FSL Phase Region Expanding Labeller for Unwrapping Discrete Estimates (PRELUDE)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Performs 3D phase unwrapping on wrapped phase images using a region-growing algorithm.
Modality: Wrapped phase image (3D NIfTI) plus optional magnitude image for masking.
Typical Use: Unwrapping phase images before fieldmap calculation for distortion correction.
Key Parameters¶
-p (wrapped phase), -a (magnitude for mask), -o (output unwrapped phase), -m (brain mask), -f (apply phase filter)
Key Points¶
Essential preprocessing for fieldmap-based distortion correction. Magnitude image improves unwrapping quality. Can handle phase wraps > 2pi.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
phase |
File |
Yes | Wrapped phase image | -p |
magnitude |
File |
No | Magnitude image (for masking) | -a |
complex_input |
File |
No | Complex input image (alternative to phase/magnitude pair) | -c |
output |
string |
Yes | Output unwrapped phase image | -o |
mask |
File |
No | Brain mask image | -m |
num_partitions |
int |
No | Number of phase partitions for initial labeling | -n |
process2d |
boolean |
No | Do 2D processing (slice by slice) | -s |
labelslices |
boolean |
No | 2D labeling with 3D unwrapping | --labelslices |
force3d |
boolean |
No | Force full 3D processing | --force3D |
removeramps |
boolean |
No | Remove phase ramps during unwrapping | --removeramps |
savemask |
string |
No | Save the generated mask volume | --savemask= |
verbose |
boolean |
No | Verbose output | -v |
Accepted Input Extensions¶
- phase:
.nii,.nii.gz - magnitude:
.nii,.nii.gz - complex_input:
.nii,.nii.gz - mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
unwrapped_phase |
File |
$(inputs.output).nii.gz, $(inputs.output).nii, $(inputs.output) |
saved_mask |
File |
$(inputs.savemask).nii.gz, $(inputs.savemask).nii |
log |
File |
prelude.log |
err_log |
File |
prelude.err.log |
Output Extensions¶
- unwrapped_phase:
.nii,.nii.gz - saved_mask:
.nii,.nii.gz
Docker Tags¶
Available versions: latest, 6.0.4-patched2, 6.0.4-patched, 6.0.4, 6.0.4-xenial, 5.0.11, 6.0.0, 6.0.1, 5.0.9
Categories¶
- Functional MRI > FSL > Distortion Correction