FMRIB's Improved Linear Model (FILM)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Fits general linear model to fMRI time series with prewhitening using autocorrelation correction.
Modality: 4D fMRI NIfTI time series plus design matrix and contrast files.
Typical Use: First-level statistical analysis within FEAT or standalone.
Key Parameters¶
--in (input 4D), --pd (design matrix), --con (contrast file), --thr (threshold), --sa (smoothed autocorrelation)
Key Points¶
Core statistical engine of FEAT. Design matrix must be pre-generated (e.g., via Feat_model). When --con is provided, directly computes COPEs, VARCOPEs, T-statistics, and Z-statistics alongside parameter estimates (pe) and residuals.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 4D data file | --in= |
design_file |
File |
Yes | Design matrix file (.mat) | --pd= |
contrast_file |
File |
No | Contrast definition file (.con) | --con= |
threshold |
double |
No | Threshold for FILM estimation (default 1000) | --thr= |
results_dir |
string |
No | Results directory name | --rn= |
autocorr_noestimate |
boolean |
No | Do not estimate autocorrelation | --noest |
autocorr_estimate_only |
boolean |
No | Only estimate autocorrelation (no GLM) | --ac |
smooth_autocorr |
boolean |
No | Smooth autocorrelation estimates | --sa |
fit_armodel |
boolean |
No | Fit autoregressive model | --ar |
use_pava |
boolean |
No | Estimate autocorrelation using PAVA | --pava |
tukey_window |
int |
No | Tukey window size for autocorrelation | --tukey= |
multitaper_product |
int |
No | Multitaper with slepian tapers | --mt= |
brightness_threshold |
int |
No | Susan brightness threshold | --epith= |
mask_size |
int |
No | Susan mask size | --ms= |
full_data |
boolean |
No | Output full data/verbose | -v |
output_pwdata |
boolean |
No | Output prewhitened data | --outputPWdata |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - design_file:
.mat - contrast_file:
.con
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
results |
Directory |
$(inputs.results_dir || 'results') |
dof |
File |
$(inputs.results_dir || 'results')/dof |
residual4d |
File |
$(inputs.results_dir || 'results')/res4d.nii.gz, $(inputs.results_dir || 'results')/res4d.nii |
param_estimates |
File[] |
$(inputs.results_dir || 'results')/pe*.nii.gz, $(inputs.results_dir || 'results')/pe*.nii |
sigmasquareds |
File |
$(inputs.results_dir || 'results')/sigmasquareds.nii.gz, $(inputs.results_dir || 'results')/sigmasquareds.nii |
threshac1 |
File |
$(inputs.results_dir || 'results')/threshac1.nii.gz, $(inputs.results_dir || 'results')/threshac1.nii |
cope |
File[] |
$(inputs.results_dir || 'results')/cope*.nii.gz, $(inputs.results_dir || 'results')/cope*.nii |
varcope |
File[] |
$(inputs.results_dir || 'results')/varcope*.nii.gz, $(inputs.results_dir || 'results')/varcope*.nii |
tstat |
File[] |
$(inputs.results_dir || 'results')/tstat*.nii.gz, $(inputs.results_dir || 'results')/tstat*.nii |
zstat |
File[] |
$(inputs.results_dir || 'results')/zstat*.nii.gz, $(inputs.results_dir || 'results')/zstat*.nii |
log |
File |
film_gls.log |
Output Extensions¶
- residual4d:
.nii,.nii.gz - param_estimates:
.nii,.nii.gz - sigmasquareds:
.nii,.nii.gz - threshac1:
.nii,.nii.gz - cope:
.nii,.nii.gz - varcope:
.nii,.nii.gz - tstat:
.nii,.nii.gz - zstat:
.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 > Statistical Analysis