niwrap-mrtrix 0.8.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- niwrap_mrtrix/mrtrix/__init__.py +263 -0
- niwrap_mrtrix/mrtrix/afdconnectivity.py +527 -0
- niwrap_mrtrix/mrtrix/amp2response.py +560 -0
- niwrap_mrtrix/mrtrix/amp2sh.py +870 -0
- niwrap_mrtrix/mrtrix/connectome2tck.py +583 -0
- niwrap_mrtrix/mrtrix/connectomeedit.py +413 -0
- niwrap_mrtrix/mrtrix/connectomestats.py +956 -0
- niwrap_mrtrix/mrtrix/dcmedit.py +552 -0
- niwrap_mrtrix/mrtrix/dcminfo.py +529 -0
- niwrap_mrtrix/mrtrix/dirflip.py +440 -0
- niwrap_mrtrix/mrtrix/dirgen.py +514 -0
- niwrap_mrtrix/mrtrix/dirmerge.py +446 -0
- niwrap_mrtrix/mrtrix/dirorder.py +421 -0
- niwrap_mrtrix/mrtrix/dirsplit.py +436 -0
- niwrap_mrtrix/mrtrix/dirstat.py +640 -0
- niwrap_mrtrix/mrtrix/dwi2adc.py +531 -0
- niwrap_mrtrix/mrtrix/dwi2fod.py +1156 -0
- niwrap_mrtrix/mrtrix/dwi2mask.py +570 -0
- niwrap_mrtrix/mrtrix/dwi2response.py +1774 -0
- niwrap_mrtrix/mrtrix/dwi2tensor.py +715 -0
- niwrap_mrtrix/mrtrix/dwibiascorrect.py +673 -0
- niwrap_mrtrix/mrtrix/dwidenoise.py +570 -0
- niwrap_mrtrix/mrtrix/dwiextract.py +1111 -0
- niwrap_mrtrix/mrtrix/dwigradcheck.py +665 -0
- niwrap_mrtrix/mrtrix/fixel2peaks.py +613 -0
- niwrap_mrtrix/mrtrix/fixel2sh.py +430 -0
- niwrap_mrtrix/mrtrix/fixel2tsf.py +435 -0
- niwrap_mrtrix/mrtrix/fixel2voxel.py +523 -0
- niwrap_mrtrix/mrtrix/fixelcfestats.py +1179 -0
- niwrap_mrtrix/mrtrix/fixelconnectivity.py +477 -0
- niwrap_mrtrix/mrtrix/fixelconvert.py +850 -0
- niwrap_mrtrix/mrtrix/fixelcorrespondence.py +455 -0
- niwrap_mrtrix/mrtrix/fixelcrop.py +422 -0
- niwrap_mrtrix/mrtrix/fixelfilter.py +882 -0
- niwrap_mrtrix/mrtrix/fixelreorient.py +435 -0
- niwrap_mrtrix/mrtrix/fod2dec.py +571 -0
- niwrap_mrtrix/mrtrix/fod2fixel.py +646 -0
- niwrap_mrtrix/mrtrix/label2colour.py +426 -0
- niwrap_mrtrix/mrtrix/label2mesh.py +417 -0
- niwrap_mrtrix/mrtrix/labelconvert.py +460 -0
- niwrap_mrtrix/mrtrix/labelstats.py +418 -0
- niwrap_mrtrix/mrtrix/maskdump.py +404 -0
- niwrap_mrtrix/mrtrix/maskfilter.py +730 -0
- niwrap_mrtrix/mrtrix/mesh2voxel.py +422 -0
- niwrap_mrtrix/mrtrix/meshconvert.py +514 -0
- niwrap_mrtrix/mrtrix/meshfilter.py +452 -0
- niwrap_mrtrix/mrtrix/mraverageheader.py +485 -0
- niwrap_mrtrix/mrtrix/mrcalc.py +4302 -0
- niwrap_mrtrix/mrtrix/mrcat.py +467 -0
- niwrap_mrtrix/mrtrix/mrcentroid.py +418 -0
- niwrap_mrtrix/mrtrix/mrcheckerboardmask.py +446 -0
- niwrap_mrtrix/mrtrix/mrclusterstats.py +930 -0
- niwrap_mrtrix/mrtrix/mrcolour.py +490 -0
- niwrap_mrtrix/mrtrix/mrconvert.py +1967 -0
- niwrap_mrtrix/mrtrix/mrdegibbs.py +535 -0
- niwrap_mrtrix/mrtrix/mrdump.py +423 -0
- niwrap_mrtrix/mrtrix/mredit.py +737 -0
- niwrap_mrtrix/mrtrix/mrfilter.py +971 -0
- niwrap_mrtrix/mrtrix/mrgrid.py +1079 -0
- niwrap_mrtrix/mrtrix/mrhistmatch.py +494 -0
- niwrap_mrtrix/mrtrix/mrhistogram.py +484 -0
- niwrap_mrtrix/mrtrix/mrinfo.py +1282 -0
- niwrap_mrtrix/mrtrix/mrmath.py +503 -0
- niwrap_mrtrix/mrtrix/mrmetric.py +525 -0
- niwrap_mrtrix/mrtrix/mrregister.py +2098 -0
- niwrap_mrtrix/mrtrix/mrstats.py +534 -0
- niwrap_mrtrix/mrtrix/mrthreshold.py +666 -0
- niwrap_mrtrix/mrtrix/mrtransform.py +1372 -0
- niwrap_mrtrix/mrtrix/mtnormalise.py +725 -0
- niwrap_mrtrix/mrtrix/peaks2amp.py +403 -0
- niwrap_mrtrix/mrtrix/peaks2fixel.py +422 -0
- niwrap_mrtrix/mrtrix/responsemean.py +385 -0
- niwrap_mrtrix/mrtrix/sh2amp.py +844 -0
- niwrap_mrtrix/mrtrix/sh2peaks.py +632 -0
- niwrap_mrtrix/mrtrix/sh2power.py +427 -0
- niwrap_mrtrix/mrtrix/sh2response.py +481 -0
- niwrap_mrtrix/mrtrix/shbasis.py +445 -0
- niwrap_mrtrix/mrtrix/shconv.py +661 -0
- niwrap_mrtrix/mrtrix/tck2connectome.py +727 -0
- niwrap_mrtrix/mrtrix/tck2fixel.py +447 -0
- niwrap_mrtrix/mrtrix/tckconvert.py +775 -0
- niwrap_mrtrix/mrtrix/tckdfc.py +684 -0
- niwrap_mrtrix/mrtrix/tckedit.py +1478 -0
- niwrap_mrtrix/mrtrix/tckgen.py +2733 -0
- niwrap_mrtrix/mrtrix/tckglobal.py +944 -0
- niwrap_mrtrix/mrtrix/tckinfo.py +402 -0
- niwrap_mrtrix/mrtrix/tckmap.py +1004 -0
- niwrap_mrtrix/mrtrix/tckresample.py +760 -0
- niwrap_mrtrix/mrtrix/tcksample.py +497 -0
- niwrap_mrtrix/mrtrix/tcksift.py +739 -0
- niwrap_mrtrix/mrtrix/tcksift2.py +902 -0
- niwrap_mrtrix/mrtrix/tckstats.py +550 -0
- niwrap_mrtrix/mrtrix/tcktransform.py +414 -0
- niwrap_mrtrix/mrtrix/tensor2metric.py +659 -0
- niwrap_mrtrix/mrtrix/transformcalc.py +421 -0
- niwrap_mrtrix/mrtrix/transformcompose.py +625 -0
- niwrap_mrtrix/mrtrix/transformconvert.py +423 -0
- niwrap_mrtrix/mrtrix/tsfdivide.py +414 -0
- niwrap_mrtrix/mrtrix/tsfinfo.py +421 -0
- niwrap_mrtrix/mrtrix/tsfmult.py +401 -0
- niwrap_mrtrix/mrtrix/tsfsmooth.py +420 -0
- niwrap_mrtrix/mrtrix/tsfthreshold.py +428 -0
- niwrap_mrtrix/mrtrix/tsfvalidate.py +398 -0
- niwrap_mrtrix/mrtrix/v_5tt2gmwmi.py +432 -0
- niwrap_mrtrix/mrtrix/v_5tt2vis.py +505 -0
- niwrap_mrtrix/mrtrix/v_5ttcheck.py +409 -0
- niwrap_mrtrix/mrtrix/v_5ttedit.py +513 -0
- niwrap_mrtrix/mrtrix/v_5ttgen.py +1107 -0
- niwrap_mrtrix/mrtrix/vectorstats.py +736 -0
- niwrap_mrtrix/mrtrix/voxel2fixel.py +430 -0
- niwrap_mrtrix/mrtrix/voxel2mesh.py +454 -0
- niwrap_mrtrix/mrtrix/warp2metric.py +556 -0
- niwrap_mrtrix/mrtrix/warpconvert.py +498 -0
- niwrap_mrtrix/mrtrix/warpcorrect.py +448 -0
- niwrap_mrtrix/mrtrix/warpinit.py +425 -0
- niwrap_mrtrix/mrtrix/warpinvert.py +448 -0
- niwrap_mrtrix-0.8.0.dist-info/METADATA +8 -0
- niwrap_mrtrix-0.8.0.dist-info/RECORD +119 -0
- niwrap_mrtrix-0.8.0.dist-info/WHEEL +4 -0
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# This file was auto generated by Styx.
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# Do not edit this file directly.
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import typing
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import pathlib
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from styxdefs import *
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TENSOR2METRIC_METADATA = Metadata(
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id="27f4e9c1379c830bcec96cfb3c8b321a7c99c245.boutiques",
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name="tensor2metric",
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package="mrtrix",
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container_image_tag="mrtrix3/mrtrix3:3.0.4",
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)
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_Tensor2metricConfigParamsDictNoTag = typing.TypedDict('_Tensor2metricConfigParamsDictNoTag', {
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"key": str,
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"value": str,
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})
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Tensor2metricConfigParamsDictTagged = typing.TypedDict('Tensor2metricConfigParamsDictTagged', {
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"@type": typing.Literal["config"],
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"key": str,
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"value": str,
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})
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Tensor2metricConfigParamsDict = _Tensor2metricConfigParamsDictNoTag | Tensor2metricConfigParamsDictTagged
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_Tensor2metricParamsDictNoTag = typing.TypedDict('_Tensor2metricParamsDictNoTag', {
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"adc": typing.NotRequired[str | None],
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"fa": typing.NotRequired[str | None],
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"ad": typing.NotRequired[str | None],
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"rd": typing.NotRequired[str | None],
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"cl": typing.NotRequired[str | None],
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"cp": typing.NotRequired[str | None],
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"cs": typing.NotRequired[str | None],
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"value": typing.NotRequired[str | None],
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"vector": typing.NotRequired[str | None],
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"num": typing.NotRequired[list[int] | None],
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"modulate": typing.NotRequired[str | None],
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"mask": typing.NotRequired[InputPathType | None],
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"info": bool,
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"quiet": bool,
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"debug": bool,
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"force": bool,
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"nthreads": typing.NotRequired[int | None],
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"config": typing.NotRequired[list[Tensor2metricConfigParamsDict] | None],
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"help": bool,
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"version": bool,
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"tensor": InputPathType,
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})
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Tensor2metricParamsDictTagged = typing.TypedDict('Tensor2metricParamsDictTagged', {
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"@type": typing.Literal["mrtrix/tensor2metric"],
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"adc": typing.NotRequired[str | None],
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"fa": typing.NotRequired[str | None],
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"ad": typing.NotRequired[str | None],
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"rd": typing.NotRequired[str | None],
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"cl": typing.NotRequired[str | None],
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"cp": typing.NotRequired[str | None],
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"cs": typing.NotRequired[str | None],
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"value": typing.NotRequired[str | None],
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"vector": typing.NotRequired[str | None],
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"num": typing.NotRequired[list[int] | None],
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"modulate": typing.NotRequired[str | None],
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"mask": typing.NotRequired[InputPathType | None],
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"info": bool,
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"quiet": bool,
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"debug": bool,
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"force": bool,
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"nthreads": typing.NotRequired[int | None],
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"config": typing.NotRequired[list[Tensor2metricConfigParamsDict] | None],
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"help": bool,
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"version": bool,
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"tensor": InputPathType,
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})
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Tensor2metricParamsDict = _Tensor2metricParamsDictNoTag | Tensor2metricParamsDictTagged
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def tensor2metric_config(
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key: str,
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value: str,
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) -> Tensor2metricConfigParamsDictTagged:
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"""
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Build parameters.
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Args:
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key: temporarily set the value of an MRtrix config file entry.
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value: temporarily set the value of an MRtrix config file entry.
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Returns:
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Parameter dictionary
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"""
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params = {
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"@type": "config",
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"key": key,
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"value": value,
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}
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return params
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def tensor2metric_config_validate(
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params: typing.Any,
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"""
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Validate parameters. Throws an error if `params` is not a valid
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`Tensor2metricConfigParamsDict` object.
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Args:
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params: The parameters object to validate.
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"""
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if params is None or not isinstance(params, dict):
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raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
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if params.get("key", None) is None:
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raise StyxValidationError("`key` must not be None")
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if not isinstance(params["key"], str):
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raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
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raise StyxValidationError("`value` must not be None")
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if not isinstance(params["value"], str):
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raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
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def tensor2metric_config_cargs(
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params: Tensor2metricConfigParamsDict,
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execution: Execution,
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) -> list[str]:
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"""
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Build command-line arguments from parameters.
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Args:
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params: The parameters.
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execution: The execution object for resolving input paths.
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Returns:
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Command-line arguments.
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"""
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cargs = []
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cargs.append("-config")
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cargs.append(params.get("key", None))
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cargs.append(params.get("value", None))
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return cargs
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class Tensor2metricOutputs(typing.NamedTuple):
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"""
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Output object returned when calling `Tensor2metricParamsDict(...)`.
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"""
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root: OutputPathType
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"""Output root folder. This is the root folder for all outputs."""
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adc: OutputPathType | None
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tensor. (sometimes also referred to as the mean diffusivity (MD)) """
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fa: OutputPathType | None
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"""compute the fractional anisotropy (FA) of the diffusion tensor. """
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ad: OutputPathType | None
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"""compute the axial diffusivity (AD) of the diffusion tensor. (equivalent
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to the principal eigenvalue) """
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rd: OutputPathType | None
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"""compute the radial diffusivity (RD) of the diffusion tensor. (equivalent
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to the mean of the two non-principal eigenvalues) """
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cl: OutputPathType | None
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"""compute the linearity metric of the diffusion tensor. (one of the three
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Westin shape metrics) """
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cp: OutputPathType | None
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"""compute the planarity metric of the diffusion tensor. (one of the three
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Westin shape metrics) """
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cs: OutputPathType | None
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"""compute the sphericity metric of the diffusion tensor. (one of the three
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Westin shape metrics) """
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value: OutputPathType | None
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"""compute the selected eigenvalue(s) of the diffusion tensor. """
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vector: OutputPathType | None
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"""compute the selected eigenvector(s) of the diffusion tensor. """
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def tensor2metric_params(
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tensor: InputPathType,
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adc: str | None = None,
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fa: str | None = None,
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ad: str | None = None,
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rd: str | None = None,
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cl: str | None = None,
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cp: str | None = None,
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value: str | None = None,
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vector: str | None = None,
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quiet: bool = False,
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debug: bool = False,
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force: bool = False,
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nthreads: int | None = None,
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config: list[Tensor2metricConfigParamsDict] | None = None,
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help_: bool = False,
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version: bool = False,
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) -> Tensor2metricParamsDictTagged:
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"""
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Build parameters.
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Args:
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tensor: the input tensor image.
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adc: compute the mean apparent diffusion coefficient (ADC) of the\
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diffusion tensor. (sometimes also referred to as the mean diffusivity\
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(MD)).
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fa: compute the fractional anisotropy (FA) of the diffusion tensor.
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ad: compute the axial diffusivity (AD) of the diffusion tensor.\
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(equivalent to the principal eigenvalue).
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rd: compute the radial diffusivity (RD) of the diffusion tensor.\
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(equivalent to the mean of the two non-principal eigenvalues).
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209
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+
cl: compute the linearity metric of the diffusion tensor. (one of the\
|
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210
|
+
three Westin shape metrics).
|
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211
|
+
cp: compute the planarity metric of the diffusion tensor. (one of the\
|
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212
|
+
three Westin shape metrics).
|
|
213
|
+
cs: compute the sphericity metric of the diffusion tensor. (one of the\
|
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214
|
+
three Westin shape metrics).
|
|
215
|
+
value: compute the selected eigenvalue(s) of the diffusion tensor.
|
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216
|
+
vector: compute the selected eigenvector(s) of the diffusion tensor.
|
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217
|
+
num: specify the desired eigenvalue/eigenvector(s). Note that several\
|
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218
|
+
eigenvalues can be specified as a number sequence. For example, '1,3'\
|
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219
|
+
specifies the principal (1) and minor (3) eigenvalues/eigenvectors\
|
|
220
|
+
(default = 1).
|
|
221
|
+
modulate: specify how to modulate the magnitude of the eigenvectors.\
|
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222
|
+
Valid choices are: none, FA, eigval (default = FA).
|
|
223
|
+
mask: only perform computation within the specified binary brain mask\
|
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|
+
image.
|
|
225
|
+
info: display information messages.
|
|
226
|
+
quiet: do not display information messages or progress status;\
|
|
227
|
+
alternatively, this can be achieved by setting the MRTRIX_QUIET\
|
|
228
|
+
environment variable to a non-empty string.
|
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229
|
+
debug: display debugging messages.
|
|
230
|
+
force: force overwrite of output files (caution: using the same file as\
|
|
231
|
+
input and output might cause unexpected behaviour).
|
|
232
|
+
nthreads: use this number of threads in multi-threaded applications\
|
|
233
|
+
(set to 0 to disable multi-threading).
|
|
234
|
+
config: temporarily set the value of an MRtrix config file entry.
|
|
235
|
+
help_: display this information page and exit.
|
|
236
|
+
version: display version information and exit.
|
|
237
|
+
Returns:
|
|
238
|
+
Parameter dictionary
|
|
239
|
+
"""
|
|
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|
+
params = {
|
|
241
|
+
"@type": "mrtrix/tensor2metric",
|
|
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|
+
"info": info,
|
|
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|
+
"quiet": quiet,
|
|
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|
+
"debug": debug,
|
|
245
|
+
"force": force,
|
|
246
|
+
"help": help_,
|
|
247
|
+
"version": version,
|
|
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|
+
"tensor": tensor,
|
|
249
|
+
}
|
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|
+
if adc is not None:
|
|
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|
+
params["adc"] = adc
|
|
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|
+
if fa is not None:
|
|
253
|
+
params["fa"] = fa
|
|
254
|
+
if ad is not None:
|
|
255
|
+
params["ad"] = ad
|
|
256
|
+
if rd is not None:
|
|
257
|
+
params["rd"] = rd
|
|
258
|
+
if cl is not None:
|
|
259
|
+
params["cl"] = cl
|
|
260
|
+
if cp is not None:
|
|
261
|
+
params["cp"] = cp
|
|
262
|
+
if cs is not None:
|
|
263
|
+
params["cs"] = cs
|
|
264
|
+
if value is not None:
|
|
265
|
+
params["value"] = value
|
|
266
|
+
if vector is not None:
|
|
267
|
+
params["vector"] = vector
|
|
268
|
+
if num is not None:
|
|
269
|
+
params["num"] = num
|
|
270
|
+
if modulate is not None:
|
|
271
|
+
params["modulate"] = modulate
|
|
272
|
+
if mask is not None:
|
|
273
|
+
params["mask"] = mask
|
|
274
|
+
if nthreads is not None:
|
|
275
|
+
params["nthreads"] = nthreads
|
|
276
|
+
if config is not None:
|
|
277
|
+
params["config"] = config
|
|
278
|
+
return params
|
|
279
|
+
|
|
280
|
+
|
|
281
|
+
def tensor2metric_validate(
|
|
282
|
+
params: typing.Any,
|
|
283
|
+
) -> None:
|
|
284
|
+
"""
|
|
285
|
+
Validate parameters. Throws an error if `params` is not a valid
|
|
286
|
+
`Tensor2metricParamsDict` object.
|
|
287
|
+
|
|
288
|
+
Args:
|
|
289
|
+
params: The parameters object to validate.
|
|
290
|
+
"""
|
|
291
|
+
if params is None or not isinstance(params, dict):
|
|
292
|
+
raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
|
|
293
|
+
if params.get("adc", None) is not None:
|
|
294
|
+
if not isinstance(params["adc"], str):
|
|
295
|
+
raise StyxValidationError(f'`adc` has the wrong type: Received `{type(params.get("adc", None))}` expected `str | None`')
|
|
296
|
+
if params.get("fa", None) is not None:
|
|
297
|
+
if not isinstance(params["fa"], str):
|
|
298
|
+
raise StyxValidationError(f'`fa` has the wrong type: Received `{type(params.get("fa", None))}` expected `str | None`')
|
|
299
|
+
if params.get("ad", None) is not None:
|
|
300
|
+
if not isinstance(params["ad"], str):
|
|
301
|
+
raise StyxValidationError(f'`ad` has the wrong type: Received `{type(params.get("ad", None))}` expected `str | None`')
|
|
302
|
+
if params.get("rd", None) is not None:
|
|
303
|
+
if not isinstance(params["rd"], str):
|
|
304
|
+
raise StyxValidationError(f'`rd` has the wrong type: Received `{type(params.get("rd", None))}` expected `str | None`')
|
|
305
|
+
if params.get("cl", None) is not None:
|
|
306
|
+
if not isinstance(params["cl"], str):
|
|
307
|
+
raise StyxValidationError(f'`cl` has the wrong type: Received `{type(params.get("cl", None))}` expected `str | None`')
|
|
308
|
+
if params.get("cp", None) is not None:
|
|
309
|
+
if not isinstance(params["cp"], str):
|
|
310
|
+
raise StyxValidationError(f'`cp` has the wrong type: Received `{type(params.get("cp", None))}` expected `str | None`')
|
|
311
|
+
if params.get("cs", None) is not None:
|
|
312
|
+
if not isinstance(params["cs"], str):
|
|
313
|
+
raise StyxValidationError(f'`cs` has the wrong type: Received `{type(params.get("cs", None))}` expected `str | None`')
|
|
314
|
+
if params.get("value", None) is not None:
|
|
315
|
+
if not isinstance(params["value"], str):
|
|
316
|
+
raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str | None`')
|
|
317
|
+
if params.get("vector", None) is not None:
|
|
318
|
+
if not isinstance(params["vector"], str):
|
|
319
|
+
raise StyxValidationError(f'`vector` has the wrong type: Received `{type(params.get("vector", None))}` expected `str | None`')
|
|
320
|
+
if params.get("num", None) is not None:
|
|
321
|
+
if not isinstance(params["num"], list):
|
|
322
|
+
raise StyxValidationError(f'`num` has the wrong type: Received `{type(params.get("num", None))}` expected `list[int] | None`')
|
|
323
|
+
for e in params["num"]:
|
|
324
|
+
if not isinstance(e, int):
|
|
325
|
+
raise StyxValidationError(f'`num` has the wrong type: Received `{type(params.get("num", None))}` expected `list[int] | None`')
|
|
326
|
+
if params.get("modulate", None) is not None:
|
|
327
|
+
if not isinstance(params["modulate"], str):
|
|
328
|
+
raise StyxValidationError(f'`modulate` has the wrong type: Received `{type(params.get("modulate", None))}` expected `str | None`')
|
|
329
|
+
if params.get("mask", None) is not None:
|
|
330
|
+
if not isinstance(params["mask"], (pathlib.Path, str)):
|
|
331
|
+
raise StyxValidationError(f'`mask` has the wrong type: Received `{type(params.get("mask", None))}` expected `InputPathType | None`')
|
|
332
|
+
if params.get("info", False) is None:
|
|
333
|
+
raise StyxValidationError("`info` must not be None")
|
|
334
|
+
if not isinstance(params["info"], bool):
|
|
335
|
+
raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
|
|
336
|
+
if params.get("quiet", False) is None:
|
|
337
|
+
raise StyxValidationError("`quiet` must not be None")
|
|
338
|
+
if not isinstance(params["quiet"], bool):
|
|
339
|
+
raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
|
|
340
|
+
if params.get("debug", False) is None:
|
|
341
|
+
raise StyxValidationError("`debug` must not be None")
|
|
342
|
+
if not isinstance(params["debug"], bool):
|
|
343
|
+
raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
|
|
344
|
+
if params.get("force", False) is None:
|
|
345
|
+
raise StyxValidationError("`force` must not be None")
|
|
346
|
+
if not isinstance(params["force"], bool):
|
|
347
|
+
raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
|
|
348
|
+
if params.get("nthreads", None) is not None:
|
|
349
|
+
if not isinstance(params["nthreads"], int):
|
|
350
|
+
raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
|
|
351
|
+
if params.get("config", None) is not None:
|
|
352
|
+
if not isinstance(params["config"], list):
|
|
353
|
+
raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[Tensor2metricConfigParamsDict] | None`')
|
|
354
|
+
for e in params["config"]:
|
|
355
|
+
tensor2metric_config_validate(e)
|
|
356
|
+
if params.get("help", False) is None:
|
|
357
|
+
raise StyxValidationError("`help` must not be None")
|
|
358
|
+
if not isinstance(params["help"], bool):
|
|
359
|
+
raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
|
|
360
|
+
if params.get("version", False) is None:
|
|
361
|
+
raise StyxValidationError("`version` must not be None")
|
|
362
|
+
if not isinstance(params["version"], bool):
|
|
363
|
+
raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
|
|
364
|
+
if params.get("tensor", None) is None:
|
|
365
|
+
raise StyxValidationError("`tensor` must not be None")
|
|
366
|
+
if not isinstance(params["tensor"], (pathlib.Path, str)):
|
|
367
|
+
raise StyxValidationError(f'`tensor` has the wrong type: Received `{type(params.get("tensor", None))}` expected `InputPathType`')
|
|
368
|
+
|
|
369
|
+
|
|
370
|
+
def tensor2metric_cargs(
|
|
371
|
+
params: Tensor2metricParamsDict,
|
|
372
|
+
execution: Execution,
|
|
373
|
+
) -> list[str]:
|
|
374
|
+
"""
|
|
375
|
+
Build command-line arguments from parameters.
|
|
376
|
+
|
|
377
|
+
Args:
|
|
378
|
+
params: The parameters.
|
|
379
|
+
execution: The execution object for resolving input paths.
|
|
380
|
+
Returns:
|
|
381
|
+
Command-line arguments.
|
|
382
|
+
"""
|
|
383
|
+
cargs = []
|
|
384
|
+
cargs.append("tensor2metric")
|
|
385
|
+
if params.get("adc", None) is not None:
|
|
386
|
+
cargs.extend([
|
|
387
|
+
"-adc",
|
|
388
|
+
params.get("adc", None)
|
|
389
|
+
])
|
|
390
|
+
if params.get("fa", None) is not None:
|
|
391
|
+
cargs.extend([
|
|
392
|
+
"-fa",
|
|
393
|
+
params.get("fa", None)
|
|
394
|
+
])
|
|
395
|
+
if params.get("ad", None) is not None:
|
|
396
|
+
cargs.extend([
|
|
397
|
+
"-ad",
|
|
398
|
+
params.get("ad", None)
|
|
399
|
+
])
|
|
400
|
+
if params.get("rd", None) is not None:
|
|
401
|
+
cargs.extend([
|
|
402
|
+
"-rd",
|
|
403
|
+
params.get("rd", None)
|
|
404
|
+
])
|
|
405
|
+
if params.get("cl", None) is not None:
|
|
406
|
+
cargs.extend([
|
|
407
|
+
"-cl",
|
|
408
|
+
params.get("cl", None)
|
|
409
|
+
])
|
|
410
|
+
if params.get("cp", None) is not None:
|
|
411
|
+
cargs.extend([
|
|
412
|
+
"-cp",
|
|
413
|
+
params.get("cp", None)
|
|
414
|
+
])
|
|
415
|
+
if params.get("cs", None) is not None:
|
|
416
|
+
cargs.extend([
|
|
417
|
+
"-cs",
|
|
418
|
+
params.get("cs", None)
|
|
419
|
+
])
|
|
420
|
+
if params.get("value", None) is not None:
|
|
421
|
+
cargs.extend([
|
|
422
|
+
"-value",
|
|
423
|
+
params.get("value", None)
|
|
424
|
+
])
|
|
425
|
+
if params.get("vector", None) is not None:
|
|
426
|
+
cargs.extend([
|
|
427
|
+
"-vector",
|
|
428
|
+
params.get("vector", None)
|
|
429
|
+
])
|
|
430
|
+
if params.get("num", None) is not None:
|
|
431
|
+
cargs.extend([
|
|
432
|
+
"-num",
|
|
433
|
+
*map(str, params.get("num", None))
|
|
434
|
+
])
|
|
435
|
+
if params.get("modulate", None) is not None:
|
|
436
|
+
cargs.extend([
|
|
437
|
+
"-modulate",
|
|
438
|
+
params.get("modulate", None)
|
|
439
|
+
])
|
|
440
|
+
if params.get("mask", None) is not None:
|
|
441
|
+
cargs.extend([
|
|
442
|
+
"-mask",
|
|
443
|
+
execution.input_file(params.get("mask", None))
|
|
444
|
+
])
|
|
445
|
+
if params.get("info", False):
|
|
446
|
+
cargs.append("-info")
|
|
447
|
+
if params.get("quiet", False):
|
|
448
|
+
cargs.append("-quiet")
|
|
449
|
+
if params.get("debug", False):
|
|
450
|
+
cargs.append("-debug")
|
|
451
|
+
if params.get("force", False):
|
|
452
|
+
cargs.append("-force")
|
|
453
|
+
if params.get("nthreads", None) is not None:
|
|
454
|
+
cargs.extend([
|
|
455
|
+
"-nthreads",
|
|
456
|
+
str(params.get("nthreads", None))
|
|
457
|
+
])
|
|
458
|
+
if params.get("config", None) is not None:
|
|
459
|
+
cargs.extend([a for c in [tensor2metric_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
|
|
460
|
+
if params.get("help", False):
|
|
461
|
+
cargs.append("-help")
|
|
462
|
+
if params.get("version", False):
|
|
463
|
+
cargs.append("-version")
|
|
464
|
+
cargs.append(execution.input_file(params.get("tensor", None)))
|
|
465
|
+
return cargs
|
|
466
|
+
|
|
467
|
+
|
|
468
|
+
def tensor2metric_outputs(
|
|
469
|
+
params: Tensor2metricParamsDict,
|
|
470
|
+
execution: Execution,
|
|
471
|
+
) -> Tensor2metricOutputs:
|
|
472
|
+
"""
|
|
473
|
+
Build outputs object containing output file paths and possibly stdout/stderr.
|
|
474
|
+
|
|
475
|
+
Args:
|
|
476
|
+
params: The parameters.
|
|
477
|
+
execution: The execution object for resolving input paths.
|
|
478
|
+
Returns:
|
|
479
|
+
Outputs object.
|
|
480
|
+
"""
|
|
481
|
+
ret = Tensor2metricOutputs(
|
|
482
|
+
root=execution.output_file("."),
|
|
483
|
+
adc=execution.output_file(params.get("adc", None)) if (params.get("adc") is not None) else None,
|
|
484
|
+
fa=execution.output_file(params.get("fa", None)) if (params.get("fa") is not None) else None,
|
|
485
|
+
ad=execution.output_file(params.get("ad", None)) if (params.get("ad") is not None) else None,
|
|
486
|
+
rd=execution.output_file(params.get("rd", None)) if (params.get("rd") is not None) else None,
|
|
487
|
+
cl=execution.output_file(params.get("cl", None)) if (params.get("cl") is not None) else None,
|
|
488
|
+
cp=execution.output_file(params.get("cp", None)) if (params.get("cp") is not None) else None,
|
|
489
|
+
cs=execution.output_file(params.get("cs", None)) if (params.get("cs") is not None) else None,
|
|
490
|
+
value=execution.output_file(params.get("value", None)) if (params.get("value") is not None) else None,
|
|
491
|
+
vector=execution.output_file(params.get("vector", None)) if (params.get("vector") is not None) else None,
|
|
492
|
+
)
|
|
493
|
+
return ret
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
def tensor2metric_execute(
|
|
497
|
+
params: Tensor2metricParamsDict,
|
|
498
|
+
runner: Runner | None = None,
|
|
499
|
+
) -> Tensor2metricOutputs:
|
|
500
|
+
"""
|
|
501
|
+
tensor2metric
|
|
502
|
+
|
|
503
|
+
Generate maps of tensor-derived parameters.
|
|
504
|
+
|
|
505
|
+
|
|
506
|
+
|
|
507
|
+
References:
|
|
508
|
+
|
|
509
|
+
Basser, P. J.; Mattiello, J. & Lebihan, D. MR diffusion tensor spectroscopy
|
|
510
|
+
and imaging. Biophysical Journal, 1994, 66, 259-267
|
|
511
|
+
|
|
512
|
+
Westin, C. F.; Peled, S.; Gudbjartsson, H.; Kikinis, R. & Jolesz, F. A.
|
|
513
|
+
Geometrical diffusion measures for MRI from tensor basis analysis. Proc Intl
|
|
514
|
+
Soc Mag Reson Med, 1997, 5, 1742.
|
|
515
|
+
|
|
516
|
+
Author: MRTrix3 Developers
|
|
517
|
+
|
|
518
|
+
URL: https://www.mrtrix.org/
|
|
519
|
+
|
|
520
|
+
Args:
|
|
521
|
+
params: The parameters.
|
|
522
|
+
runner: Command runner.
|
|
523
|
+
Returns:
|
|
524
|
+
NamedTuple of outputs (described in `Tensor2metricOutputs`).
|
|
525
|
+
"""
|
|
526
|
+
tensor2metric_validate(params)
|
|
527
|
+
runner = runner or get_global_runner()
|
|
528
|
+
execution = runner.start_execution(TENSOR2METRIC_METADATA)
|
|
529
|
+
params = execution.params(params)
|
|
530
|
+
cargs = tensor2metric_cargs(params, execution)
|
|
531
|
+
ret = tensor2metric_outputs(params, execution)
|
|
532
|
+
execution.run(cargs)
|
|
533
|
+
return ret
|
|
534
|
+
|
|
535
|
+
|
|
536
|
+
def tensor2metric(
|
|
537
|
+
tensor: InputPathType,
|
|
538
|
+
adc: str | None = None,
|
|
539
|
+
fa: str | None = None,
|
|
540
|
+
ad: str | None = None,
|
|
541
|
+
rd: str | None = None,
|
|
542
|
+
cl: str | None = None,
|
|
543
|
+
cp: str | None = None,
|
|
544
|
+
cs: str | None = None,
|
|
545
|
+
value: str | None = None,
|
|
546
|
+
vector: str | None = None,
|
|
547
|
+
num: list[int] | None = None,
|
|
548
|
+
modulate: str | None = None,
|
|
549
|
+
mask: InputPathType | None = None,
|
|
550
|
+
info: bool = False,
|
|
551
|
+
quiet: bool = False,
|
|
552
|
+
debug: bool = False,
|
|
553
|
+
force: bool = False,
|
|
554
|
+
nthreads: int | None = None,
|
|
555
|
+
config: list[Tensor2metricConfigParamsDict] | None = None,
|
|
556
|
+
help_: bool = False,
|
|
557
|
+
version: bool = False,
|
|
558
|
+
runner: Runner | None = None,
|
|
559
|
+
) -> Tensor2metricOutputs:
|
|
560
|
+
"""
|
|
561
|
+
tensor2metric
|
|
562
|
+
|
|
563
|
+
Generate maps of tensor-derived parameters.
|
|
564
|
+
|
|
565
|
+
|
|
566
|
+
|
|
567
|
+
References:
|
|
568
|
+
|
|
569
|
+
Basser, P. J.; Mattiello, J. & Lebihan, D. MR diffusion tensor spectroscopy
|
|
570
|
+
and imaging. Biophysical Journal, 1994, 66, 259-267
|
|
571
|
+
|
|
572
|
+
Westin, C. F.; Peled, S.; Gudbjartsson, H.; Kikinis, R. & Jolesz, F. A.
|
|
573
|
+
Geometrical diffusion measures for MRI from tensor basis analysis. Proc Intl
|
|
574
|
+
Soc Mag Reson Med, 1997, 5, 1742.
|
|
575
|
+
|
|
576
|
+
Author: MRTrix3 Developers
|
|
577
|
+
|
|
578
|
+
URL: https://www.mrtrix.org/
|
|
579
|
+
|
|
580
|
+
Args:
|
|
581
|
+
tensor: the input tensor image.
|
|
582
|
+
adc: compute the mean apparent diffusion coefficient (ADC) of the\
|
|
583
|
+
diffusion tensor. (sometimes also referred to as the mean diffusivity\
|
|
584
|
+
(MD)).
|
|
585
|
+
fa: compute the fractional anisotropy (FA) of the diffusion tensor.
|
|
586
|
+
ad: compute the axial diffusivity (AD) of the diffusion tensor.\
|
|
587
|
+
(equivalent to the principal eigenvalue).
|
|
588
|
+
rd: compute the radial diffusivity (RD) of the diffusion tensor.\
|
|
589
|
+
(equivalent to the mean of the two non-principal eigenvalues).
|
|
590
|
+
cl: compute the linearity metric of the diffusion tensor. (one of the\
|
|
591
|
+
three Westin shape metrics).
|
|
592
|
+
cp: compute the planarity metric of the diffusion tensor. (one of the\
|
|
593
|
+
three Westin shape metrics).
|
|
594
|
+
cs: compute the sphericity metric of the diffusion tensor. (one of the\
|
|
595
|
+
three Westin shape metrics).
|
|
596
|
+
value: compute the selected eigenvalue(s) of the diffusion tensor.
|
|
597
|
+
vector: compute the selected eigenvector(s) of the diffusion tensor.
|
|
598
|
+
num: specify the desired eigenvalue/eigenvector(s). Note that several\
|
|
599
|
+
eigenvalues can be specified as a number sequence. For example, '1,3'\
|
|
600
|
+
specifies the principal (1) and minor (3) eigenvalues/eigenvectors\
|
|
601
|
+
(default = 1).
|
|
602
|
+
modulate: specify how to modulate the magnitude of the eigenvectors.\
|
|
603
|
+
Valid choices are: none, FA, eigval (default = FA).
|
|
604
|
+
mask: only perform computation within the specified binary brain mask\
|
|
605
|
+
image.
|
|
606
|
+
info: display information messages.
|
|
607
|
+
quiet: do not display information messages or progress status;\
|
|
608
|
+
alternatively, this can be achieved by setting the MRTRIX_QUIET\
|
|
609
|
+
environment variable to a non-empty string.
|
|
610
|
+
debug: display debugging messages.
|
|
611
|
+
force: force overwrite of output files (caution: using the same file as\
|
|
612
|
+
input and output might cause unexpected behaviour).
|
|
613
|
+
nthreads: use this number of threads in multi-threaded applications\
|
|
614
|
+
(set to 0 to disable multi-threading).
|
|
615
|
+
config: temporarily set the value of an MRtrix config file entry.
|
|
616
|
+
help_: display this information page and exit.
|
|
617
|
+
version: display version information and exit.
|
|
618
|
+
runner: Command runner.
|
|
619
|
+
Returns:
|
|
620
|
+
NamedTuple of outputs (described in `Tensor2metricOutputs`).
|
|
621
|
+
"""
|
|
622
|
+
params = tensor2metric_params(
|
|
623
|
+
adc=adc,
|
|
624
|
+
fa=fa,
|
|
625
|
+
ad=ad,
|
|
626
|
+
rd=rd,
|
|
627
|
+
cl=cl,
|
|
628
|
+
cp=cp,
|
|
629
|
+
cs=cs,
|
|
630
|
+
value=value,
|
|
631
|
+
vector=vector,
|
|
632
|
+
num=num,
|
|
633
|
+
modulate=modulate,
|
|
634
|
+
mask=mask,
|
|
635
|
+
info=info,
|
|
636
|
+
quiet=quiet,
|
|
637
|
+
debug=debug,
|
|
638
|
+
force=force,
|
|
639
|
+
nthreads=nthreads,
|
|
640
|
+
config=config,
|
|
641
|
+
help_=help_,
|
|
642
|
+
version=version,
|
|
643
|
+
tensor=tensor,
|
|
644
|
+
)
|
|
645
|
+
return tensor2metric_execute(params, runner)
|
|
646
|
+
|
|
647
|
+
|
|
648
|
+
__all__ = [
|
|
649
|
+
"TENSOR2METRIC_METADATA",
|
|
650
|
+
"Tensor2metricConfigParamsDict",
|
|
651
|
+
"Tensor2metricConfigParamsDictTagged",
|
|
652
|
+
"Tensor2metricOutputs",
|
|
653
|
+
"Tensor2metricParamsDict",
|
|
654
|
+
"Tensor2metricParamsDictTagged",
|
|
655
|
+
"tensor2metric",
|
|
656
|
+
"tensor2metric_config",
|
|
657
|
+
"tensor2metric_execute",
|
|
658
|
+
"tensor2metric_params",
|
|
659
|
+
]
|