{"id":18142415,"url":"https://github.com/benoitberanger/openrecon-ants","last_synced_at":"2026-03-02T21:39:18.648Z","repository":{"id":255486774,"uuid":"851602238","full_name":"benoitberanger/openrecon-ants","owner":"benoitberanger","description":"Perform ANTs transformations using 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Terra.X](doc/OpenRecon_ANTS_V2_FLAIR-CP_FLAIR-UP_DIR-UP_SAG_blur.png)  \n_Sequence_: Non-selective 3D SPACE.  \n_From left to right_: Original, brain mask (SynthStrip), N4BiasFieldCorrection (ANTs) in brain mask, DenoiseImage (ANTs) in brain mask after N4BiasFieldCorrection.  \n_From top to bottom_: 3D FLAIR with Circular Polarization (CP), 3D FLAIR with Universal Pulses (UP), 3D DIR with UP.  \n\n[ANTs](https://github.com/ANTsX/ANTs) using [ANTsPy](https://github.com/ANTsX/ANTsPy) in OpenRecon.  \nBrain masking is performed by [SynthStrip](https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/)\n\n\n## SkullStripping\n\n![ANTs V3 in XA60 on a 7T Terra.x](doc/V3_TOF_SkullStripping_MIP_blur.PNG)\n_Sequence_: Angio TOF  \n_From left to right_: Original, SkullStripped using brainmask from Synthstrip, N4BiasFieldCorrection, DenoiseImage  \n_From top to bottom_: SAG MIP, COR MIP, TRA MIP\n\n\n# Features\n\nThis OR performs ANTs image operations : \n- N4BiasFieldCorrection\n- DenoiseImage\n- N4BiasFieldCorrection then DenoiseImage (default)\n- DenoiseImage then N4BiasFieldCorrection\n- None (only for brain masking / skull stripping)\n\nBrain mask usage :\n- Apply ANTs in brainmask (keep outside the mask intact)\n- Skull stripping then ANTs (keep only in mask)\n- None (only ANTs, no masking)\n\nThere is an option, a checkbox, to **save original images** and intermediate images. (default is _True_)\n\nBased on https://github.com/benoitberanger/openrecon-template\n\n\n# Build\n\nRequirements for building :\n- python **3.12**\n- jsonschema\n\n Python environment manager is **strongly** recomanded :\n```bash\nconda create --name openrecon-ants\nconda install python=3.12\npip install jsonschema\n```\n\nBuild with :\n```bash\npython build.py\n```\n\n\n# Offline test and dev\n\nPython modules :\n- ismrmrd\n- pydicom\n- pynetdicom\n- antspyx\n- torch\n- surfa\n\n``` bash\npip install ismrmrd pydicom pynetdicom antspyx torch surfa\n```\nFollow guidelines in https://github.com/benoitberanger/openrecon-template\n\n# TODO\n\n- Add fields in the UI to tune `N4BiasFieldCorrection` and `DenoiseImage`\n- Add fields in the UI to tune the mask (erode ? delate ? ...)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenoitberanger%2Fopenrecon-ants","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbenoitberanger%2Fopenrecon-ants","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenoitberanger%2Fopenrecon-ants/lists"}