omni.pipelines.anat.align#
Functions
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Align T1/T2 images. |
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Align T1/T2 images to atlas. |
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Deoblique images. |
- omni.pipelines.anat.align.align_anat(output_path: str, t1_debias: str, t2_debias: str, ref: str = 'T1', program: str = 'fsl', other_args: str = None)[source]#
Align T1/T2 images.
- Parameters:
- output_pathstr
Output path to write out files to.
- t1_debiasstr
Debiased T1 image.
- t2_debiasstr
Debiased T2 image.
- refstr
Set the image to use as a reference [T1/T2].
- programstr
Program to use for alignment (‘afni’: AFNI 3dAllineate or ‘fsl’: fsl flirt).
- other_argsstr
Other arguments to pass to alignment program.
- Returns:
- str
Anatomical aligned T1 (aligned to ref)
- str
Anatomical aligned T2 (aligned to ref).
- str
Affine aligning T1/T2 (depends on what ref was set to).
- omni.pipelines.anat.align.align_atlas(output_path: str, t1_debias: str, t2_debias: str, t1_debias_bet: str, t2_debias_bet: str, anat_align_affine: str, atlas: str = 'mni', atlas_label: str = 'atlas', ref: str = 'T1', program: str = 'fsl', other_args: str = None)[source]#
Align T1/T2 images to atlas.
- Parameters:
- output_pathstr
Output path to write out files to.
- t1_debiasstr
Debiased T1 image.
- t2_debiasstr
Debiased T2 image.
- t1_debias_betstr
Debiased bet T1 image.
- t2_debias_betstr
Debiased bet T2 image.
- anat_align_affinestr
Anatomical image to atlas.
- atlasstr
Atlas to align to.
- atlas_labelstr
Label suffix for atlas outputs
- refstr
Set anatomical reference image that was used.
- programstr
Program to use for alignment (‘afni’: AFNI 3dAllineate or ‘fsl’: fsl flirt).
- other_argsstr
Other arguments to pass to alignment program.
- Returns:
- str
Atlas aligned T1.
- str
Atlas aligned T2.