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.
Files changed (119) hide show
  1. niwrap_mrtrix/mrtrix/__init__.py +263 -0
  2. niwrap_mrtrix/mrtrix/afdconnectivity.py +527 -0
  3. niwrap_mrtrix/mrtrix/amp2response.py +560 -0
  4. niwrap_mrtrix/mrtrix/amp2sh.py +870 -0
  5. niwrap_mrtrix/mrtrix/connectome2tck.py +583 -0
  6. niwrap_mrtrix/mrtrix/connectomeedit.py +413 -0
  7. niwrap_mrtrix/mrtrix/connectomestats.py +956 -0
  8. niwrap_mrtrix/mrtrix/dcmedit.py +552 -0
  9. niwrap_mrtrix/mrtrix/dcminfo.py +529 -0
  10. niwrap_mrtrix/mrtrix/dirflip.py +440 -0
  11. niwrap_mrtrix/mrtrix/dirgen.py +514 -0
  12. niwrap_mrtrix/mrtrix/dirmerge.py +446 -0
  13. niwrap_mrtrix/mrtrix/dirorder.py +421 -0
  14. niwrap_mrtrix/mrtrix/dirsplit.py +436 -0
  15. niwrap_mrtrix/mrtrix/dirstat.py +640 -0
  16. niwrap_mrtrix/mrtrix/dwi2adc.py +531 -0
  17. niwrap_mrtrix/mrtrix/dwi2fod.py +1156 -0
  18. niwrap_mrtrix/mrtrix/dwi2mask.py +570 -0
  19. niwrap_mrtrix/mrtrix/dwi2response.py +1774 -0
  20. niwrap_mrtrix/mrtrix/dwi2tensor.py +715 -0
  21. niwrap_mrtrix/mrtrix/dwibiascorrect.py +673 -0
  22. niwrap_mrtrix/mrtrix/dwidenoise.py +570 -0
  23. niwrap_mrtrix/mrtrix/dwiextract.py +1111 -0
  24. niwrap_mrtrix/mrtrix/dwigradcheck.py +665 -0
  25. niwrap_mrtrix/mrtrix/fixel2peaks.py +613 -0
  26. niwrap_mrtrix/mrtrix/fixel2sh.py +430 -0
  27. niwrap_mrtrix/mrtrix/fixel2tsf.py +435 -0
  28. niwrap_mrtrix/mrtrix/fixel2voxel.py +523 -0
  29. niwrap_mrtrix/mrtrix/fixelcfestats.py +1179 -0
  30. niwrap_mrtrix/mrtrix/fixelconnectivity.py +477 -0
  31. niwrap_mrtrix/mrtrix/fixelconvert.py +850 -0
  32. niwrap_mrtrix/mrtrix/fixelcorrespondence.py +455 -0
  33. niwrap_mrtrix/mrtrix/fixelcrop.py +422 -0
  34. niwrap_mrtrix/mrtrix/fixelfilter.py +882 -0
  35. niwrap_mrtrix/mrtrix/fixelreorient.py +435 -0
  36. niwrap_mrtrix/mrtrix/fod2dec.py +571 -0
  37. niwrap_mrtrix/mrtrix/fod2fixel.py +646 -0
  38. niwrap_mrtrix/mrtrix/label2colour.py +426 -0
  39. niwrap_mrtrix/mrtrix/label2mesh.py +417 -0
  40. niwrap_mrtrix/mrtrix/labelconvert.py +460 -0
  41. niwrap_mrtrix/mrtrix/labelstats.py +418 -0
  42. niwrap_mrtrix/mrtrix/maskdump.py +404 -0
  43. niwrap_mrtrix/mrtrix/maskfilter.py +730 -0
  44. niwrap_mrtrix/mrtrix/mesh2voxel.py +422 -0
  45. niwrap_mrtrix/mrtrix/meshconvert.py +514 -0
  46. niwrap_mrtrix/mrtrix/meshfilter.py +452 -0
  47. niwrap_mrtrix/mrtrix/mraverageheader.py +485 -0
  48. niwrap_mrtrix/mrtrix/mrcalc.py +4302 -0
  49. niwrap_mrtrix/mrtrix/mrcat.py +467 -0
  50. niwrap_mrtrix/mrtrix/mrcentroid.py +418 -0
  51. niwrap_mrtrix/mrtrix/mrcheckerboardmask.py +446 -0
  52. niwrap_mrtrix/mrtrix/mrclusterstats.py +930 -0
  53. niwrap_mrtrix/mrtrix/mrcolour.py +490 -0
  54. niwrap_mrtrix/mrtrix/mrconvert.py +1967 -0
  55. niwrap_mrtrix/mrtrix/mrdegibbs.py +535 -0
  56. niwrap_mrtrix/mrtrix/mrdump.py +423 -0
  57. niwrap_mrtrix/mrtrix/mredit.py +737 -0
  58. niwrap_mrtrix/mrtrix/mrfilter.py +971 -0
  59. niwrap_mrtrix/mrtrix/mrgrid.py +1079 -0
  60. niwrap_mrtrix/mrtrix/mrhistmatch.py +494 -0
  61. niwrap_mrtrix/mrtrix/mrhistogram.py +484 -0
  62. niwrap_mrtrix/mrtrix/mrinfo.py +1282 -0
  63. niwrap_mrtrix/mrtrix/mrmath.py +503 -0
  64. niwrap_mrtrix/mrtrix/mrmetric.py +525 -0
  65. niwrap_mrtrix/mrtrix/mrregister.py +2098 -0
  66. niwrap_mrtrix/mrtrix/mrstats.py +534 -0
  67. niwrap_mrtrix/mrtrix/mrthreshold.py +666 -0
  68. niwrap_mrtrix/mrtrix/mrtransform.py +1372 -0
  69. niwrap_mrtrix/mrtrix/mtnormalise.py +725 -0
  70. niwrap_mrtrix/mrtrix/peaks2amp.py +403 -0
  71. niwrap_mrtrix/mrtrix/peaks2fixel.py +422 -0
  72. niwrap_mrtrix/mrtrix/responsemean.py +385 -0
  73. niwrap_mrtrix/mrtrix/sh2amp.py +844 -0
  74. niwrap_mrtrix/mrtrix/sh2peaks.py +632 -0
  75. niwrap_mrtrix/mrtrix/sh2power.py +427 -0
  76. niwrap_mrtrix/mrtrix/sh2response.py +481 -0
  77. niwrap_mrtrix/mrtrix/shbasis.py +445 -0
  78. niwrap_mrtrix/mrtrix/shconv.py +661 -0
  79. niwrap_mrtrix/mrtrix/tck2connectome.py +727 -0
  80. niwrap_mrtrix/mrtrix/tck2fixel.py +447 -0
  81. niwrap_mrtrix/mrtrix/tckconvert.py +775 -0
  82. niwrap_mrtrix/mrtrix/tckdfc.py +684 -0
  83. niwrap_mrtrix/mrtrix/tckedit.py +1478 -0
  84. niwrap_mrtrix/mrtrix/tckgen.py +2733 -0
  85. niwrap_mrtrix/mrtrix/tckglobal.py +944 -0
  86. niwrap_mrtrix/mrtrix/tckinfo.py +402 -0
  87. niwrap_mrtrix/mrtrix/tckmap.py +1004 -0
  88. niwrap_mrtrix/mrtrix/tckresample.py +760 -0
  89. niwrap_mrtrix/mrtrix/tcksample.py +497 -0
  90. niwrap_mrtrix/mrtrix/tcksift.py +739 -0
  91. niwrap_mrtrix/mrtrix/tcksift2.py +902 -0
  92. niwrap_mrtrix/mrtrix/tckstats.py +550 -0
  93. niwrap_mrtrix/mrtrix/tcktransform.py +414 -0
  94. niwrap_mrtrix/mrtrix/tensor2metric.py +659 -0
  95. niwrap_mrtrix/mrtrix/transformcalc.py +421 -0
  96. niwrap_mrtrix/mrtrix/transformcompose.py +625 -0
  97. niwrap_mrtrix/mrtrix/transformconvert.py +423 -0
  98. niwrap_mrtrix/mrtrix/tsfdivide.py +414 -0
  99. niwrap_mrtrix/mrtrix/tsfinfo.py +421 -0
  100. niwrap_mrtrix/mrtrix/tsfmult.py +401 -0
  101. niwrap_mrtrix/mrtrix/tsfsmooth.py +420 -0
  102. niwrap_mrtrix/mrtrix/tsfthreshold.py +428 -0
  103. niwrap_mrtrix/mrtrix/tsfvalidate.py +398 -0
  104. niwrap_mrtrix/mrtrix/v_5tt2gmwmi.py +432 -0
  105. niwrap_mrtrix/mrtrix/v_5tt2vis.py +505 -0
  106. niwrap_mrtrix/mrtrix/v_5ttcheck.py +409 -0
  107. niwrap_mrtrix/mrtrix/v_5ttedit.py +513 -0
  108. niwrap_mrtrix/mrtrix/v_5ttgen.py +1107 -0
  109. niwrap_mrtrix/mrtrix/vectorstats.py +736 -0
  110. niwrap_mrtrix/mrtrix/voxel2fixel.py +430 -0
  111. niwrap_mrtrix/mrtrix/voxel2mesh.py +454 -0
  112. niwrap_mrtrix/mrtrix/warp2metric.py +556 -0
  113. niwrap_mrtrix/mrtrix/warpconvert.py +498 -0
  114. niwrap_mrtrix/mrtrix/warpcorrect.py +448 -0
  115. niwrap_mrtrix/mrtrix/warpinit.py +425 -0
  116. niwrap_mrtrix/mrtrix/warpinvert.py +448 -0
  117. niwrap_mrtrix-0.8.0.dist-info/METADATA +8 -0
  118. niwrap_mrtrix-0.8.0.dist-info/RECORD +119 -0
  119. niwrap_mrtrix-0.8.0.dist-info/WHEEL +4 -0
@@ -0,0 +1,1282 @@
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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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+
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+ import typing
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+ import pathlib
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+ from styxdefs import *
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+
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+ MRINFO_METADATA = Metadata(
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+ id="8282cf2096dd2c6c171488cc71738cd947e2697c.boutiques",
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+ name="mrinfo",
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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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+
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+
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+ _MrinfoPropertyParamsDictNoTag = typing.TypedDict('_MrinfoPropertyParamsDictNoTag', {
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+ "key": str,
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+ })
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+ MrinfoPropertyParamsDictTagged = typing.TypedDict('MrinfoPropertyParamsDictTagged', {
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+ "@type": typing.Literal["property"],
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+ "key": str,
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+ })
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+ MrinfoPropertyParamsDict = _MrinfoPropertyParamsDictNoTag | MrinfoPropertyParamsDictTagged
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+
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+
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+ _MrinfoFslgradParamsDictNoTag = typing.TypedDict('_MrinfoFslgradParamsDictNoTag', {
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+ "bvecs": InputPathType,
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+ "bvals": InputPathType,
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+ })
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+ MrinfoFslgradParamsDictTagged = typing.TypedDict('MrinfoFslgradParamsDictTagged', {
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+ "@type": typing.Literal["fslgrad"],
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+ "bvecs": InputPathType,
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+ "bvals": InputPathType,
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+ })
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+ MrinfoFslgradParamsDict = _MrinfoFslgradParamsDictNoTag | MrinfoFslgradParamsDictTagged
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+
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+
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+ _MrinfoExportGradFslParamsDictNoTag = typing.TypedDict('_MrinfoExportGradFslParamsDictNoTag', {
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+ "bvecs_path": str,
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+ "bvals_path": str,
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+ })
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+ MrinfoExportGradFslParamsDictTagged = typing.TypedDict('MrinfoExportGradFslParamsDictTagged', {
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+ "@type": typing.Literal["export_grad_fsl"],
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+ "bvecs_path": str,
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+ "bvals_path": str,
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+ })
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+ MrinfoExportGradFslParamsDict = _MrinfoExportGradFslParamsDictNoTag | MrinfoExportGradFslParamsDictTagged
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+
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+
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+ _MrinfoExportPeEddyParamsDictNoTag = typing.TypedDict('_MrinfoExportPeEddyParamsDictNoTag', {
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+ "config": str,
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+ "indices": str,
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+ })
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+ MrinfoExportPeEddyParamsDictTagged = typing.TypedDict('MrinfoExportPeEddyParamsDictTagged', {
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+ "@type": typing.Literal["export_pe_eddy"],
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+ "config": str,
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+ "indices": str,
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+ })
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+ MrinfoExportPeEddyParamsDict = _MrinfoExportPeEddyParamsDictNoTag | MrinfoExportPeEddyParamsDictTagged
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+
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+
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+ _MrinfoConfigParamsDictNoTag = typing.TypedDict('_MrinfoConfigParamsDictNoTag', {
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+ "key": str,
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+ "value": str,
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+ })
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+ MrinfoConfigParamsDictTagged = typing.TypedDict('MrinfoConfigParamsDictTagged', {
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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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+ MrinfoConfigParamsDict = _MrinfoConfigParamsDictNoTag | MrinfoConfigParamsDictTagged
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+
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+
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+ _MrinfoParamsDictNoTag = typing.TypedDict('_MrinfoParamsDictNoTag', {
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+ "all": bool,
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+ "name": bool,
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+ "format": bool,
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+ "ndim": bool,
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+ "size": bool,
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+ "spacing": bool,
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+ "datatype": bool,
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+ "strides": bool,
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+ "offset": bool,
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+ "multiplier": bool,
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+ "transform": bool,
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+ "property": typing.NotRequired[list[MrinfoPropertyParamsDict] | None],
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+ "json_keyval": typing.NotRequired[str | None],
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+ "json_all": typing.NotRequired[str | None],
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+ "grad": typing.NotRequired[InputPathType | None],
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+ "fslgrad": typing.NotRequired[MrinfoFslgradParamsDict | None],
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+ "bvalue_scaling": typing.NotRequired[str | None],
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+ "export_grad_mrtrix": typing.NotRequired[str | None],
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+ "export_grad_fsl": typing.NotRequired[MrinfoExportGradFslParamsDict | None],
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+ "dwgrad": bool,
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+ "shell_bvalues": bool,
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+ "shell_sizes": bool,
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+ "shell_indices": bool,
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+ "export_pe_table": typing.NotRequired[str | None],
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+ "export_pe_eddy": typing.NotRequired[MrinfoExportPeEddyParamsDict | None],
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+ "petable": bool,
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+ "nodelete": bool,
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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[MrinfoConfigParamsDict] | None],
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+ "help": bool,
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+ "version": bool,
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+ "image": list[InputPathType],
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+ })
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+ MrinfoParamsDictTagged = typing.TypedDict('MrinfoParamsDictTagged', {
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+ "@type": typing.Literal["mrtrix/mrinfo"],
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+ "all": bool,
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+ "name": bool,
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+ "format": bool,
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+ "ndim": bool,
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+ "size": bool,
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+ "spacing": bool,
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+ "datatype": bool,
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+ "strides": bool,
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+ "offset": bool,
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+ "multiplier": bool,
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+ "transform": bool,
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+ "property": typing.NotRequired[list[MrinfoPropertyParamsDict] | None],
126
+ "json_keyval": typing.NotRequired[str | None],
127
+ "json_all": typing.NotRequired[str | None],
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+ "grad": typing.NotRequired[InputPathType | None],
129
+ "fslgrad": typing.NotRequired[MrinfoFslgradParamsDict | None],
130
+ "bvalue_scaling": typing.NotRequired[str | None],
131
+ "export_grad_mrtrix": typing.NotRequired[str | None],
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+ "export_grad_fsl": typing.NotRequired[MrinfoExportGradFslParamsDict | None],
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+ "dwgrad": bool,
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+ "shell_bvalues": bool,
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+ "shell_sizes": bool,
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+ "shell_indices": bool,
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+ "export_pe_table": typing.NotRequired[str | None],
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+ "export_pe_eddy": typing.NotRequired[MrinfoExportPeEddyParamsDict | None],
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+ "petable": bool,
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+ "nodelete": bool,
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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],
146
+ "config": typing.NotRequired[list[MrinfoConfigParamsDict] | None],
147
+ "help": bool,
148
+ "version": bool,
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+ "image": list[InputPathType],
150
+ })
151
+ MrinfoParamsDict = _MrinfoParamsDictNoTag | MrinfoParamsDictTagged
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+
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+
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+ def mrinfo_property(
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+ key: str,
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+ ) -> MrinfoPropertyParamsDictTagged:
157
+ """
158
+ Build parameters.
159
+
160
+ Args:
161
+ key: any text properties embedded in the image header under the\
162
+ specified key (use 'all' to list all keys found).
163
+ Returns:
164
+ Parameter dictionary
165
+ """
166
+ params = {
167
+ "@type": "property",
168
+ "key": key,
169
+ }
170
+ return params
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+
172
+
173
+ def mrinfo_property_validate(
174
+ params: typing.Any,
175
+ ) -> None:
176
+ """
177
+ Validate parameters. Throws an error if `params` is not a valid
178
+ `MrinfoPropertyParamsDict` object.
179
+
180
+ Args:
181
+ params: The parameters object to validate.
182
+ """
183
+ if params is None or not isinstance(params, dict):
184
+ raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
185
+ if params.get("key", None) is None:
186
+ raise StyxValidationError("`key` must not be None")
187
+ if not isinstance(params["key"], str):
188
+ raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
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+
190
+
191
+ def mrinfo_property_cargs(
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+ params: MrinfoPropertyParamsDict,
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+ execution: Execution,
194
+ ) -> list[str]:
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+ """
196
+ Build command-line arguments from parameters.
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+
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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.
203
+ """
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+ cargs = []
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+ cargs.append("-property")
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+ cargs.append(params.get("key", None))
207
+ return cargs
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+
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+
210
+ def mrinfo_fslgrad(
211
+ bvecs: InputPathType,
212
+ bvals: InputPathType,
213
+ ) -> MrinfoFslgradParamsDictTagged:
214
+ """
215
+ Build parameters.
216
+
217
+ Args:
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+ bvecs: Provide the diffusion-weighted gradient scheme used in the\
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+ acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
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+ scheme is present in the input image header, the data provided with\
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+ this option will be instead used.
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+ bvals: Provide the diffusion-weighted gradient scheme used in the\
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+ acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
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+ scheme is present in the input image header, the data provided with\
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+ this option will be instead used.
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+ Returns:
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+ Parameter dictionary
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+ """
229
+ params = {
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+ "@type": "fslgrad",
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+ "bvecs": bvecs,
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+ "bvals": bvals,
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+ }
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+ return params
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+
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+
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+ def mrinfo_fslgrad_validate(
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+ params: typing.Any,
239
+ ) -> None:
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+ """
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+ Validate parameters. Throws an error if `params` is not a valid
242
+ `MrinfoFslgradParamsDict` object.
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+
244
+ Args:
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+ params: The parameters object to validate.
246
+ """
247
+ if params is None or not isinstance(params, dict):
248
+ raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
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+ if params.get("bvecs", None) is None:
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+ raise StyxValidationError("`bvecs` must not be None")
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+ if not isinstance(params["bvecs"], (pathlib.Path, str)):
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+ raise StyxValidationError(f'`bvecs` has the wrong type: Received `{type(params.get("bvecs", None))}` expected `InputPathType`')
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+ if params.get("bvals", None) is None:
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+ raise StyxValidationError("`bvals` must not be None")
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+ if not isinstance(params["bvals"], (pathlib.Path, str)):
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+ raise StyxValidationError(f'`bvals` has the wrong type: Received `{type(params.get("bvals", None))}` expected `InputPathType`')
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+
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+
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+ def mrinfo_fslgrad_cargs(
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+ params: MrinfoFslgradParamsDict,
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+ execution: Execution,
262
+ ) -> list[str]:
263
+ """
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+ Build command-line arguments from parameters.
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+
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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("-fslgrad")
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+ cargs.append(execution.input_file(params.get("bvecs", None)))
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+ cargs.append(execution.input_file(params.get("bvals", None)))
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+ return cargs
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+
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+
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+ class MrinfoExportGradFslOutputs(typing.NamedTuple):
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+ """
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+ Output object returned when calling `MrinfoExportGradFslParamsDict | None(...)`.
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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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+ bvecs_path: OutputPathType
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+ """export the diffusion-weighted gradient table to files in FSL (bvecs /
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+ bvals) format"""
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+ bvals_path: OutputPathType
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+ """export the diffusion-weighted gradient table to files in FSL (bvecs /
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+ bvals) format"""
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+
292
+
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+ def mrinfo_export_grad_fsl(
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+ bvecs_path: str,
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+ bvals_path: str,
296
+ ) -> MrinfoExportGradFslParamsDictTagged:
297
+ """
298
+ Build parameters.
299
+
300
+ Args:
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+ bvecs_path: export the diffusion-weighted gradient table to files in\
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+ FSL (bvecs / bvals) format.
303
+ bvals_path: export the diffusion-weighted gradient table to files in\
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+ FSL (bvecs / bvals) format.
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+ Returns:
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+ Parameter dictionary
307
+ """
308
+ params = {
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+ "@type": "export_grad_fsl",
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+ "bvecs_path": bvecs_path,
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+ "bvals_path": bvals_path,
312
+ }
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+ return params
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+
315
+
316
+ def mrinfo_export_grad_fsl_validate(
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+ params: typing.Any,
318
+ ) -> None:
319
+ """
320
+ Validate parameters. Throws an error if `params` is not a valid
321
+ `MrinfoExportGradFslParamsDict` object.
322
+
323
+ Args:
324
+ params: The parameters object to validate.
325
+ """
326
+ if params is None or not isinstance(params, dict):
327
+ raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
328
+ if params.get("bvecs_path", None) is None:
329
+ raise StyxValidationError("`bvecs_path` must not be None")
330
+ if not isinstance(params["bvecs_path"], str):
331
+ raise StyxValidationError(f'`bvecs_path` has the wrong type: Received `{type(params.get("bvecs_path", None))}` expected `str`')
332
+ if params.get("bvals_path", None) is None:
333
+ raise StyxValidationError("`bvals_path` must not be None")
334
+ if not isinstance(params["bvals_path"], str):
335
+ raise StyxValidationError(f'`bvals_path` has the wrong type: Received `{type(params.get("bvals_path", None))}` expected `str`')
336
+
337
+
338
+ def mrinfo_export_grad_fsl_cargs(
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+ params: MrinfoExportGradFslParamsDict,
340
+ execution: Execution,
341
+ ) -> list[str]:
342
+ """
343
+ Build command-line arguments from parameters.
344
+
345
+ Args:
346
+ params: The parameters.
347
+ execution: The execution object for resolving input paths.
348
+ Returns:
349
+ Command-line arguments.
350
+ """
351
+ cargs = []
352
+ cargs.append("-export_grad_fsl")
353
+ cargs.append(params.get("bvecs_path", None))
354
+ cargs.append(params.get("bvals_path", None))
355
+ return cargs
356
+
357
+
358
+ def mrinfo_export_grad_fsl_outputs(
359
+ params: MrinfoExportGradFslParamsDict,
360
+ execution: Execution,
361
+ ) -> MrinfoExportGradFslOutputs:
362
+ """
363
+ Build outputs object containing output file paths and possibly stdout/stderr.
364
+
365
+ Args:
366
+ params: The parameters.
367
+ execution: The execution object for resolving input paths.
368
+ Returns:
369
+ Outputs object.
370
+ """
371
+ ret = MrinfoExportGradFslOutputs(
372
+ root=execution.output_file("."),
373
+ bvecs_path=execution.output_file(params.get("bvecs_path", None)),
374
+ bvals_path=execution.output_file(params.get("bvals_path", None)),
375
+ )
376
+ return ret
377
+
378
+
379
+ class MrinfoExportPeEddyOutputs(typing.NamedTuple):
380
+ """
381
+ Output object returned when calling `MrinfoExportPeEddyParamsDict | None(...)`.
382
+ """
383
+ root: OutputPathType
384
+ """Output root folder. This is the root folder for all outputs."""
385
+ config: OutputPathType
386
+ """export phase-encoding information to an EDDY-style config / index file
387
+ pair"""
388
+ indices: OutputPathType
389
+ """export phase-encoding information to an EDDY-style config / index file
390
+ pair"""
391
+
392
+
393
+ def mrinfo_export_pe_eddy(
394
+ config: str,
395
+ indices: str,
396
+ ) -> MrinfoExportPeEddyParamsDictTagged:
397
+ """
398
+ Build parameters.
399
+
400
+ Args:
401
+ config: export phase-encoding information to an EDDY-style config /\
402
+ index file pair.
403
+ indices: export phase-encoding information to an EDDY-style config /\
404
+ index file pair.
405
+ Returns:
406
+ Parameter dictionary
407
+ """
408
+ params = {
409
+ "@type": "export_pe_eddy",
410
+ "config": config,
411
+ "indices": indices,
412
+ }
413
+ return params
414
+
415
+
416
+ def mrinfo_export_pe_eddy_validate(
417
+ params: typing.Any,
418
+ ) -> None:
419
+ """
420
+ Validate parameters. Throws an error if `params` is not a valid
421
+ `MrinfoExportPeEddyParamsDict` object.
422
+
423
+ Args:
424
+ params: The parameters object to validate.
425
+ """
426
+ if params is None or not isinstance(params, dict):
427
+ raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
428
+ if params.get("config", None) is None:
429
+ raise StyxValidationError("`config` must not be None")
430
+ if not isinstance(params["config"], str):
431
+ raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `str`')
432
+ if params.get("indices", None) is None:
433
+ raise StyxValidationError("`indices` must not be None")
434
+ if not isinstance(params["indices"], str):
435
+ raise StyxValidationError(f'`indices` has the wrong type: Received `{type(params.get("indices", None))}` expected `str`')
436
+
437
+
438
+ def mrinfo_export_pe_eddy_cargs(
439
+ params: MrinfoExportPeEddyParamsDict,
440
+ execution: Execution,
441
+ ) -> list[str]:
442
+ """
443
+ Build command-line arguments from parameters.
444
+
445
+ Args:
446
+ params: The parameters.
447
+ execution: The execution object for resolving input paths.
448
+ Returns:
449
+ Command-line arguments.
450
+ """
451
+ cargs = []
452
+ cargs.append("-export_pe_eddy")
453
+ cargs.append(params.get("config", None))
454
+ cargs.append(params.get("indices", None))
455
+ return cargs
456
+
457
+
458
+ def mrinfo_export_pe_eddy_outputs(
459
+ params: MrinfoExportPeEddyParamsDict,
460
+ execution: Execution,
461
+ ) -> MrinfoExportPeEddyOutputs:
462
+ """
463
+ Build outputs object containing output file paths and possibly stdout/stderr.
464
+
465
+ Args:
466
+ params: The parameters.
467
+ execution: The execution object for resolving input paths.
468
+ Returns:
469
+ Outputs object.
470
+ """
471
+ ret = MrinfoExportPeEddyOutputs(
472
+ root=execution.output_file("."),
473
+ config=execution.output_file(params.get("config", None)),
474
+ indices=execution.output_file(params.get("indices", None)),
475
+ )
476
+ return ret
477
+
478
+
479
+ def mrinfo_config(
480
+ key: str,
481
+ value: str,
482
+ ) -> MrinfoConfigParamsDictTagged:
483
+ """
484
+ Build parameters.
485
+
486
+ Args:
487
+ key: temporarily set the value of an MRtrix config file entry.
488
+ value: temporarily set the value of an MRtrix config file entry.
489
+ Returns:
490
+ Parameter dictionary
491
+ """
492
+ params = {
493
+ "@type": "config",
494
+ "key": key,
495
+ "value": value,
496
+ }
497
+ return params
498
+
499
+
500
+ def mrinfo_config_validate(
501
+ params: typing.Any,
502
+ ) -> None:
503
+ """
504
+ Validate parameters. Throws an error if `params` is not a valid
505
+ `MrinfoConfigParamsDict` object.
506
+
507
+ Args:
508
+ params: The parameters object to validate.
509
+ """
510
+ if params is None or not isinstance(params, dict):
511
+ raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
512
+ if params.get("key", None) is None:
513
+ raise StyxValidationError("`key` must not be None")
514
+ if not isinstance(params["key"], str):
515
+ raise StyxValidationError(f'`key` has the wrong type: Received `{type(params.get("key", None))}` expected `str`')
516
+ if params.get("value", None) is None:
517
+ raise StyxValidationError("`value` must not be None")
518
+ if not isinstance(params["value"], str):
519
+ raise StyxValidationError(f'`value` has the wrong type: Received `{type(params.get("value", None))}` expected `str`')
520
+
521
+
522
+ def mrinfo_config_cargs(
523
+ params: MrinfoConfigParamsDict,
524
+ execution: Execution,
525
+ ) -> list[str]:
526
+ """
527
+ Build command-line arguments from parameters.
528
+
529
+ Args:
530
+ params: The parameters.
531
+ execution: The execution object for resolving input paths.
532
+ Returns:
533
+ Command-line arguments.
534
+ """
535
+ cargs = []
536
+ cargs.append("-config")
537
+ cargs.append(params.get("key", None))
538
+ cargs.append(params.get("value", None))
539
+ return cargs
540
+
541
+
542
+ class MrinfoOutputs(typing.NamedTuple):
543
+ """
544
+ Output object returned when calling `MrinfoParamsDict(...)`.
545
+ """
546
+ root: OutputPathType
547
+ """Output root folder. This is the root folder for all outputs."""
548
+ json_keyval: OutputPathType | None
549
+ """export header key/value entries to a JSON file """
550
+ json_all: OutputPathType | None
551
+ """export all header contents to a JSON file """
552
+ export_grad_mrtrix: OutputPathType | None
553
+ """export the diffusion-weighted gradient table to file in MRtrix format """
554
+ export_pe_table: OutputPathType | None
555
+ """export phase-encoding table to file """
556
+ export_grad_fsl: MrinfoExportGradFslOutputs | None
557
+ """Outputs from `mrinfo_export_grad_fsl_outputs`."""
558
+ export_pe_eddy: MrinfoExportPeEddyOutputs | None
559
+ """Outputs from `mrinfo_export_pe_eddy_outputs`."""
560
+
561
+
562
+ def mrinfo_params(
563
+ image: list[InputPathType],
564
+ all_: bool = False,
565
+ name: bool = False,
566
+ format_: bool = False,
567
+ ndim: bool = False,
568
+ size: bool = False,
569
+ spacing: bool = False,
570
+ datatype: bool = False,
571
+ strides: bool = False,
572
+ offset: bool = False,
573
+ multiplier: bool = False,
574
+ transform: bool = False,
575
+ property_: list[MrinfoPropertyParamsDict] | None = None,
576
+ json_keyval: str | None = None,
577
+ json_all: str | None = None,
578
+ grad: InputPathType | None = None,
579
+ fslgrad: MrinfoFslgradParamsDict | None = None,
580
+ bvalue_scaling: str | None = None,
581
+ export_grad_mrtrix: str | None = None,
582
+ export_grad_fsl: MrinfoExportGradFslParamsDict | None = None,
583
+ dwgrad: bool = False,
584
+ shell_bvalues: bool = False,
585
+ shell_sizes: bool = False,
586
+ shell_indices: bool = False,
587
+ export_pe_table: str | None = None,
588
+ export_pe_eddy: MrinfoExportPeEddyParamsDict | None = None,
589
+ petable: bool = False,
590
+ nodelete: bool = False,
591
+ info: bool = False,
592
+ quiet: bool = False,
593
+ debug: bool = False,
594
+ force: bool = False,
595
+ nthreads: int | None = None,
596
+ config: list[MrinfoConfigParamsDict] | None = None,
597
+ help_: bool = False,
598
+ version: bool = False,
599
+ ) -> MrinfoParamsDictTagged:
600
+ """
601
+ Build parameters.
602
+
603
+ Args:
604
+ image: the input image(s).
605
+ all_: print all properties, rather than the first and last 2 of each.
606
+ name: print the file system path of the image.
607
+ format_: image file format.
608
+ ndim: number of image dimensions.
609
+ size: image size along each axis.
610
+ spacing: voxel spacing along each image dimension.
611
+ datatype: data type used for image data storage.
612
+ strides: data strides i.e. order and direction of axes data layout.
613
+ offset: image intensity offset.
614
+ multiplier: image intensity multiplier.
615
+ transform: the transformation from image coordinates [mm] to scanner /\
616
+ real world coordinates [mm].
617
+ property_: any text properties embedded in the image header under the\
618
+ specified key (use 'all' to list all keys found).
619
+ json_keyval: export header key/value entries to a JSON file.
620
+ json_all: export all header contents to a JSON file.
621
+ grad: Provide the diffusion-weighted gradient scheme used in the\
622
+ acquisition in a text file. This should be supplied as a 4xN text file\
623
+ with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
624
+ the direction of the applied gradient, and b gives the b-value in units\
625
+ of s/mm^2. If a diffusion gradient scheme is present in the input image\
626
+ header, the data provided with this option will be instead used.
627
+ fslgrad: Provide the diffusion-weighted gradient scheme used in the\
628
+ acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
629
+ scheme is present in the input image header, the data provided with\
630
+ this option will be instead used.
631
+ bvalue_scaling: enable or disable scaling of diffusion b-values by the\
632
+ square of the corresponding DW gradient norm (see Desciption). Valid\
633
+ choices are yes/no, true/false, 0/1 (default: automatic).
634
+ export_grad_mrtrix: export the diffusion-weighted gradient table to\
635
+ file in MRtrix format.
636
+ export_grad_fsl: export the diffusion-weighted gradient table to files\
637
+ in FSL (bvecs / bvals) format.
638
+ dwgrad: the diffusion-weighting gradient table, as interpreted by\
639
+ MRtrix3.
640
+ shell_bvalues: list the average b-value of each shell.
641
+ shell_sizes: list the number of volumes in each shell.
642
+ shell_indices: list the image volumes attributed to each b-value shell.
643
+ export_pe_table: export phase-encoding table to file.
644
+ export_pe_eddy: export phase-encoding information to an EDDY-style\
645
+ config / index file pair.
646
+ petable: print the phase encoding table.
647
+ nodelete: don't delete temporary images or images passed to mrinfo via\
648
+ Unix pipes.
649
+ info: display information messages.
650
+ quiet: do not display information messages or progress status;\
651
+ alternatively, this can be achieved by setting the MRTRIX_QUIET\
652
+ environment variable to a non-empty string.
653
+ debug: display debugging messages.
654
+ force: force overwrite of output files (caution: using the same file as\
655
+ input and output might cause unexpected behaviour).
656
+ nthreads: use this number of threads in multi-threaded applications\
657
+ (set to 0 to disable multi-threading).
658
+ config: temporarily set the value of an MRtrix config file entry.
659
+ help_: display this information page and exit.
660
+ version: display version information and exit.
661
+ Returns:
662
+ Parameter dictionary
663
+ """
664
+ params = {
665
+ "@type": "mrtrix/mrinfo",
666
+ "all": all_,
667
+ "name": name,
668
+ "format": format_,
669
+ "ndim": ndim,
670
+ "size": size,
671
+ "spacing": spacing,
672
+ "datatype": datatype,
673
+ "strides": strides,
674
+ "offset": offset,
675
+ "multiplier": multiplier,
676
+ "transform": transform,
677
+ "dwgrad": dwgrad,
678
+ "shell_bvalues": shell_bvalues,
679
+ "shell_sizes": shell_sizes,
680
+ "shell_indices": shell_indices,
681
+ "petable": petable,
682
+ "nodelete": nodelete,
683
+ "info": info,
684
+ "quiet": quiet,
685
+ "debug": debug,
686
+ "force": force,
687
+ "help": help_,
688
+ "version": version,
689
+ "image": image,
690
+ }
691
+ if property_ is not None:
692
+ params["property"] = property_
693
+ if json_keyval is not None:
694
+ params["json_keyval"] = json_keyval
695
+ if json_all is not None:
696
+ params["json_all"] = json_all
697
+ if grad is not None:
698
+ params["grad"] = grad
699
+ if fslgrad is not None:
700
+ params["fslgrad"] = fslgrad
701
+ if bvalue_scaling is not None:
702
+ params["bvalue_scaling"] = bvalue_scaling
703
+ if export_grad_mrtrix is not None:
704
+ params["export_grad_mrtrix"] = export_grad_mrtrix
705
+ if export_grad_fsl is not None:
706
+ params["export_grad_fsl"] = export_grad_fsl
707
+ if export_pe_table is not None:
708
+ params["export_pe_table"] = export_pe_table
709
+ if export_pe_eddy is not None:
710
+ params["export_pe_eddy"] = export_pe_eddy
711
+ if nthreads is not None:
712
+ params["nthreads"] = nthreads
713
+ if config is not None:
714
+ params["config"] = config
715
+ return params
716
+
717
+
718
+ def mrinfo_validate(
719
+ params: typing.Any,
720
+ ) -> None:
721
+ """
722
+ Validate parameters. Throws an error if `params` is not a valid
723
+ `MrinfoParamsDict` object.
724
+
725
+ Args:
726
+ params: The parameters object to validate.
727
+ """
728
+ if params is None or not isinstance(params, dict):
729
+ raise StyxValidationError(f'Params object has the wrong type \'{type(params)}\'')
730
+ if params.get("all", False) is None:
731
+ raise StyxValidationError("`all` must not be None")
732
+ if not isinstance(params["all"], bool):
733
+ raise StyxValidationError(f'`all` has the wrong type: Received `{type(params.get("all", False))}` expected `bool`')
734
+ if params.get("name", False) is None:
735
+ raise StyxValidationError("`name` must not be None")
736
+ if not isinstance(params["name"], bool):
737
+ raise StyxValidationError(f'`name` has the wrong type: Received `{type(params.get("name", False))}` expected `bool`')
738
+ if params.get("format", False) is None:
739
+ raise StyxValidationError("`format` must not be None")
740
+ if not isinstance(params["format"], bool):
741
+ raise StyxValidationError(f'`format` has the wrong type: Received `{type(params.get("format", False))}` expected `bool`')
742
+ if params.get("ndim", False) is None:
743
+ raise StyxValidationError("`ndim` must not be None")
744
+ if not isinstance(params["ndim"], bool):
745
+ raise StyxValidationError(f'`ndim` has the wrong type: Received `{type(params.get("ndim", False))}` expected `bool`')
746
+ if params.get("size", False) is None:
747
+ raise StyxValidationError("`size` must not be None")
748
+ if not isinstance(params["size"], bool):
749
+ raise StyxValidationError(f'`size` has the wrong type: Received `{type(params.get("size", False))}` expected `bool`')
750
+ if params.get("spacing", False) is None:
751
+ raise StyxValidationError("`spacing` must not be None")
752
+ if not isinstance(params["spacing"], bool):
753
+ raise StyxValidationError(f'`spacing` has the wrong type: Received `{type(params.get("spacing", False))}` expected `bool`')
754
+ if params.get("datatype", False) is None:
755
+ raise StyxValidationError("`datatype` must not be None")
756
+ if not isinstance(params["datatype"], bool):
757
+ raise StyxValidationError(f'`datatype` has the wrong type: Received `{type(params.get("datatype", False))}` expected `bool`')
758
+ if params.get("strides", False) is None:
759
+ raise StyxValidationError("`strides` must not be None")
760
+ if not isinstance(params["strides"], bool):
761
+ raise StyxValidationError(f'`strides` has the wrong type: Received `{type(params.get("strides", False))}` expected `bool`')
762
+ if params.get("offset", False) is None:
763
+ raise StyxValidationError("`offset` must not be None")
764
+ if not isinstance(params["offset"], bool):
765
+ raise StyxValidationError(f'`offset` has the wrong type: Received `{type(params.get("offset", False))}` expected `bool`')
766
+ if params.get("multiplier", False) is None:
767
+ raise StyxValidationError("`multiplier` must not be None")
768
+ if not isinstance(params["multiplier"], bool):
769
+ raise StyxValidationError(f'`multiplier` has the wrong type: Received `{type(params.get("multiplier", False))}` expected `bool`')
770
+ if params.get("transform", False) is None:
771
+ raise StyxValidationError("`transform` must not be None")
772
+ if not isinstance(params["transform"], bool):
773
+ raise StyxValidationError(f'`transform` has the wrong type: Received `{type(params.get("transform", False))}` expected `bool`')
774
+ if params.get("property", None) is not None:
775
+ if not isinstance(params["property"], list):
776
+ raise StyxValidationError(f'`property` has the wrong type: Received `{type(params.get("property", None))}` expected `list[MrinfoPropertyParamsDict] | None`')
777
+ for e in params["property"]:
778
+ mrinfo_property_validate(e)
779
+ if params.get("json_keyval", None) is not None:
780
+ if not isinstance(params["json_keyval"], str):
781
+ raise StyxValidationError(f'`json_keyval` has the wrong type: Received `{type(params.get("json_keyval", None))}` expected `str | None`')
782
+ if params.get("json_all", None) is not None:
783
+ if not isinstance(params["json_all"], str):
784
+ raise StyxValidationError(f'`json_all` has the wrong type: Received `{type(params.get("json_all", None))}` expected `str | None`')
785
+ if params.get("grad", None) is not None:
786
+ if not isinstance(params["grad"], (pathlib.Path, str)):
787
+ raise StyxValidationError(f'`grad` has the wrong type: Received `{type(params.get("grad", None))}` expected `InputPathType | None`')
788
+ if params.get("fslgrad", None) is not None:
789
+ mrinfo_fslgrad_validate(params["fslgrad"])
790
+ if params.get("bvalue_scaling", None) is not None:
791
+ if not isinstance(params["bvalue_scaling"], str):
792
+ raise StyxValidationError(f'`bvalue_scaling` has the wrong type: Received `{type(params.get("bvalue_scaling", None))}` expected `str | None`')
793
+ if params.get("export_grad_mrtrix", None) is not None:
794
+ if not isinstance(params["export_grad_mrtrix"], str):
795
+ raise StyxValidationError(f'`export_grad_mrtrix` has the wrong type: Received `{type(params.get("export_grad_mrtrix", None))}` expected `str | None`')
796
+ if params.get("export_grad_fsl", None) is not None:
797
+ mrinfo_export_grad_fsl_validate(params["export_grad_fsl"])
798
+ if params.get("dwgrad", False) is None:
799
+ raise StyxValidationError("`dwgrad` must not be None")
800
+ if not isinstance(params["dwgrad"], bool):
801
+ raise StyxValidationError(f'`dwgrad` has the wrong type: Received `{type(params.get("dwgrad", False))}` expected `bool`')
802
+ if params.get("shell_bvalues", False) is None:
803
+ raise StyxValidationError("`shell_bvalues` must not be None")
804
+ if not isinstance(params["shell_bvalues"], bool):
805
+ raise StyxValidationError(f'`shell_bvalues` has the wrong type: Received `{type(params.get("shell_bvalues", False))}` expected `bool`')
806
+ if params.get("shell_sizes", False) is None:
807
+ raise StyxValidationError("`shell_sizes` must not be None")
808
+ if not isinstance(params["shell_sizes"], bool):
809
+ raise StyxValidationError(f'`shell_sizes` has the wrong type: Received `{type(params.get("shell_sizes", False))}` expected `bool`')
810
+ if params.get("shell_indices", False) is None:
811
+ raise StyxValidationError("`shell_indices` must not be None")
812
+ if not isinstance(params["shell_indices"], bool):
813
+ raise StyxValidationError(f'`shell_indices` has the wrong type: Received `{type(params.get("shell_indices", False))}` expected `bool`')
814
+ if params.get("export_pe_table", None) is not None:
815
+ if not isinstance(params["export_pe_table"], str):
816
+ raise StyxValidationError(f'`export_pe_table` has the wrong type: Received `{type(params.get("export_pe_table", None))}` expected `str | None`')
817
+ if params.get("export_pe_eddy", None) is not None:
818
+ mrinfo_export_pe_eddy_validate(params["export_pe_eddy"])
819
+ if params.get("petable", False) is None:
820
+ raise StyxValidationError("`petable` must not be None")
821
+ if not isinstance(params["petable"], bool):
822
+ raise StyxValidationError(f'`petable` has the wrong type: Received `{type(params.get("petable", False))}` expected `bool`')
823
+ if params.get("nodelete", False) is None:
824
+ raise StyxValidationError("`nodelete` must not be None")
825
+ if not isinstance(params["nodelete"], bool):
826
+ raise StyxValidationError(f'`nodelete` has the wrong type: Received `{type(params.get("nodelete", False))}` expected `bool`')
827
+ if params.get("info", False) is None:
828
+ raise StyxValidationError("`info` must not be None")
829
+ if not isinstance(params["info"], bool):
830
+ raise StyxValidationError(f'`info` has the wrong type: Received `{type(params.get("info", False))}` expected `bool`')
831
+ if params.get("quiet", False) is None:
832
+ raise StyxValidationError("`quiet` must not be None")
833
+ if not isinstance(params["quiet"], bool):
834
+ raise StyxValidationError(f'`quiet` has the wrong type: Received `{type(params.get("quiet", False))}` expected `bool`')
835
+ if params.get("debug", False) is None:
836
+ raise StyxValidationError("`debug` must not be None")
837
+ if not isinstance(params["debug"], bool):
838
+ raise StyxValidationError(f'`debug` has the wrong type: Received `{type(params.get("debug", False))}` expected `bool`')
839
+ if params.get("force", False) is None:
840
+ raise StyxValidationError("`force` must not be None")
841
+ if not isinstance(params["force"], bool):
842
+ raise StyxValidationError(f'`force` has the wrong type: Received `{type(params.get("force", False))}` expected `bool`')
843
+ if params.get("nthreads", None) is not None:
844
+ if not isinstance(params["nthreads"], int):
845
+ raise StyxValidationError(f'`nthreads` has the wrong type: Received `{type(params.get("nthreads", None))}` expected `int | None`')
846
+ if params.get("config", None) is not None:
847
+ if not isinstance(params["config"], list):
848
+ raise StyxValidationError(f'`config` has the wrong type: Received `{type(params.get("config", None))}` expected `list[MrinfoConfigParamsDict] | None`')
849
+ for e in params["config"]:
850
+ mrinfo_config_validate(e)
851
+ if params.get("help", False) is None:
852
+ raise StyxValidationError("`help` must not be None")
853
+ if not isinstance(params["help"], bool):
854
+ raise StyxValidationError(f'`help` has the wrong type: Received `{type(params.get("help", False))}` expected `bool`')
855
+ if params.get("version", False) is None:
856
+ raise StyxValidationError("`version` must not be None")
857
+ if not isinstance(params["version"], bool):
858
+ raise StyxValidationError(f'`version` has the wrong type: Received `{type(params.get("version", False))}` expected `bool`')
859
+ if params.get("image", None) is None:
860
+ raise StyxValidationError("`image` must not be None")
861
+ if not isinstance(params["image"], list):
862
+ raise StyxValidationError(f'`image` has the wrong type: Received `{type(params.get("image", None))}` expected `list[InputPathType]`')
863
+ for e in params["image"]:
864
+ if not isinstance(e, (pathlib.Path, str)):
865
+ raise StyxValidationError(f'`image` has the wrong type: Received `{type(params.get("image", None))}` expected `list[InputPathType]`')
866
+
867
+
868
+ def mrinfo_cargs(
869
+ params: MrinfoParamsDict,
870
+ execution: Execution,
871
+ ) -> list[str]:
872
+ """
873
+ Build command-line arguments from parameters.
874
+
875
+ Args:
876
+ params: The parameters.
877
+ execution: The execution object for resolving input paths.
878
+ Returns:
879
+ Command-line arguments.
880
+ """
881
+ cargs = []
882
+ cargs.append("mrinfo")
883
+ if params.get("all", False):
884
+ cargs.append("-all")
885
+ if params.get("name", False):
886
+ cargs.append("-name")
887
+ if params.get("format", False):
888
+ cargs.append("-format")
889
+ if params.get("ndim", False):
890
+ cargs.append("-ndim")
891
+ if params.get("size", False):
892
+ cargs.append("-size")
893
+ if params.get("spacing", False):
894
+ cargs.append("-spacing")
895
+ if params.get("datatype", False):
896
+ cargs.append("-datatype")
897
+ if params.get("strides", False):
898
+ cargs.append("-strides")
899
+ if params.get("offset", False):
900
+ cargs.append("-offset")
901
+ if params.get("multiplier", False):
902
+ cargs.append("-multiplier")
903
+ if params.get("transform", False):
904
+ cargs.append("-transform")
905
+ if params.get("property", None) is not None:
906
+ cargs.extend([a for c in [mrinfo_property_cargs(s, execution) for s in params.get("property", None)] for a in c])
907
+ if params.get("json_keyval", None) is not None:
908
+ cargs.extend([
909
+ "-json_keyval",
910
+ params.get("json_keyval", None)
911
+ ])
912
+ if params.get("json_all", None) is not None:
913
+ cargs.extend([
914
+ "-json_all",
915
+ params.get("json_all", None)
916
+ ])
917
+ if params.get("grad", None) is not None:
918
+ cargs.extend([
919
+ "-grad",
920
+ execution.input_file(params.get("grad", None))
921
+ ])
922
+ if params.get("fslgrad", None) is not None:
923
+ cargs.extend(mrinfo_fslgrad_cargs(params.get("fslgrad", None), execution))
924
+ if params.get("bvalue_scaling", None) is not None:
925
+ cargs.extend([
926
+ "-bvalue_scaling",
927
+ params.get("bvalue_scaling", None)
928
+ ])
929
+ if params.get("export_grad_mrtrix", None) is not None:
930
+ cargs.extend([
931
+ "-export_grad_mrtrix",
932
+ params.get("export_grad_mrtrix", None)
933
+ ])
934
+ if params.get("export_grad_fsl", None) is not None:
935
+ cargs.extend(mrinfo_export_grad_fsl_cargs(params.get("export_grad_fsl", None), execution))
936
+ if params.get("dwgrad", False):
937
+ cargs.append("-dwgrad")
938
+ if params.get("shell_bvalues", False):
939
+ cargs.append("-shell_bvalues")
940
+ if params.get("shell_sizes", False):
941
+ cargs.append("-shell_sizes")
942
+ if params.get("shell_indices", False):
943
+ cargs.append("-shell_indices")
944
+ if params.get("export_pe_table", None) is not None:
945
+ cargs.extend([
946
+ "-export_pe_table",
947
+ params.get("export_pe_table", None)
948
+ ])
949
+ if params.get("export_pe_eddy", None) is not None:
950
+ cargs.extend(mrinfo_export_pe_eddy_cargs(params.get("export_pe_eddy", None), execution))
951
+ if params.get("petable", False):
952
+ cargs.append("-petable")
953
+ if params.get("nodelete", False):
954
+ cargs.append("-nodelete")
955
+ if params.get("info", False):
956
+ cargs.append("-info")
957
+ if params.get("quiet", False):
958
+ cargs.append("-quiet")
959
+ if params.get("debug", False):
960
+ cargs.append("-debug")
961
+ if params.get("force", False):
962
+ cargs.append("-force")
963
+ if params.get("nthreads", None) is not None:
964
+ cargs.extend([
965
+ "-nthreads",
966
+ str(params.get("nthreads", None))
967
+ ])
968
+ if params.get("config", None) is not None:
969
+ cargs.extend([a for c in [mrinfo_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
970
+ if params.get("help", False):
971
+ cargs.append("-help")
972
+ if params.get("version", False):
973
+ cargs.append("-version")
974
+ cargs.extend([execution.input_file(f) for f in params.get("image", None)])
975
+ return cargs
976
+
977
+
978
+ def mrinfo_outputs(
979
+ params: MrinfoParamsDict,
980
+ execution: Execution,
981
+ ) -> MrinfoOutputs:
982
+ """
983
+ Build outputs object containing output file paths and possibly stdout/stderr.
984
+
985
+ Args:
986
+ params: The parameters.
987
+ execution: The execution object for resolving input paths.
988
+ Returns:
989
+ Outputs object.
990
+ """
991
+ ret = MrinfoOutputs(
992
+ root=execution.output_file("."),
993
+ json_keyval=execution.output_file(params.get("json_keyval", None)) if (params.get("json_keyval") is not None) else None,
994
+ json_all=execution.output_file(params.get("json_all", None)) if (params.get("json_all") is not None) else None,
995
+ export_grad_mrtrix=execution.output_file(params.get("export_grad_mrtrix", None)) if (params.get("export_grad_mrtrix") is not None) else None,
996
+ export_pe_table=execution.output_file(params.get("export_pe_table", None)) if (params.get("export_pe_table") is not None) else None,
997
+ export_grad_fsl=mrinfo_export_grad_fsl_outputs(params.get("export_grad_fsl"), execution) if params.get("export_grad_fsl") else None,
998
+ export_pe_eddy=mrinfo_export_pe_eddy_outputs(params.get("export_pe_eddy"), execution) if params.get("export_pe_eddy") else None,
999
+ )
1000
+ return ret
1001
+
1002
+
1003
+ def mrinfo_execute(
1004
+ params: MrinfoParamsDict,
1005
+ runner: Runner | None = None,
1006
+ ) -> MrinfoOutputs:
1007
+ """
1008
+ mrinfo
1009
+
1010
+ Display image header information, or extract specific information from the
1011
+ header.
1012
+
1013
+ By default, all information contained in each image header will be printed
1014
+ to the console in a reader-friendly format.
1015
+
1016
+ Alternatively, command-line options may be used to extract specific details
1017
+ from the header(s); these are printed to the console in a format more
1018
+ appropriate for scripting purposes or piping to file. If multiple options
1019
+ and/or images are provided, the requested header fields will be printed in
1020
+ the order in which they appear in the help page, with all requested details
1021
+ from each input image in sequence printed before the next image is
1022
+ processed.
1023
+
1024
+ The command can also write the diffusion gradient table from a single input
1025
+ image to file; either in the MRtrix or FSL format (bvecs/bvals file pair;
1026
+ includes appropriate diffusion gradient vector reorientation)
1027
+
1028
+ The -dwgrad, -export_* and -shell_* options provide (information about) the
1029
+ diffusion weighting gradient table after it has been processed by the
1030
+ MRtrix3 back-end (vectors normalised, b-values scaled by the square of the
1031
+ vector norm, depending on the -bvalue_scaling option). To see the raw
1032
+ gradient table information as stored in the image header, i.e. without
1033
+ MRtrix3 back-end processing, use "-property dw_scheme".
1034
+
1035
+ The -bvalue_scaling option controls an aspect of the import of diffusion
1036
+ gradient tables. When the input diffusion-weighting direction vectors have
1037
+ norms that differ substantially from unity, the b-values will be scaled by
1038
+ the square of their corresponding vector norm (this is how multi-shell
1039
+ acquisitions are frequently achieved on scanner platforms). However in some
1040
+ rare instances, the b-values may be correct, despite the vectors not being
1041
+ of unit norm (or conversely, the b-values may need to be rescaled even
1042
+ though the vectors are close to unit norm). This option allows the user to
1043
+ control this operation and override MRrtix3's automatic detection.
1044
+
1045
+ References:
1046
+
1047
+ .
1048
+
1049
+ Author: MRTrix3 Developers
1050
+
1051
+ URL: https://www.mrtrix.org/
1052
+
1053
+ Args:
1054
+ params: The parameters.
1055
+ runner: Command runner.
1056
+ Returns:
1057
+ NamedTuple of outputs (described in `MrinfoOutputs`).
1058
+ """
1059
+ mrinfo_validate(params)
1060
+ runner = runner or get_global_runner()
1061
+ execution = runner.start_execution(MRINFO_METADATA)
1062
+ params = execution.params(params)
1063
+ cargs = mrinfo_cargs(params, execution)
1064
+ ret = mrinfo_outputs(params, execution)
1065
+ execution.run(cargs)
1066
+ return ret
1067
+
1068
+
1069
+ def mrinfo(
1070
+ image: list[InputPathType],
1071
+ all_: bool = False,
1072
+ name: bool = False,
1073
+ format_: bool = False,
1074
+ ndim: bool = False,
1075
+ size: bool = False,
1076
+ spacing: bool = False,
1077
+ datatype: bool = False,
1078
+ strides: bool = False,
1079
+ offset: bool = False,
1080
+ multiplier: bool = False,
1081
+ transform: bool = False,
1082
+ property_: list[MrinfoPropertyParamsDict] | None = None,
1083
+ json_keyval: str | None = None,
1084
+ json_all: str | None = None,
1085
+ grad: InputPathType | None = None,
1086
+ fslgrad: MrinfoFslgradParamsDict | None = None,
1087
+ bvalue_scaling: str | None = None,
1088
+ export_grad_mrtrix: str | None = None,
1089
+ export_grad_fsl: MrinfoExportGradFslParamsDict | None = None,
1090
+ dwgrad: bool = False,
1091
+ shell_bvalues: bool = False,
1092
+ shell_sizes: bool = False,
1093
+ shell_indices: bool = False,
1094
+ export_pe_table: str | None = None,
1095
+ export_pe_eddy: MrinfoExportPeEddyParamsDict | None = None,
1096
+ petable: bool = False,
1097
+ nodelete: bool = False,
1098
+ info: bool = False,
1099
+ quiet: bool = False,
1100
+ debug: bool = False,
1101
+ force: bool = False,
1102
+ nthreads: int | None = None,
1103
+ config: list[MrinfoConfigParamsDict] | None = None,
1104
+ help_: bool = False,
1105
+ version: bool = False,
1106
+ runner: Runner | None = None,
1107
+ ) -> MrinfoOutputs:
1108
+ """
1109
+ mrinfo
1110
+
1111
+ Display image header information, or extract specific information from the
1112
+ header.
1113
+
1114
+ By default, all information contained in each image header will be printed
1115
+ to the console in a reader-friendly format.
1116
+
1117
+ Alternatively, command-line options may be used to extract specific details
1118
+ from the header(s); these are printed to the console in a format more
1119
+ appropriate for scripting purposes or piping to file. If multiple options
1120
+ and/or images are provided, the requested header fields will be printed in
1121
+ the order in which they appear in the help page, with all requested details
1122
+ from each input image in sequence printed before the next image is
1123
+ processed.
1124
+
1125
+ The command can also write the diffusion gradient table from a single input
1126
+ image to file; either in the MRtrix or FSL format (bvecs/bvals file pair;
1127
+ includes appropriate diffusion gradient vector reorientation)
1128
+
1129
+ The -dwgrad, -export_* and -shell_* options provide (information about) the
1130
+ diffusion weighting gradient table after it has been processed by the
1131
+ MRtrix3 back-end (vectors normalised, b-values scaled by the square of the
1132
+ vector norm, depending on the -bvalue_scaling option). To see the raw
1133
+ gradient table information as stored in the image header, i.e. without
1134
+ MRtrix3 back-end processing, use "-property dw_scheme".
1135
+
1136
+ The -bvalue_scaling option controls an aspect of the import of diffusion
1137
+ gradient tables. When the input diffusion-weighting direction vectors have
1138
+ norms that differ substantially from unity, the b-values will be scaled by
1139
+ the square of their corresponding vector norm (this is how multi-shell
1140
+ acquisitions are frequently achieved on scanner platforms). However in some
1141
+ rare instances, the b-values may be correct, despite the vectors not being
1142
+ of unit norm (or conversely, the b-values may need to be rescaled even
1143
+ though the vectors are close to unit norm). This option allows the user to
1144
+ control this operation and override MRrtix3's automatic detection.
1145
+
1146
+ References:
1147
+
1148
+ .
1149
+
1150
+ Author: MRTrix3 Developers
1151
+
1152
+ URL: https://www.mrtrix.org/
1153
+
1154
+ Args:
1155
+ image: the input image(s).
1156
+ all_: print all properties, rather than the first and last 2 of each.
1157
+ name: print the file system path of the image.
1158
+ format_: image file format.
1159
+ ndim: number of image dimensions.
1160
+ size: image size along each axis.
1161
+ spacing: voxel spacing along each image dimension.
1162
+ datatype: data type used for image data storage.
1163
+ strides: data strides i.e. order and direction of axes data layout.
1164
+ offset: image intensity offset.
1165
+ multiplier: image intensity multiplier.
1166
+ transform: the transformation from image coordinates [mm] to scanner /\
1167
+ real world coordinates [mm].
1168
+ property_: any text properties embedded in the image header under the\
1169
+ specified key (use 'all' to list all keys found).
1170
+ json_keyval: export header key/value entries to a JSON file.
1171
+ json_all: export all header contents to a JSON file.
1172
+ grad: Provide the diffusion-weighted gradient scheme used in the\
1173
+ acquisition in a text file. This should be supplied as a 4xN text file\
1174
+ with each line is in the format [ X Y Z b ], where [ X Y Z ] describe\
1175
+ the direction of the applied gradient, and b gives the b-value in units\
1176
+ of s/mm^2. If a diffusion gradient scheme is present in the input image\
1177
+ header, the data provided with this option will be instead used.
1178
+ fslgrad: Provide the diffusion-weighted gradient scheme used in the\
1179
+ acquisition in FSL bvecs/bvals format files. If a diffusion gradient\
1180
+ scheme is present in the input image header, the data provided with\
1181
+ this option will be instead used.
1182
+ bvalue_scaling: enable or disable scaling of diffusion b-values by the\
1183
+ square of the corresponding DW gradient norm (see Desciption). Valid\
1184
+ choices are yes/no, true/false, 0/1 (default: automatic).
1185
+ export_grad_mrtrix: export the diffusion-weighted gradient table to\
1186
+ file in MRtrix format.
1187
+ export_grad_fsl: export the diffusion-weighted gradient table to files\
1188
+ in FSL (bvecs / bvals) format.
1189
+ dwgrad: the diffusion-weighting gradient table, as interpreted by\
1190
+ MRtrix3.
1191
+ shell_bvalues: list the average b-value of each shell.
1192
+ shell_sizes: list the number of volumes in each shell.
1193
+ shell_indices: list the image volumes attributed to each b-value shell.
1194
+ export_pe_table: export phase-encoding table to file.
1195
+ export_pe_eddy: export phase-encoding information to an EDDY-style\
1196
+ config / index file pair.
1197
+ petable: print the phase encoding table.
1198
+ nodelete: don't delete temporary images or images passed to mrinfo via\
1199
+ Unix pipes.
1200
+ info: display information messages.
1201
+ quiet: do not display information messages or progress status;\
1202
+ alternatively, this can be achieved by setting the MRTRIX_QUIET\
1203
+ environment variable to a non-empty string.
1204
+ debug: display debugging messages.
1205
+ force: force overwrite of output files (caution: using the same file as\
1206
+ input and output might cause unexpected behaviour).
1207
+ nthreads: use this number of threads in multi-threaded applications\
1208
+ (set to 0 to disable multi-threading).
1209
+ config: temporarily set the value of an MRtrix config file entry.
1210
+ help_: display this information page and exit.
1211
+ version: display version information and exit.
1212
+ runner: Command runner.
1213
+ Returns:
1214
+ NamedTuple of outputs (described in `MrinfoOutputs`).
1215
+ """
1216
+ params = mrinfo_params(
1217
+ all_=all_,
1218
+ name=name,
1219
+ format_=format_,
1220
+ ndim=ndim,
1221
+ size=size,
1222
+ spacing=spacing,
1223
+ datatype=datatype,
1224
+ strides=strides,
1225
+ offset=offset,
1226
+ multiplier=multiplier,
1227
+ transform=transform,
1228
+ property_=property_,
1229
+ json_keyval=json_keyval,
1230
+ json_all=json_all,
1231
+ grad=grad,
1232
+ fslgrad=fslgrad,
1233
+ bvalue_scaling=bvalue_scaling,
1234
+ export_grad_mrtrix=export_grad_mrtrix,
1235
+ export_grad_fsl=export_grad_fsl,
1236
+ dwgrad=dwgrad,
1237
+ shell_bvalues=shell_bvalues,
1238
+ shell_sizes=shell_sizes,
1239
+ shell_indices=shell_indices,
1240
+ export_pe_table=export_pe_table,
1241
+ export_pe_eddy=export_pe_eddy,
1242
+ petable=petable,
1243
+ nodelete=nodelete,
1244
+ info=info,
1245
+ quiet=quiet,
1246
+ debug=debug,
1247
+ force=force,
1248
+ nthreads=nthreads,
1249
+ config=config,
1250
+ help_=help_,
1251
+ version=version,
1252
+ image=image,
1253
+ )
1254
+ return mrinfo_execute(params, runner)
1255
+
1256
+
1257
+ __all__ = [
1258
+ "MRINFO_METADATA",
1259
+ "MrinfoConfigParamsDict",
1260
+ "MrinfoConfigParamsDictTagged",
1261
+ "MrinfoExportGradFslOutputs",
1262
+ "MrinfoExportGradFslParamsDict",
1263
+ "MrinfoExportGradFslParamsDictTagged",
1264
+ "MrinfoExportPeEddyOutputs",
1265
+ "MrinfoExportPeEddyParamsDict",
1266
+ "MrinfoExportPeEddyParamsDictTagged",
1267
+ "MrinfoFslgradParamsDict",
1268
+ "MrinfoFslgradParamsDictTagged",
1269
+ "MrinfoOutputs",
1270
+ "MrinfoParamsDict",
1271
+ "MrinfoParamsDictTagged",
1272
+ "MrinfoPropertyParamsDict",
1273
+ "MrinfoPropertyParamsDictTagged",
1274
+ "mrinfo",
1275
+ "mrinfo_config",
1276
+ "mrinfo_execute",
1277
+ "mrinfo_export_grad_fsl",
1278
+ "mrinfo_export_pe_eddy",
1279
+ "mrinfo_fslgrad",
1280
+ "mrinfo_params",
1281
+ "mrinfo_property",
1282
+ ]