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# workflows.fmri.fsl.estimate

## `create_fixed_effects_flow()`

Link to code

Create a fixed-effects workflow

This workflow is used to combine registered copes and varcopes across runs for an individual subject

### Example

    >>> fixedfx = create_fixed_effects_flow()
    >>> fixedfx.base_dir = '.'
    >>> fixedfx.inputs.inputspec.copes = [['cope1run1.nii.gz', 'cope1run2.nii.gz'], ['cope2run1.nii.gz', 'cope2run2.nii.gz']] # per contrast
    >>> fixedfx.inputs.inputspec.varcopes = [['varcope1run1.nii.gz', 'varcope1run2.nii.gz'], ['varcope2run1.nii.gz', 'varcope2run2.nii.gz']] # per contrast
    >>> fixedfx.inputs.inputspec.dof_files = ['dofrun1', 'dofrun2'] # per run
    >>> fixedfx.run()

Inputs:

    inputspec.copes : list of list of cope files (one list per contrast)
    inputspec.varcopes : list of list of varcope files (one list per
                         contrast)
    inputspec.dof_files : degrees of freedom files for each run

Outputs:

    outputspec.res4d : 4d residual time series
    outputspec.copes : contrast parameter estimates
    outputspec.varcopes : variance of contrast parameter estimates
    outputspec.zstats : z statistics of contrasts
    outputspec.tstats : t statistics of contrasts

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## `create_modelfit_workflow()`

Link to code

Create an FSL individual modelfitting workflow

### Example

    >>> modelfit = create_modelfit_workflow()
    >>> modelfit.base_dir = '.'
    >>> info = dict()
    >>> modelfit.inputs.inputspec.session_info = info
    >>> modelfit.inputs.inputspec.interscan_interval = 3.
    >>> modelfit.inputs.inputspec.film_threshold = 1000
    >>> modelfit.run()

Inputs:

    inputspec.session_info : info generated by modelgen.SpecifyModel
    inputspec.interscan_interval : interscan interval
    inputspec.contrasts : list of contrasts
    inputspec.film_threshold : image threshold for FILM estimation

Outputs:

    outputspec.realignment_parameters : realignment parameter files
    outputspec.smoothed_files : smoothed functional files
    outputspec.outlier_files : list of outliers
    outputspec.outlier_stats : statistics of outliers
    outputspec.outlier_plots : images of outliers
    outputspec.mask_file : binary mask file in reference image space
    outputspec.reg_file : registration file that maps reference image to
                          freesurfer space
    outputspec.reg_cost : cost of registration (useful for detecting
                          misalignment)

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## `create_overlay_workflow()`

Link to code

Setup overlay workflow

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