FSL Robust Field of View Reduction¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Automatically identifies and removes neck/non-brain tissue by estimating the brain center and reducing the field of view to a standard size.
Modality: T1-weighted 3D NIfTI volume (full head coverage).
Typical Use: Preprocessing step before brain extraction to remove neck and improve BET robustness.
Key Parameters¶
-i (input), -r (output ROI volume), -m (output transformation matrix), -b (brain size estimate in mm, default 170)
Key Points¶
Useful for images with extensive neck coverage. Run before BET for more robust brain extraction. Does not resample, just crops.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input image (full head coverage) | -i |
output |
string |
Yes | Output cropped image filename | -r |
matrix_output |
string |
No | Output transformation matrix filename | -m |
brain_size |
int |
No | Brain size estimate in mm (default 170) | -b |
Accepted Input Extensions¶
- input:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
cropped_image |
File |
$(inputs.output).nii.gz, $(inputs.output).nii, $(inputs.output) |
transform_matrix |
File |
$(inputs.matrix_output) |
log |
File |
robustfov.log |
err_log |
File |
robustfov.err.log |
Output Extensions¶
- cropped_image:
.nii,.nii.gz - transform_matrix:
.mat
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¶
- Utilities > FSL > Volume Operations