harmonization_clinicalcombat
ComBAT harmonization of clinical MRI data. It’s a ComBAT implementations for adapting sites to a reference site along with ready-to-run scripts to prepare datasets, fit a model, apply the harmonization and analyze the outputs. Two harmonization methods are available pairwise (linear) and clinic (non-linear).
Keywords : Harmonization, Pairwise, Clinical, ComBAT
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple path(ref_site), path(move_site)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| ref_site | file | CSV for Reference site data for one metric, all bundles and subjects. Must include sid,site,bundle,metric,mean,age,sex,handedness,disease. The Disease column must include at least the label HC. | True | *.{csv,csv.gz} |
| move_site | file | CSV for Moving site data for one metric, all bundles and subjects. Must include sid,site,bundle,metric,mean,age,sex,handedness,disease. The Disease column must include at least the label HC. | True | *.{csv,csv.gz} |
Outputs
Section titled “Outputs”Format : path(*.model.csv)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| *.model.csv | file | Harmonization fitted model. | True | *.model.csv |
harmonizedsite
Section titled “harmonizedsite”Format : path(*.harmonized.csv.gz)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| *.harmonized.csv.gz | file | Harmonized moving site data. | True | *.harmonized.csv.gz |
Format : path(qc_reports)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| qc_reports | directory | BDQC reports for harmonized data. | True | qc_reports/ |
figures
Section titled “figures”Format : path(figures)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| figures | directory | Figures generated to visualize harmonization results. | True | figures/ |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| method | string | Harmonization strategy to use clinic (non-linear) or pairwise (linear) | clinic | |
| bundles | list | List of bundles subset used to plot. By default all bundles in the csv input file were used to compute model harmonization. | all | |
| limit_age_range | boolean | Drop reference subjects outside the moving age range. | disabled | |
| ignore_sex | boolean | Remove sex variable when estimating the model. If all subjects have the same value, it will be automatically applied. | disabled | |
| ignore_handedness | boolean | Remove handedness variable when estimating the model. If all subjects have the same value, it will be automatically applied. | disabled | |
| no_empiral_bayes | boolean | Ignore the empirical Bayesian estimate | disabled | |
| regul_ref | integer | Ridge penalty applied to reference regression. Parameter use for clinic method only. | 0 | |
| regul_mov | string | Moving site penalty or auto-tuning. Parameter use for clinic method only. | -1 | |
| degree | integer | Polynomial degree used for age. It depend on method used (1 for parwise, 2 for clinic) | None | - 1 - 2 |
| nu | integer | Variance hyperparameter for the moving site. Parameter use for clinic method only. | 5 | |
| tau | integer | Covariate hyperparameter for the moving site. Parameter use for clinic method only. | 2 | |
| degree_qc | integer | QC model degree override (0 reuses the harmonization degree). | 0 |
| Description | DOI | |
|---|---|---|
| clinical-ComBAT | Method for harmonizing MRI data across different sites. | 10.48550/arXiv.2511.04871 |
Authors
Section titled “Authors”Last updated : 2025-12-22