Module: registration/easyreg
Image registration and SynthSeg v2 segmentation with easyreg from freesurfer
Inputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | |
| reference | file | the reference image in .nii(.gz) or .mgz format (note that, since the method is symmetric, the choice of reference vs floating is arbitrary). | *.{nii,nii.gz,mgz} |
| floating | file | the floating image in .nii(.gz) or .mgz format. | *.{nii,nii.gz,mgz} |
| ref_segmentation | file | file with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image. If it does not exist, EasyReg will create it. If it already exists (e.g., from a previous EasyReg run), then EasyReg will read it from disk (which is faster than segmenting). | *.{nii,nii.gz} |
| flo_segmentation | file | file with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image. If it does not exist, EasyReg will create it. If it already exists (e.g., from a previous EasyReg run), then EasyReg will read it from disk (which is faster than segmenting). | *.{nii,nii.gz} |
Outputs
| Type | Description | Pattern | |
|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] | |
| ref_reg | file | this is the file where the deformed (registered) reference image is written. | *_reference_registered.nii.gz |
| flo_reg | file | this is the file where the deformed (registered) floating image is written. | *_floating_registered.nii.gz |
| ref_seg | file | file with the SynthSeg v2 (non-robust) segmentation + parcellation of the reference image. Will produce image only if not passed as input. | *_reference_segmentation.nii.gz |
| flo_seg | file | file with the SynthSeg v2 (non-robust) segmentation + parcellation of the floating image. Will produce image only if not passed as input. | *_floating_segmentation.nii.gz |
| fwd_field | file | this is the file where the forward deformation field is written. The deformation includes both the affine and nonlinear components. Must be a nifti (.nii/.nii.gz) or .mgz file; it is encoded as the real world (RAS) coordinates of the target location for each voxel. | *_forward_field.nii.gz |
| bak_field | file | this is the file where the backward deformation field is written. It must also be a nifty or mgz file. | *_backward_field.nii.gz |
| versions | file | File containing software versions | versions.yml |
Tools
| Description | Homepage | DOI | |
|---|---|---|---|
| Freesurfer | Software package for the analysis and visualization of structural and functional neuroimaging data. | https://surfer.nmr.mgh.harvard.edu/fswiki |
Keywords
| nifti |
| registration |
| segmentation |
| easyreg |
| freesurfer |
Authors
@ThoumyreStanislas
Maintainers
@ThoumyreStanislas