tensor2Metric
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from .transformcalc import TransformCalc
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from .transformcompose import TransformCompose
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from .transformconvert import TransformConvert
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from .tsfdivide import TsfDivide
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from .tsfinfo import TsfInfo
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from .tsfmult import TsfMult
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from .tsfsmooth import TsfSmooth
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from .tsfthreshold import TsfThreshold
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from .tsfvalidate import TsfValidate
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from .vectorstats import VectorStats
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from .voxel2fixel import Voxel2Fixel
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from .voxel2mesh import Voxel2Mesh
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from .warp2metric import Warp2Metric
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from .warpconvert import WarpConvert
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from .warpcorrect import WarpCorrect
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from .warpinit import WarpInit
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from .warpinvert import WarpInvert
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from ..manual.mrcalc import MrCalc

‎pydra/tasks/mrtrix3/v3_1/afdconnectivity.py‎

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# Auto-generated from MRtrix C++ command with '__print_pydra_code__' secret option
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import typing as ty
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from pathlib import Path # noqa: F401
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from fileformats.generic import File, Directory # noqa: F401
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from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks # noqa: F401
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from pydra.compose import shell
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from pydra.utils.typing import MultiInputObj
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@shell.define
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class AfdConnectivity(shell.Task["AfdConnectivity.Outputs"]):
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"""This estimate is obtained by determining a fibre volume (AFD) occupied by the pathway of interest, and dividing by the streamline length.
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If only the streamlines belonging to the pathway of interest are provided, then ALL of the fibre volume within each fixel selected will contribute to the result. If the -wbft option is used to provide whole-brain fibre-tracking (of which the pathway of interest should contain a subset), only the fraction of the fibre volume in each fixel estimated to belong to the pathway of interest will contribute to the result.
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Use -quiet to suppress progress messages and output fibre connectivity value only.
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For valid comparisons of AFD connectivity across scans, images MUST be intensity normalised and bias field corrected, and a common response function for all subjects must be used.
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Note that the sum of the AFD is normalised by streamline length to account for subject differences in fibre bundle length. This normalisation results in a measure that is more related to the cross-sectional volume of the tract (and therefore 'connectivity'). Note that SIFT-ed tract count is a superior measure because it is unaffected by tangential yet unrelated fibres. However, AFD connectivity may be used as a substitute when Anatomically Constrained Tractography is not possible due to uncorrectable EPI distortions, and SIFT may therefore not be as effective.
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Longer discussion regarding this command can additionally be found at: https://mrtrix.readthedocs.io/en/3.0.4/concepts/afd_connectivity.html (as well as in the relevant reference).
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References
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----------
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Smith, R. E.; Raffelt, D.; Tournier, J.-D.; Connelly, A. Quantitative Streamlines Tractography: Methods and Inter-Subject Normalisation. Open Science Framework, https://doi.org/10.31219/osf.io/c67kn.
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Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137
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MRtrix
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------
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Version:3.0.4-1402-gd28b95cd, built Aug 22 2025
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Author: David Raffelt ([email protected]) and Robert E. Smith ([email protected])
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Copyright: Copyright (c) 2008-2025 the MRtrix3 contributors.
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This Source Code Form is subject to the terms of the Mozilla Public
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License, v. 2.0. If a copy of the MPL was not distributed with this
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file, You can obtain one at http://mozilla.org/MPL/2.0/.
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Covered Software is provided under this License on an "as is"
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basis, without warranty of any kind, either expressed, implied, or
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statutory, including, without limitation, warranties that the
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Covered Software is free of defects, merchantable, fit for a
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particular purpose or non-infringing.
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See the Mozilla Public License v. 2.0 for more details.
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For more details, see http://www.mrtrix.org/.
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"""
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executable = "afdconnectivity"
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# Arguments
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image_: ImageIn = shell.arg(
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argstr="",
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position=1,
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help="""the input FOD image.""",
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)
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tracks: Tracks = shell.arg(
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argstr="",
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position=2,
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help="""the input track file defining the bundle of interest.""",
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)
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# Options
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wbft: Tracks | None = shell.arg(
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default=None,
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argstr="-wbft",
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help="""provide a whole-brain fibre-tracking data set (of which the input track file should be a subset), to improve the estimate of fibre bundle volume in the presence of partial volume""",
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)
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all_fixels: bool = shell.arg(
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default=False,
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argstr="-all_fixels",
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help="""if whole-brain fibre-tracking is NOT provided, then if multiple fixels within a voxel are traversed by the pathway of interest, by default the fixel with the greatest streamlines density is selected to contribute to the AFD in that voxel. If this option is provided, then ALL fixels with non-zero streamlines density will contribute to the result, even if multiple fixels per voxel are selected.""",
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)
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# Standard options
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info: bool = shell.arg(
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default=False,
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argstr="-info",
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help="""display information messages.""",
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)
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quiet: bool = shell.arg(
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default=False,
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argstr="-quiet",
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help="""do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.""",
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)
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debug: bool = shell.arg(
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default=False,
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argstr="-debug",
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help="""display debugging messages.""",
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)
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force: bool = shell.arg(
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default=False,
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argstr="-force",
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help="""force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).""",
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)
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nthreads: int | None = shell.arg(
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default=None,
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argstr="-nthreads",
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help="""use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).""",
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)
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config: MultiInputObj[tuple[str, str]] | None = shell.arg(
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default=None,
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argstr="-config",
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help="""temporarily set the value of an MRtrix config file entry.""",
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sep=" ",
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)
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class Outputs(shell.Outputs):
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afd_map: ImageOut | bool | None = shell.outarg(
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default=None,
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argstr="-afd_map",
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path_template="afd_map.mif",
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help="""output a 3D image containing the AFD estimated for each voxel.""",
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)

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