FSL Randomise Permutation Testing¶
Library: FSL | Docker Image: brainlife/fsl
Function¶
Non-parametric permutation testing for statistical inference with multiple correction methods including TFCE.
Modality: 4D NIfTI of stacked subject images plus design matrix and contrast files.
Typical Use: Group-level inference with family-wise error correction (VBM, TBSS, etc.).
Key Parameters¶
-i (input 4D), -o (output basename), -d (design matrix), -t (contrast file), -n (num permutations), -T (TFCE)
Key Points¶
Use -T for TFCE (recommended). 5000+ permutations for publication. Computationally intensive but provides strong family-wise error control.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | 4D input image | -i |
output |
string |
Yes | Output file root name | -o |
design_mat |
File |
No | Design matrix file (.mat) | -d |
tcon |
File |
No | T-contrast file (.con) | -t |
fcon |
File |
No | F-contrast file (.fts) | -f |
mask |
File |
No | Mask image | -m |
num_perm |
int |
No | Number of permutations (default 5000) | -n |
seed |
int |
No | Random seed | --seed= |
one_sample_group_mean |
boolean |
No | Perform one-sample group mean test | -1 |
tfce |
boolean |
No | Use Threshold-Free Cluster Enhancement | -T |
tfce2D |
boolean |
No | Use 2D TFCE optimization (for TBSS) | --T2 |
tfce_H |
double |
No | TFCE height parameter (default 2) | --tfce_H= |
tfce_E |
double |
No | TFCE extent parameter (default 0.5) | --tfce_E= |
tfce_C |
double |
No | TFCE connectivity parameter (default 6) | --tfce_C= |
c_thresh |
double |
No | Cluster-forming threshold for t-statistics | -c |
cm_thresh |
double |
No | Cluster-mass threshold for t-statistics | -C |
f_c_thresh |
double |
No | Cluster-forming threshold for F-statistics | -F |
f_cm_thresh |
double |
No | Cluster-mass threshold for F-statistics | -S |
demean |
boolean |
No | Demean data temporally before analysis | -D |
vox_p_values |
boolean |
No | Output voxelwise (uncorrected) p-values | -x |
f_only |
boolean |
No | Calculate F-statistics only | --fonly |
raw_stats_imgs |
boolean |
No | Output raw (unpermuted) statistic images | -R |
p_vec_n_dist_files |
boolean |
No | Output permutation vector and null distribution | -P |
var_smooth |
int |
No | Variance smoothing in mm | -v |
x_block_labels |
File |
No | Exchangeability block labels file | -e |
show_total_perms |
boolean |
No | Print total number of permutations and exit | -q |
show_info_parallel_mode |
boolean |
No | Print parallel mode info | -Q |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - design_mat:
.mat - tcon:
.con - fcon:
.fts - mask:
.nii,.nii.gz - x_block_labels:
.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
t_corrp |
File[] |
$(inputs.output)_tfce_corrp_tstat*.nii.gz, $(inputs.output)_vox_corrp_tstat*.nii.gz, $(inputs.output)_clustere_corrp_tstat*.nii.gz, $(inputs.output)_clusterm_corrp_tstat*.nii.gz |
t_p |
File[] |
$(inputs.output)_tfce_p_tstat*.nii.gz, $(inputs.output)_vox_p_tstat*.nii.gz |
tstat |
File[] |
$(inputs.output)_tstat*.nii.gz, $(inputs.output)_tstat*.nii |
f_corrp |
File[] |
$(inputs.output)_tfce_corrp_fstat*.nii.gz, $(inputs.output)_vox_corrp_fstat*.nii.gz |
f_p |
File[] |
$(inputs.output)_tfce_p_fstat*.nii.gz, $(inputs.output)_vox_p_fstat*.nii.gz |
fstat |
File[] |
$(inputs.output)_fstat*.nii.gz, $(inputs.output)_fstat*.nii |
log |
File |
randomise.log |
Output Extensions¶
- t_corrp:
.nii.gz - t_p:
.nii.gz - tstat:
.nii,.nii.gz - f_corrp:
.nii.gz - f_p:
.nii.gz - fstat:
.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