Code: file:///build/buildd/nipype-0.5.3/nipype/workflows/fmri/fsl/estimate.py#L134
Create a fixed-effects workflow
This workflow is used to combine registered copes and varcopes across runs for an individual subject
>>> 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
Code: file:///build/buildd/nipype-0.5.3/nipype/workflows/fmri/fsl/estimate.py#L8
Create an FSL individual modelfitting workflow
>>> 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)
Code: file:///build/buildd/nipype-0.5.3/nipype/workflows/fmri/fsl/estimate.py#L114
Setup overlay workflow