FMRIB's Local Analysis of Mixed Effects (FLAME)¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Group-level mixed-effects analysis accounting for both within-subject and between-subject variance using MCMC-based Bayesian estimation.
Modality: 4D NIfTI of stacked subject-level COPEs, VARCOPEs, plus group design matrix and contrast files.
Typical Use: Second-level group analyses with proper random effects.
Key Parameters¶
--cope (cope image), --vc (varcope image), --dm (design matrix), --cs (contrast file), --runmode (fe/ols/flame1/flame12)
Key Points¶
FLAME1 is recommended (good accuracy with reasonable speed). OLS is fast but ignores within-subject variance. FLAME1+2 is most accurate but slowest.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
cope_file |
File |
Yes | COPE (contrast of parameter estimates) file | --copefile= |
var_cope_file |
File |
No | Variance of COPE file | --varcopefile= |
mask_file |
File |
Yes | Mask file | --maskfile= |
design_file |
File |
Yes | Design matrix file (.mat) | --designfile= |
t_con_file |
File |
Yes | T-contrast file (.con) | --tcontrastsfile= |
cov_split_file |
File |
Yes | Covariance split file | --covsplitfile= |
run_mode |
enum |
Yes | Inference mode (fe=fixed effects, ols=OLS, flame1=FLAME stage 1, flame12=FLAME stages 1+2) | --runmode= |
log_dir |
string |
No | Output directory name (default stats) | --ld= |
f_con_file |
File |
No | F-contrast file (.fts) | --fcontrastsfile= |
dof_var_cope_file |
File |
No | Degrees of freedom for varcope | --dofvarcopefile= |
n_jumps |
int |
No | Number of MCMC jumps | --njumps= |
burnin |
int |
No | Number of MCMC burnin jumps | --burnin= |
sample_every |
int |
No | MCMC sample every N jumps | --sampleevery= |
infer_outliers |
boolean |
No | Infer outliers | --inferoutliers |
outlier_iter |
int |
No | Outlier inference iterations | --ioni= |
fix_mean |
boolean |
No | Fix mean for tfit | --fixmean |
no_pe_outputs |
boolean |
No | Do not output parameter estimates | --nopeoutput |
sigma_dofs |
int |
No | Sigma for DOF Gaussian smoothing | --sigma_dofs= |
Accepted Input Extensions¶
- cope_file:
.nii,.nii.gz - var_cope_file:
.nii,.nii.gz - mask_file:
.nii,.nii.gz - design_file:
.mat - t_con_file:
.con - cov_split_file:
.grp - f_con_file:
.fts - dof_var_cope_file:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
stats_dir |
Directory |
$(inputs.log_dir || 'stats') |
copes |
File[] |
$(inputs.log_dir || 'stats')/cope*.nii.gz, $(inputs.log_dir || 'stats')/cope*.nii |
var_copes |
File[] |
$(inputs.log_dir || 'stats')/varcope*.nii.gz, $(inputs.log_dir || 'stats')/varcope*.nii |
tstats |
File[] |
$(inputs.log_dir || 'stats')/tstat*.nii.gz, $(inputs.log_dir || 'stats')/tstat*.nii |
zstats |
File[] |
$(inputs.log_dir || 'stats')/zstat*.nii.gz, $(inputs.log_dir || 'stats')/zstat*.nii |
fstats |
File[] |
$(inputs.log_dir || 'stats')/fstat*.nii.gz, $(inputs.log_dir || 'stats')/fstat*.nii |
zfstats |
File[] |
$(inputs.log_dir || 'stats')/zfstat*.nii.gz, $(inputs.log_dir || 'stats')/zfstat*.nii |
tdof |
File |
$(inputs.log_dir || 'stats')/tdof_t*.nii.gz, $(inputs.log_dir || 'stats')/tdof_t*.nii |
res4d |
File |
$(inputs.log_dir || 'stats')/res4d.nii.gz, $(inputs.log_dir || 'stats')/res4d.nii |
weights |
File |
$(inputs.log_dir || 'stats')/weights*.nii.gz, $(inputs.log_dir || 'stats')/weights*.nii |
log |
File |
flameo.log |
Output Extensions¶
- copes:
.nii,.nii.gz - var_copes:
.nii,.nii.gz - tstats:
.nii,.nii.gz - zstats:
.nii,.nii.gz - fstats:
.nii,.nii.gz - zfstats:
.nii,.nii.gz - tdof:
.nii,.nii.gz - res4d:
.nii,.nii.gz - weights:
.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