File format:
[base output]_[main input]_[algorithm acronym]_[type(optional)].[extension]
Only the primary outputs are written to disk, unless an argument --output-all is provided.
| Algorithm | main input | acronym | type | extension | primary |
|---|---|---|---|---|---|
| N4 bias correction | t1 | n4 | .nii.gz | ||
| Skull strip | t1 | ss | .nii.gz | ✓ | |
| Skull strip | t1 | ss | scaling | .csv | ✓ |
| Skull strip | t1 | ss | mask | .nii.gz | |
| Skull strip | t1 | ss | cutplane | .csv | |
| Bias field correction | t1 | bfc | .nii.gz | ||
| Bias field correction | t1 | bfc | ss | .nii.gz | |
| Hypointensity correction | t1 | hic | .nii.gz | ||
| Hypointensity correct | t1 | hic | ss | .nii.gz | |
| Expectation maximization segmentation | t1 | em | tissue | .nii.gz | |
| Multi-atlas segmentation | t1 | ma | .nii.gz | ✓ | |
| Multi-atlas segmentation | t1 | ma | .csv | ✓ | |
| Multi-atlas segmentation | t1 | ma | cmta | .csv | ✓ |
| Multi-atlas segmentation | t1 | ma | tissue | .nii.gz | ✓ |
| Multi-atlas segmentation | t1 | ma | tissue | .csv | ✓ |
| Tensor-based morpohmetry | t1 | tbm | .nii.gz | ✓ | |
| Tensor-based morpohmetry | t1 | tbm | .csv | ✓ | |
| Tensor-based morpohmetry | t1 | tbm | dsi-scd-ad | .nii.gz | |
| Tensor-based morpohmetry | t1 | tbm | dsi-scd-ftd | .nii.gz | |
| Tensor-based morpohmetry | t1 | tbm | dsi-scd-dlb | .nii.gz | |
| Tensor-based morpohmetry | t1 | tbm | dsi-ftd-dlb | .nii.gz | |
| Tensor-based morpohmetry | t1 | tbm | dsi-ad-ftd | .nii.gz | |
| Tensor-based morpohmetry | t1 | tbm | dsi-ad-dlb | .nii.gz | |
| Tensor-based morpohmetry | t1 | tbm | affine | .trf | |
| Tensor-based morpohmetry | t1 | tbm | nonrigid | .asc | |
| Tensor-based morpohmetry | t1 | tbm | nonrigid | .e3d.gz | |
| Voxel-based morpohmetry | t1 | vbm | .nii.gz | ✓ | |
| Voxel-based morpohmetry | t1 | vbm | .csv | ✓ | |
| Voxel-based morpohmetry | t1 | vbm | cgca | .csv | ✓ |
| Voxel-based morpohmetry | t1 | vbm | dsi-scd-ad | .nii.gz | |
| Voxel-based morpohmetry | t1 | vbm | dsi-scd-ftd | .nii.gz | |
| Voxel-based morpohmetry | t1 | vbm | dsi-scd-dlb | .nii.gz | |
| Voxel-based morpohmetry | t1 | vbm | dsi-ftd-dlb | .nii.gz | |
| Voxel-based morpohmetry | t1 | vbm | dsi-ad-ftd | .nii.gz | |
| Voxel-based morpohmetry | t1 | vbm | dsi-ad-dlb | .nii.gz | |
| Voxel-based morpohmetry | t1 | vbm | normality | .csv | |
| Voxel-based morpohmetry | t1 | vbm | nonrigid | .asc | |
| Voxel-based morpohmetry | t1 | vbm | nonrigid | .e3d.gz | |
| Grading | t1 | grading | .csv | ✓ | |
| Vascular burden | flair | vb | .nii.gz | ✓ | |
| Vascular burden | flair | vb | .csv | ✓ | |
| Vascular burden | flair | vb | cfazekas | .csv | ✓ |
| Vascular burden | flair | vb | li | .nii.gz | |
| Vascular burden | flair | vb | ci | .nii.gz | |
| Vascular burden | flair | vb | wmh | .nii.gz |
output_t1_ss.nii.gz
output_t1_ss_scaling.csv
output_t1_ma.nii.gz
output_t1_ma.csv
output_t1_ma_cmta.csv
output_t1_ma_tissue.nii.gz
output_t1_ma_tissue.csv
output_t1_tbm.nii.gz
output_t1_tbm.csv
output_t1_vbm.nii.gz
output_t1_vbm.csv
output_t1_vbm_cgca.csv
output_t1_grading.csv
output_flair_vb.nii.gz
output_flair_vb.csv
output_flair_vb_cfazekas.csv