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base repository: styx-api/niwrap
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base: v0.1.3
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head repository: styx-api/niwrap
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compare: v0.2.0
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  • 8 commits
  • 15 files changed
  • 4 contributors

Commits on Sep 23, 2024

  1. Add Mrtrix3Tissue fork (#156)

    * Add mrtrix3tissue ss3t
    
    * Compiled
    kaitj authored Sep 23, 2024
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    28620f1 View commit details

Commits on Oct 4, 2024

  1. Add dwigradcheck descriptor (#157)

    kaitj authored Oct 4, 2024
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    0d36c3e View commit details
  2. Prettified Code!

    nx10 authored and actions-user committed Oct 4, 2024
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    23347d3 View commit details
  3. Compile

    github-actions[bot] committed Oct 4, 2024
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    33d6f45 View commit details

Commits on Oct 15, 2024

  1. Mutable inputs

    nx10 committed Oct 15, 2024
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    cead23e View commit details
  2. 3drefit mutable input

    nx10 committed Oct 15, 2024
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    d9c9845 View commit details
  3. Merge branch 'main' of https://github.com/childmindresearch/niwrap

    nx10 committed Oct 15, 2024
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    b14a525 View commit details
  4. Compile

    github-actions[bot] committed Oct 15, 2024
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1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -25,6 +25,7 @@
| [FreeSurfer](https://github.com/freesurfer/freesurfer) | In progress | [`7.4.1`](https://hub.docker.com/r/freesurfer/freesurfer) | 2/104 (1.9%) |
| [Greedy](https://sites.google.com/view/greedyreg/about) | In progress | [`1.0.1`](https://hub.docker.com/r/pyushkevich/itksnap) | 1/1 (100% 🎉) |
| [MRTrix3](https://www.mrtrix.org/) | Testing | [`3.0.4`](https://hub.docker.com/r/mrtrix3/mrtrix3) | 116/125 (92.8%) |
| [MRTrix3Tissue](https://3tissue.github.io/) | Testing | [`5.2.8`](https://hub.docker.com/r/brainlife/3tissue) | 1/1 (100% 🎉) |
| [NiftyReg](http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg) | In progress | [`1.4.0`](https://hub.docker.com/r/vnmd/niftyreg_1.4.0) | 7/7 (100% 🎉) |

<!-- END_PACKAGES_TABLE -->
3 changes: 2 additions & 1 deletion descriptors/afni/3drefit.json
Original file line number Diff line number Diff line change
@@ -77,7 +77,8 @@
"type": "File",
"value-key": "[IN_FILE]",
"description": "Input file to 3drefit.",
"optional": false
"optional": false,
"mutable": true
},
{
"id": "nosaveatr",
254 changes: 254 additions & 0 deletions descriptors/mrtrix/dwigradcheck.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,254 @@
{
"name": "dwigradcheck",
"tool-version": "1.0",
"author": "Ben Jeurrisen",
"description": "Check the orientation of the diffusion gradient table",
"url": "http://www.mrtrix.org/",
"command-line": "dwigradcheck [INPUT_IMAGE] [GRAD] [FSLGRAD_BVECS] [MASK_IMAGE] [NUMBER] [EXPORT_GRAD_MRTRIX] [EXPORT_GRAD_FSL] [NOCLEANUP] [SCRATCH] [CONTINUE_SCRATCH] [INFO] [QUIET] [DEBUG] [FORCE] [NTHREADS] [CONFIG] [HELP] [VERSION]",
"schema-version": "0.5",
"container-image": {
"image": "mrtrix3/mrtrix3:3.0.4",
"type": "docker"
},
"inputs": [
{
"id": "input_image",
"name": "Input Image",
"type": "File",
"value-key": "[INPUT_IMAGE]",
"description": "The input DWI series to be checked",
"optional": false
},
{
"id": "grad",
"name": "Gradient Table (MRtrix format)",
"type": "File",
"value-key": "[GRAD]",
"command-line-flag": "-grad",
"description": "Provide the diffusion gradient table in MRtrix format",
"optional": true
},
{
"id": "fslgrad",
"name": "fslgrad",
"value-key": "[FSLGRAD_BVECS]",
"description": "Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.",
"type": {
"id": "fslgrad",
"name": "fslgrad",
"description": "Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.",
"command-line": "-fslgrad [BVECS] [BVALS]",
"inputs": [
{
"id": "bvecs",
"name": "bvecs",
"value-key": "[BVECS]",
"description": "Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.",
"type": "File",
"optional": false
},
{
"id": "bvals",
"name": "bvals",
"value-key": "[BVALS]",
"description": "Provide the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files. If a diffusion gradient scheme is present in the input image header, the data provided with this option will be instead used.",
"type": "File",
"optional": false
}
],
"output-files": []
},
"optional": true
},
{
"id": "mask_image",
"name": "Mask Image",
"type": "File",
"value-key": "[MASK_IMAGE]",
"command-line-flag": "-mask",
"description": "Provide a brain mask image",
"optional": true
},
{
"id": "number",
"name": "number",
"type": "Number",
"value-key": "[NUMBER]",
"command-line-flag": "-number",
"integer": true,
"description": "Set the number of tracks to generate for each test",
"optional": true
},
{
"id": "export_grad_mrtrix",
"name": "export_grad_mrtrix",
"command-line-flag": "-export_grad_mrtrix",
"value-key": "[EXPORT_GRAD_MRTRIX]",
"description": "export the diffusion-weighted gradient table to file in MRtrix format",
"type": "String",
"optional": true
},
{
"id": "export_grad_fsl",
"name": "export_grad_fsl",
"value-key": "[EXPORT_GRAD_FSL]",
"description": "export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format",
"type": {
"id": "export_grad_fsl",
"name": "export_grad_fsl",
"description": "export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format",
"command-line": "-export_grad_fsl [BVECS_PATH] [BVALS_PATH]",
"inputs": [
{
"id": "bvecs_path",
"name": "bvecs_path",
"value-key": "[BVECS_PATH]",
"description": "export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format",
"type": "String",
"optional": false
},
{
"id": "bvals_path",
"name": "bvals_path",
"value-key": "[BVALS_PATH]",
"description": "export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format",
"type": "String",
"optional": false
}
],
"output-files": [
{
"id": "bvecs_path",
"name": "bvecs_path",
"path-template": "[BVECS_PATH]",
"description": "export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format"
},
{
"id": "bvals_path",
"name": "bvals_path",
"path-template": "[BVALS_PATH]",
"description": "export the diffusion-weighted gradient table to files in FSL (bvecs / bvals) format"
}
]
},
"optional": true
},
{
"id": "nocleanup",
"name": "No Cleanup",
"type": "Flag",
"value-key": "[NOCLEANUP]",
"command-line-flag": "-nocleanup",
"description": "Do not delete intermediate files during script execution, and do not delete scratch directory at script completion",
"optional": true
},
{
"id": "scratch_dir",
"name": "Scratch Directory",
"type": "File",
"value-key": "[SCRATCH]",
"command-line-flag": "-scratch",
"description": "Manually specify the path in which to generate the scratch directory",
"optional": true
},
{
"id": "continue_scratch_dir",
"name": "Continue Scratch Directory",
"type": "File",
"value-key": "[CONTINUE_SCRATCH]",
"command-line-flag": "-continue",
"description": "Continue the script from a previous execution; must provide the scratch directory path",
"optional": true,
"list": true,
"min-list-entries": 2,
"max-list-entries": 2
},
{
"id": "info",
"name": "Display Information Messages",
"type": "Flag",
"value-key": "[INFO]",
"command-line-flag": "-info",
"description": "Display information messages",
"optional": true
},
{
"id": "quiet",
"name": "Quiet Mode",
"type": "Flag",
"value-key": "[QUIET]",
"command-line-flag": "-quiet",
"description": "Do not display information messages or progress status",
"optional": true
},
{
"id": "debug",
"name": "Debug Mode",
"type": "Flag",
"value-key": "[DEBUG]",
"command-line-flag": "-debug",
"description": "Display debugging messages",
"optional": true
},
{
"id": "force",
"name": "Force Overwrite",
"type": "Flag",
"value-key": "[FORCE]",
"command-line-flag": "-force",
"description": "Force overwrite of output files",
"optional": true
},
{
"id": "nthreads",
"name": "Number of Threads",
"type": "Number",
"value-key": "[NTHREADS]",
"command-line-flag": "-nthreads",
"description": "Use this number of threads in multi-threaded applications (set to 0 to disable multi-threading)",
"optional": true
},
{
"id": "config",
"name": "Config Key Value",
"type": "String",
"value-key": "[CONFIG]",
"command-line-flag": "-config",
"description": "Temporarily set the value of an MRtrix config file entry",
"optional": true,
"list": true
},
{
"id": "help",
"name": "Display Help",
"type": "Flag",
"value-key": "[HELP]",
"command-line-flag": "-help",
"description": "Display help information and exit",
"optional": true
},
{
"id": "version",
"name": "Display Version",
"type": "Flag",
"value-key": "[VERSION]",
"command-line-flag": "-version",
"description": "Display version information and exit",
"optional": true
}
],
"output-files": [
{
"id": "export_grad_mrtrix",
"name": "export_grad_mrtrix",
"path-template": "[EXPORT_GRAD_MRTRIX]",
"description": "export the diffusion-weighted gradient table to file in MRtrix format "
},
{
"id": "export_grad_fsl",
"name": "export_grad_fsl",
"path-template": "[EXPORT_GRAD_MRTRIX]",
"description": "export the diffusion-weighted gradient table to file in FSL format "
}
]
}
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