ICA-based Automatic Removal of Motion Artifacts (ICA-AROMA)¶
Library: ICA-AROMA | Docker Image: rtrhd/ica-aroma
Function¶
Multi-step denoising pipeline for fMRI motion artifact removal. Internally chains MELODIC ICA decomposition, motion artifact feature extraction, classifier-based component labeling, and non-aggressive denoising.
Modality: Preprocessed 4D fMRI NIfTI in standard (MNI) space with motion parameters.
Typical Use: Removing motion artifacts from resting-state or task fMRI data after standard preprocessing.
Key Parameters¶
-i (input 4D), -mc (motion parameters), -o (output directory), -a (affine matrix), -w (warp field), -den (denoising type)
Key Points¶
Requires data in MNI space. Classifier uses four features: max RP correlation, edge fraction, HFC spatial fraction, and CSF fraction. Non-aggressive denoising recommended.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 4D fMRI data (preprocessed, in standard space) | -i |
output_dir |
string |
Yes | Output directory | -o |
mc |
File |
Yes | Motion parameters file (6 columns) | -mc |
affmat |
File |
No | Affine registration matrix (func to MNI) | -a |
warp |
File |
No | Non-linear warp field (func to MNI) | -w |
mask |
File |
No | Brain mask in functional space | -m |
denoise_type |
enum |
No | Denoising strategy (nonaggr=non-aggressive, aggr=aggressive, both) | -den |
melodic_dir |
Directory |
No | Pre-computed MELODIC directory (skip ICA step) | -md |
dim |
int |
No | Dimensionality for MELODIC (default auto) | -dim |
TR |
double |
No | TR in seconds (extracted from data if not provided) | -tr |
Accepted Input Extensions¶
- input:
.nii,.nii.gz - mc:
.txt,.par,.1D - affmat:
.mat - warp:
.nii,.nii.gz - mask:
.nii,.nii.gz
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
output_directory |
Directory |
$(inputs.output_dir) |
denoised_func |
File |
$(inputs.output_dir)/denoised_func_data_nonaggr.nii.gz, $(inputs.output_dir)/denoised_func_data_aggr.nii.gz, $(inputs.output_dir)/denoised_func_data_nonaggr.nii |
classified_motion |
File |
$(inputs.output_dir)/classified_motion_ICs.txt |
melodic_mixing |
File |
$(inputs.output_dir)/melodic.ica/melodic_mix |
log |
File |
ICA_AROMA.log |
Output Extensions¶
- denoised_func:
.nii,.nii.gz - classified_motion:
.txt
Docker Tags¶
Available versions: latest
Categories¶
- Functional MRI > ICA-AROMA > Denoising
- Pipelines > ICA-AROMA > Denoising