workflows.fmri.fsl.estimate

create_fixed_effects_flow()

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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() #doctest: +SKIP

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

Graph

digraph fixedfx{ label="fixedfx"; fixedfx_l2model[label="l2model (fsl)"]; fixedfx_inputspec[label="inputspec (utility)"]; fixedfx_varcopemerge[label="varcopemerge (fsl)"]; fixedfx_copemerge[label="copemerge (fsl)"]; fixedfx_gendofvolume[label="gendofvolume (utility)"]; fixedfx_flameo[label="flameo (fsl)"]; fixedfx_outputspec[label="outputspec (utility)"]; fixedfx_l2model -> fixedfx_flameo; fixedfx_l2model -> fixedfx_flameo; fixedfx_l2model -> fixedfx_flameo; fixedfx_inputspec -> fixedfx_copemerge; fixedfx_inputspec -> fixedfx_varcopemerge; fixedfx_inputspec -> fixedfx_gendofvolume; fixedfx_varcopemerge -> fixedfx_flameo; fixedfx_copemerge -> fixedfx_gendofvolume; fixedfx_copemerge -> fixedfx_flameo; fixedfx_gendofvolume -> fixedfx_flameo; fixedfx_flameo -> fixedfx_outputspec; fixedfx_flameo -> fixedfx_outputspec; fixedfx_flameo -> fixedfx_outputspec; fixedfx_flameo -> fixedfx_outputspec; fixedfx_flameo -> fixedfx_outputspec; }

create_modelfit_workflow()

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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() #doctest: +SKIP

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
inputspec.model_serial_correlations
inputspec.bases

Outputs:

outputspec.copes
outputspec.varcopes
outputspec.dof_file
outputspec.pfiles
outputspec.zfiles
outputspec.parameter_estimates

Graph

digraph modelfit{ label="modelfit"; modelfit_inputspec[label="inputspec (utility)"]; modelfit_level1design[label="level1design (fsl)"]; modelfit_modelgen[label="modelgen (fsl)"]; modelfit_modelestimate[label="modelestimate (fsl)"]; modelfit_merge_contrasts[label="merge_contrasts (utility)"]; modelfit_ztop[label="ztop (fsl)"]; modelfit_outputspec[label="outputspec (utility)"]; modelfit_inputspec -> modelfit_level1design; modelfit_inputspec -> modelfit_level1design; modelfit_inputspec -> modelfit_level1design; modelfit_inputspec -> modelfit_level1design; modelfit_inputspec -> modelfit_level1design; modelfit_inputspec -> modelfit_modelestimate; modelfit_inputspec -> modelfit_modelestimate; modelfit_level1design -> modelfit_modelgen; modelfit_level1design -> modelfit_modelgen; modelfit_modelgen -> modelfit_modelestimate; modelfit_modelgen -> modelfit_modelestimate; modelfit_modelgen -> modelfit_modelestimate; modelfit_modelestimate -> modelfit_outputspec; modelfit_modelestimate -> modelfit_outputspec; modelfit_modelestimate -> modelfit_outputspec; modelfit_modelestimate -> modelfit_outputspec; modelfit_modelestimate -> modelfit_merge_contrasts; modelfit_modelestimate -> modelfit_merge_contrasts; modelfit_merge_contrasts -> modelfit_ztop; modelfit_merge_contrasts -> modelfit_outputspec; modelfit_ztop -> modelfit_outputspec; }

create_overlay_workflow()

Link to code

Setup overlay workflow

Graph

digraph overlay{ label="overlay"; overlay_overlaystats[label="overlaystats (fsl)"]; overlay_slicestats[label="slicestats (fsl)"]; overlay_overlaystats -> overlay_slicestats; }