FSL Fieldmap Preparation¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Prepares a fieldmap for use with FUGUE by converting phase difference images to radians per second.
Modality: Phase difference image and magnitude image from gradient echo fieldmap acquisition.
Typical Use: Converting raw fieldmap images to FUGUE-compatible format for EPI distortion correction.
Key Parameters¶
Key Points¶
Scanner type determines unwrapping method (SIEMENS most common). Delta TE is the echo time difference in milliseconds. Output is in rad/s for use with FUGUE.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
scanner |
string |
Yes | Scanner type (e.g., SIEMENS) | |
phase_image |
File |
Yes | Phase difference image | |
magnitude_image |
File |
Yes | Brain-extracted magnitude image | |
output |
string |
Yes | Output fieldmap filename | |
delta_TE |
double |
Yes | Echo time difference in milliseconds | |
nocheck |
boolean |
No | Suppress sanity checking of image size/range/dimensions | --nocheck |
Accepted Input Extensions¶
- phase_image:
.nii,.nii.gz - magnitude_image:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
fieldmap |
File |
$(inputs.output).nii.gz, $(inputs.output).nii, $(inputs.output) |
log |
File |
fsl_prepare_fieldmap.log |
err_log |
File |
fsl_prepare_fieldmap.err.log |
Output Extensions¶
- fieldmap:
.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