FMRIB's Slice Timing Correction (SliceTimer)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Corrects for differences in slice acquisition times within each volume using sinc interpolation.
Modality: 4D fMRI NIfTI time series.
Typical Use: Temporal alignment of slices acquired at different times within each TR.
Key Parameters¶
-r (TR in seconds), --odd (interleaved odd slices first), --down (reverse slice order), --tcustom (custom timing file)
Key Points¶
Must match actual acquisition order. Important for event-related designs with short TRs. Less critical for long TRs or block designs.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 4D timeseries | --in= |
output |
string |
Yes | Output filename | --out= |
tr |
double |
No | TR in seconds | --repeat= |
global_shift |
double |
No | Global shift as fraction of TR (0-1, default 0.5) | --tglobal= |
slice_order |
record(interleaved) | record(down) | record(custom_order) | record(custom_timings) |
No | ||
direction |
int |
No | Slice acquisition direction (1=x, 2=y, 3=z, default 3) | --direction= |
verbose |
boolean |
No | Verbose output | -v |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - custom_order:
.txt - custom_timings:
.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
slice_time_corrected |
File |
$(inputs.output).nii.gz, $(inputs.output).nii |
log |
File |
slicetimer.log |
Output Extensions¶
- slice_time_corrected:
.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 > Slice Timing