FreeSurfer General Linear Model (mri_glmfit)¶
Library: FreeSurfer | Docker Image: freesurfer/freesurfer
Function¶
Fits a general linear model on surface or volume data for group-level statistical analysis.
Modality: Concatenated surface data from mris_preproc or stacked volume data.
Typical Use: Surface-based or volume-based group statistical analysis.
Key Parameters¶
--y (input data), --fsgd (FreeSurfer group descriptor), --C (contrast file), --surf (surface subject), --glmdir (output directory)
Key Points¶
Uses FSGD file for design specification. Supports DODS and DOSS design types. Can run on surface or volume data.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
subjects_dir |
Directory |
Yes | FreeSurfer SUBJECTS_DIR | |
fs_license |
File |
Yes | FreeSurfer license file | |
y |
File |
Yes | Input data file | --y |
glmdir |
string |
Yes | Output GLM directory | --glmdir |
fsgd |
File |
No | FreeSurfer Group Descriptor file | --fsgd |
design |
File |
No | Design matrix file | --X |
osgm |
boolean |
No | One-sample group mean | --osgm |
C |
File[] |
No | Contrast matrix file(s) | --C |
surface |
string |
No | Surface subject and hemisphere (e.g., fsaverage lh) | --surface |
cortex |
boolean |
No | Use cortex label as mask | --cortex |
fwhm |
double |
No | Smooth input by FWHM in mm | --fwhm |
var_fwhm |
double |
No | Smooth variance by FWHM in mm | --var-fwhm |
mask |
File |
No | Mask volume or label | --mask |
mask_inv |
boolean |
No | Invert mask | --mask-inv |
prune |
boolean |
No | Prune design matrix | --prune |
no_prune |
boolean |
No | Do not prune | --no-prune |
wls |
File |
No | Weighted least squares variance file | --wls |
self |
int |
No | Self regressor column | --self |
pca |
boolean |
No | Perform PCA on residuals | --pca |
save_eres |
boolean |
No | Save residual error | --eres-save |
save_yhat |
boolean |
No | Save signal estimate | --yhat-save |
nii |
boolean |
No | Use NIfTI output format | --nii |
nii_gz |
boolean |
No | Use compressed NIfTI output | --nii.gz |
sim |
string |
No | Simulation parameters (nulltype nsim thresh csd) | --sim |
sim_sign |
enum |
No | Simulation sign | --sim-sign |
seed |
int |
No | Random seed | --seed |
synth |
boolean |
No | Replace input with Gaussian noise | --synth |
allowsubjrep |
boolean |
No | Allow subject repetition in FSGD | --allowsubjrep |
Accepted Input Extensions¶
- y:
.mgh,.mgz,.nii,.nii.gz - fsgd:
.fsgd - design:
.mat,.txt - C:
.mat,.txt,.mtx - mask:
.mgh,.mgz,.nii,.nii.gz,.label - wls:
.mgh,.mgz,.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
glm_dir |
Directory |
$(inputs.glmdir) |
log |
File |
mri_glmfit.log |
Docker Tags¶
Available versions: latest, 8.1.0, 8.0.0, 7.2.0, 7.3.0, 7.3.1, 7.3.2, 7.4.1, 7.1.1, 6.0
Categories¶
- Functional MRI > FreeSurfer > Functional Analysis