.. AUTO-GENERATED FILE -- DO NOT EDIT!

nipype.interfaces.freesurfer.model
==================================


:class:`Binarize`
-----------------


Wraps command **mri_binarize**

Use FreeSurfer mri_binarize to threshold an input volume

Examples
~~~~~~~~

>>> binvol = Binarize(in_file='structural.nii', min=10, binary_file='foo_out.nii')
>>> binvol.cmdline
'mri_binarize --o foo_out.nii --i structural.nii --min 10.000000'

Inputs:: 

	[Mandatory]
	in_file : (an existing file name)
		input volume

	[Optional]
	abs : (a boolean)
		take abs of invol first (ie, make unsigned)
	args : (a string)
		Additional parameters to the command
	bin_col_num : (a boolean)
		set binarized voxel value to its column number
	bin_val : (an integer)
		set vox within thresh to val (default is 1)
	bin_val_not : (an integer)
		set vox outside range to val (default is 0)
	binary_file : (a file name)
		binary output volume
	count_file : (a boolean or a file name)
		save number of hits in ascii file (hits,ntotvox,pct)
	dilate : (an integer)
		niters: dilate binarization in 3D
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	erode : (an integer)
		nerode: erode binarization in 3D (after any dilation)
	erode2d : (an integer)
		nerode2d: erode binarization in 2D (after any 3D erosion)
	frame_no : (an integer)
		use 0-based frame of input (default is 0)
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	invert : (a boolean)
		set binval=0, binvalnot=1
	mask_file : (an existing file name)
		must be within mask
	mask_thresh : (a float)
		set thresh for mask
	match : (a list of items which are an integer)
		match instead of threshold
	max : (a float)
		max thresh
	merge_file : (an existing file name)
		merge with mergevol
	min : (a float)
		min thresh
	out_type : ('nii' or 'nii.gz' or 'mgz')
		output file type
	rmax : (a float)
		compute max based on rmax*globalmean
	rmin : (a float)
		compute min based on rmin*globalmean
	subjects_dir : (an existing directory name)
		subjects directory
	ventricles : (a boolean)
		set match vals those for aseg ventricles+choroid (not 4th)
	wm : (a boolean)
		set match vals to 2 and 41 (aseg for cerebral WM)
	wm_ven_csf : (a boolean)
		WM and ventricular CSF, including choroid (not 4th)
	zero_edges : (a boolean)
		zero the edge voxels
	zero_slice_edge : (a boolean)
		zero the edge slice voxels


Outputs:: 

	binary_file : (an existing file name)
		binarized output volume
	count_file : (a file name)
		ascii file containing number of hits

:class:`Concatenate`
--------------------


Wraps command **mri_concat**

Use Freesurfer mri_concat to combine several input volumes
into one output volume.  Can concatenate by frames, or compute
a variety of statistics on the input volumes.

Examples
~~~~~~~~

Combine two input volumes into one volume with two frames

>>> concat = Concatenate()
>>> concat.inputs.in_files = ['cont1.nii','cont2.nii']
>>> concat.inputs.concatenated_file = 'bar.nii'
>>> concat.cmdline
'mri_concat --o bar.nii --i cont1.nii --i cont2.nii'

Inputs:: 

	[Mandatory]
	in_files : (an existing file name)
		Individual volumes to be concatenated

	[Optional]
	add_val : (a float)
		Add some amount to the input volume
	args : (a string)
		Additional parameters to the command
	combine : (a boolean)
		Combine non-zero values into single frame volume
	concatenated_file : (a file name)
		Output volume
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	gmean : (an integer)
		create matrix to average Ng groups, Nper=Ntot/Ng
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	keep_dtype : (a boolean)
		Keep voxelwise precision type (default is float
	mask_file : (an existing file name)
		Mask input with a volume
	max_bonfcor : (a boolean)
		Compute max and bonferroni correct (assumes -log10(ps))
	max_index : (a boolean)
		Compute the index of max voxel in concatenated volumes
	mean_div_n : (a boolean)
		compute mean/nframes (good for var)
	multiply_by : (a float)
		Multiply input volume by some amount
	multiply_matrix_file : (an existing file name)
		Multiply input by an ascii matrix in file
	paired_stats : ('sum' or 'avg' or 'diff' or 'diff-norm' or 'diff-norm1' or 'diff-norm2')
		Compute paired sum, avg, or diff
	sign : ('abs' or 'pos' or 'neg')
		Take only pos or neg voxles from input, or take abs
	sort : (a boolean)
		Sort each voxel by ascending frame value
	stats : ('sum' or 'var' or 'std' or 'max' or 'min' or 'mean')
		Compute the sum, var, std, max, min or mean of the input volumes
	subjects_dir : (an existing directory name)
		subjects directory
	vote : (a boolean)
		Most frequent value at each voxel and fraction of occurances


Outputs:: 

	concatenated_file : (an existing file name)
		Path/name of the output volume

:class:`GLMFit`
---------------


Wraps command **mri_glmfit**

Use FreeSurfer's mri_glmfit to specify and estimate a general linear model.

Examples
~~~~~~~~

>>> glmfit = GLMFit()
>>> glmfit.inputs.in_file = 'functional.nii'
>>> glmfit.inputs.one_sample = True
>>> glmfit.cmdline == 'mri_glmfit --glmdir %s --y functional.nii --osgm'%os.getcwd()
True

Inputs:: 

	[Mandatory]
	in_file : (a file name)
		input 4D file

	[Optional]
	allow_ill_cond : (a boolean)
		allow ill-conditioned design matrices
	allow_repeated_subjects : (a boolean)
		allow subject names to repeat in the fsgd file (must appear before --fsgd
	args : (a string)
		Additional parameters to the command
	calc_AR1 : (a boolean)
		compute and save temporal AR1 of residual
	check_opts : (a boolean)
		don't run anything, just check options and exit
	compute_log_y : (a boolean)
		compute natural log of y prior to analysis
	contrast : (an existing file name)
		contrast file
	cortex : (a boolean)
		use subjects ?h.cortex.label as label
		exclusive: label_file
	debug : (a boolean)
		turn on debugging
	design : (an existing file name)
		design matrix file
		exclusive: fsgd,design,one_sample
	diag : (an integer)
		Gdiag_no : set diagnositc level
	diag_cluster : (a boolean)
		save sig volume and exit from first sim loop
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	fixed_fx_dof : (an integer)
		dof for fixed effects analysis
		exclusive: fixed_fx_dof_file
	fixed_fx_dof_file : (a file name)
		text file with dof for fixed effects analysis
		exclusive: fixed_fx_dof
	fixed_fx_var : (an existing file name)
		for fixed effects analysis
	force_perm : (a boolean)
		force perumtation test, even when design matrix is not orthog
	fsgd : (a tuple of the form: (an existing file name, 'doss' or 'dods'))
		freesurfer descriptor file
		exclusive: fsgd,design,one_sample
	fwhm : (a float)
		smooth input by fwhm
	glm_dir : (a string)
		save outputs to dir
	hemi : ('lh' or 'rh')
		surface hemisphere
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	invert_mask : (a boolean)
		invert mask
	label_file : (an existing file name)
		use label as mask, surfaces only
		exclusive: cortex
	mask_file : (an existing file name)
		binary mask
	no_contrast_sok : (a boolean)
		do not fail if no contrasts specified
	no_est_fwhm : (a boolean)
		turn off FWHM output estimation
	no_mask_smooth : (a boolean)
		do not mask when smoothing
	no_prune : (a boolean)
		do not prune
		exclusive: prunethresh
	one_sample : (a boolean)
		construct X and C as a one-sample group mean
		exclusive: one_sample,fsgd,design,contrast
	pca : (a boolean)
		perform pca/svd analysis on residual
	per_voxel_reg : (an existing file name)
		per-voxel regressors
	profile : (an integer)
		niters : test speed
	prune : (a boolean)
		remove voxels that do not have a non-zero value at each frame (def)
	prune_thresh : (a float)
		prune threshold. Default is FLT_MIN
		exclusive: noprune
	resynth_test : (an integer)
		test GLM by resynthsis
	save_cond : (a boolean)
		flag to save design matrix condition at each voxel
	save_estimate : (a boolean)
		save signal estimate (yhat)
	save_res_corr_mtx : (a boolean)
		save residual error spatial correlation matrix (eres.scm). Big!
	save_residual : (a boolean)
		save residual error (eres)
	seed : (an integer)
		used for synthesizing noise
	self_reg : (a tuple of the form: (an integer, an integer, an integer))
		self-regressor from index col row slice
	sim_done_file : (a file name)
		create file when simulation finished
	sim_sign : ('abs' or 'pos' or 'neg')
		abs, pos, or neg
	simulation : (a tuple of the form: ('perm' or 'mc-full' or 'mc-z', an integer, a float, a string))
		nulltype nsim thresh csdbasename
	subject_id : (a string)
		subject id for surface geometry
	subjects_dir : (an existing directory name)
		subjects directory
	surf : (a boolean)
		analysis is on a surface mesh
		requires: subject_id,hemi
	surf_geo : (a string)
		surface geometry name (e.g. white, pial)
	synth : (a boolean)
		replace input with gaussian
	uniform : (a tuple of the form: (a float, a float))
		use uniform distribution instead of gaussian
	var_fwhm : (a float)
		smooth variance by fwhm
	vox_dump : (a tuple of the form: (an integer, an integer, an integer))
		dump voxel GLM and exit
	weight_file : (an existing file name)
		weight for each input at each voxel
		exclusive: weighted_ls
	weight_inv : (a boolean)
		invert weights
		exclusive: weighted_ls
	weight_sqrt : (a boolean)
		sqrt of weights
		exclusive: weighted_ls
	weighted_ls : (an existing file name)
		weighted least squares
		exclusive: weight_file,weight_inv,weight_sqrt


Outputs:: 

	beta_file : (an existing file name)
		map of regression coefficients
	dof_file : (a file name)
		text file with effective degrees-of-freedom for the analysis
	error_file : (a file name)
		map of residual error
	error_stddev_file : (a file name)
		map of residual error standard deviation
	error_var_file : (a file name)
		map of residual error variance
	estimate_file : (a file name)
		map of the estimated Y values
	frame_eigenvectors : (a file name)
		matrix of frame eigenvectors from residual PCA
	ftest_file	map of test statistic values
	fwhm_file : (a file name)
		text file with estimated smoothness
	gamma_file	map of contrast of regression coefficients
	gamma_var_file	map of regression contrast variance
	glm_dir : (an existing directory name)
		output directory
	mask_file : (a file name)
		map of the mask used in the analysis
	sig_file	map of F-test significance (in -log10p)
	singular_values : (a file name)
		matrix singular values from residual PCA
	spatial_eigenvectors : (a file name)
		map of spatial eigenvectors from residual PCA
	svd_stats_file : (a file name)
		text file summarizing the residual PCA

:class:`Label2Vol`
------------------


Wraps command **mri_label2vol**

Make a binary volume from a Freesurfer label

Examples
~~~~~~~~

>>> binvol = Label2Vol(label_file='cortex.label', template_file='structural.nii', reg_file='register.dat', fill_thresh=0.5, vol_label_file='foo_out.nii')
>>> binvol.cmdline
'mri_label2vol --fillthresh 0 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii'

Inputs:: 

	[Mandatory]
	annot_file : (an existing file name)
		surface annotation file
		exclusive: label_file,annot_file,seg_file,aparc_aseg
		requires: subjectid,hemi
	aparc_aseg : (a boolean)
		use aparc+aseg.mgz in subjectdir as seg
		exclusive: label_file,annot_file,seg_file,aparc_aseg
	label_file : (an existing file name)
		list of label files
		exclusive: label_file,annot_file,seg_file,aparc_aseg
	seg_file : (an existing file name)
		segmentation file
		exclusive: label_file,annot_file,seg_file,aparc_aseg
	template_file : (an existing file name)
		output template volume

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	fill_thresh : (0.0 <= a floating point number <= 1.0)
		thresh : between 0 and 1
	hemi : ('lh' or 'rh')
		hemisphere to use lh or rh
	identity : (a boolean)
		set R=I
		exclusive: reg_file,reg_header,identity
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	invert_mtx : (a boolean)
		Invert the registration matrix
	label_hit_file : (a file name)
		file with each frame is nhits for a label
	label_voxel_volume : (a float)
		volume of each label point (def 1mm3)
	map_label_stat : (a file name)
		map the label stats field into the vol
	native_vox2ras : (a boolean)
		use native vox2ras xform instead of  tkregister-style
	proj : (a tuple of the form: ('abs' or 'frac', a float, a float, a float))
		project along surface normal
	reg_file : (an existing file name)
		tkregister style matrix VolXYZ = R*LabelXYZ
		exclusive: reg_file,reg_header,identity
	reg_header : (an existing file name)
		label template volume
		exclusive: reg_file,reg_header,identity
	subject_id : (a string)
		subject id
	subjects_dir : (an existing directory name)
		subjects directory
	surface : (a string)
		use surface instead of white
	vol_label_file : (a file name)
		output volume


Outputs:: 

	vol_label_file : (an existing file name)
		output volume

:class:`MRISPreproc`
--------------------


Wraps command **mris_preproc**

Use FreeSurfer mris_preproc to prepare a group of contrasts for
a second level analysis

Examples
~~~~~~~~

>>> preproc = MRISPreproc()
>>> preproc.inputs.target = 'fsaverage'
>>> preproc.inputs.hemi = 'lh'
>>> preproc.inputs.vol_measure_file = [('cont1.nii', 'register.dat'),                                            ('cont1a.nii', 'register.dat')]
>>> preproc.inputs.out_file = 'concatenated_file.mgz'
>>> preproc.cmdline
'mris_preproc --hemi lh --out concatenated_file.mgz --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat'

Inputs:: 

	[Mandatory]
	hemi : ('lh' or 'rh')
		hemisphere for source and target
	target : (a string)
		target subject name

	[Optional]
	args : (a string)
		Additional parameters to the command
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	fsgd_file : (an existing file name)
		specify subjects using fsgd file
		exclusive: subjects,fsgd_file,subject_file
	fwhm : (a float)
		smooth by fwhm mm on the target surface
		exclusive: num_iters
	fwhm_source : (a float)
		smooth by fwhm mm on the source surface
		exclusive: num_iters_source
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	num_iters : (an integer)
		niters : smooth by niters on the target surface
		exclusive: fwhm
	num_iters_source : (an integer)
		niters : smooth by niters on the source surface
		exclusive: fwhm_source
	out_file : (a file name)
		output filename
	proj_frac : (a float)
		projection fraction for vol2surf
	smooth_cortex_only : (a boolean)
		only smooth cortex (ie, exclude medial wall)
	source_format : (a string)
		source format
	subject_file : (an existing file name)
		file specifying subjects separated by white space
		exclusive: subjects,fsgd_file,subject_file
	subjects : (a list of items which are any value)
		subjects from who measures are calculated
		exclusive: subjects,fsgd_file,subject_file
	subjects_dir : (an existing directory name)
		subjects directory
	surf_area : (a string)
		Extract vertex area from subject/surf/hemi.surfname to use as input.
		exclusive: surf_measure,surf_measure_file,surf_area
	surf_dir : (a string)
		alternative directory (instead of surf)
	surf_measure : (a string)
		Use subject/surf/hemi.surf_measure as input
		exclusive: surf_measure,surf_measure_file,surf_area
	surf_measure_file : (an existing file name)
		file alternative to surfmeas, still requires list of subjects
		exclusive: surf_measure,surf_measure_file,surf_area
	vol_measure_file : (a tuple of the form: (an existing file name, an existing file name))
		list of volume measure and reg file tuples


Outputs:: 

	out_file : (an existing file name)
		preprocessed output file

:class:`OneSampleTTest`
-----------------------


Wraps command **mri_glmfit**



Inputs:: 

	[Mandatory]
	in_file : (a file name)
		input 4D file

	[Optional]
	allow_ill_cond : (a boolean)
		allow ill-conditioned design matrices
	allow_repeated_subjects : (a boolean)
		allow subject names to repeat in the fsgd file (must appear before --fsgd
	args : (a string)
		Additional parameters to the command
	calc_AR1 : (a boolean)
		compute and save temporal AR1 of residual
	check_opts : (a boolean)
		don't run anything, just check options and exit
	compute_log_y : (a boolean)
		compute natural log of y prior to analysis
	contrast : (an existing file name)
		contrast file
	cortex : (a boolean)
		use subjects ?h.cortex.label as label
		exclusive: label_file
	debug : (a boolean)
		turn on debugging
	design : (an existing file name)
		design matrix file
		exclusive: fsgd,design,one_sample
	diag : (an integer)
		Gdiag_no : set diagnositc level
	diag_cluster : (a boolean)
		save sig volume and exit from first sim loop
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	fixed_fx_dof : (an integer)
		dof for fixed effects analysis
		exclusive: fixed_fx_dof_file
	fixed_fx_dof_file : (a file name)
		text file with dof for fixed effects analysis
		exclusive: fixed_fx_dof
	fixed_fx_var : (an existing file name)
		for fixed effects analysis
	force_perm : (a boolean)
		force perumtation test, even when design matrix is not orthog
	fsgd : (a tuple of the form: (an existing file name, 'doss' or 'dods'))
		freesurfer descriptor file
		exclusive: fsgd,design,one_sample
	fwhm : (a float)
		smooth input by fwhm
	glm_dir : (a string)
		save outputs to dir
	hemi : ('lh' or 'rh')
		surface hemisphere
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	invert_mask : (a boolean)
		invert mask
	label_file : (an existing file name)
		use label as mask, surfaces only
		exclusive: cortex
	mask_file : (an existing file name)
		binary mask
	no_contrast_sok : (a boolean)
		do not fail if no contrasts specified
	no_est_fwhm : (a boolean)
		turn off FWHM output estimation
	no_mask_smooth : (a boolean)
		do not mask when smoothing
	no_prune : (a boolean)
		do not prune
		exclusive: prunethresh
	one_sample : (a boolean)
		construct X and C as a one-sample group mean
		exclusive: one_sample,fsgd,design,contrast
	pca : (a boolean)
		perform pca/svd analysis on residual
	per_voxel_reg : (an existing file name)
		per-voxel regressors
	profile : (an integer)
		niters : test speed
	prune : (a boolean)
		remove voxels that do not have a non-zero value at each frame (def)
	prune_thresh : (a float)
		prune threshold. Default is FLT_MIN
		exclusive: noprune
	resynth_test : (an integer)
		test GLM by resynthsis
	save_cond : (a boolean)
		flag to save design matrix condition at each voxel
	save_estimate : (a boolean)
		save signal estimate (yhat)
	save_res_corr_mtx : (a boolean)
		save residual error spatial correlation matrix (eres.scm). Big!
	save_residual : (a boolean)
		save residual error (eres)
	seed : (an integer)
		used for synthesizing noise
	self_reg : (a tuple of the form: (an integer, an integer, an integer))
		self-regressor from index col row slice
	sim_done_file : (a file name)
		create file when simulation finished
	sim_sign : ('abs' or 'pos' or 'neg')
		abs, pos, or neg
	simulation : (a tuple of the form: ('perm' or 'mc-full' or 'mc-z', an integer, a float, a string))
		nulltype nsim thresh csdbasename
	subject_id : (a string)
		subject id for surface geometry
	subjects_dir : (an existing directory name)
		subjects directory
	surf : (a boolean)
		analysis is on a surface mesh
		requires: subject_id,hemi
	surf_geo : (a string)
		surface geometry name (e.g. white, pial)
	synth : (a boolean)
		replace input with gaussian
	uniform : (a tuple of the form: (a float, a float))
		use uniform distribution instead of gaussian
	var_fwhm : (a float)
		smooth variance by fwhm
	vox_dump : (a tuple of the form: (an integer, an integer, an integer))
		dump voxel GLM and exit
	weight_file : (an existing file name)
		weight for each input at each voxel
		exclusive: weighted_ls
	weight_inv : (a boolean)
		invert weights
		exclusive: weighted_ls
	weight_sqrt : (a boolean)
		sqrt of weights
		exclusive: weighted_ls
	weighted_ls : (an existing file name)
		weighted least squares
		exclusive: weight_file,weight_inv,weight_sqrt


Outputs:: 

	beta_file : (an existing file name)
		map of regression coefficients
	dof_file : (a file name)
		text file with effective degrees-of-freedom for the analysis
	error_file : (a file name)
		map of residual error
	error_stddev_file : (a file name)
		map of residual error standard deviation
	error_var_file : (a file name)
		map of residual error variance
	estimate_file : (a file name)
		map of the estimated Y values
	frame_eigenvectors : (a file name)
		matrix of frame eigenvectors from residual PCA
	ftest_file	map of test statistic values
	fwhm_file : (a file name)
		text file with estimated smoothness
	gamma_file	map of contrast of regression coefficients
	gamma_var_file	map of regression contrast variance
	glm_dir : (an existing directory name)
		output directory
	mask_file : (a file name)
		map of the mask used in the analysis
	sig_file	map of F-test significance (in -log10p)
	singular_values : (a file name)
		matrix singular values from residual PCA
	spatial_eigenvectors : (a file name)
		map of spatial eigenvectors from residual PCA
	svd_stats_file : (a file name)
		text file summarizing the residual PCA

:class:`SegStats`
-----------------


Wraps command **mri_segstats**

Use FreeSurfer mri_segstats for ROI analysis

Examples
~~~~~~~~

>>> import nipype.interfaces.freesurfer as fs
>>> ss = fs.SegStats()
>>> ss.inputs.annot = ('PWS04', 'lh', 'aparc')
>>> ss.inputs.in_file = 'functional.nii'
>>> ss.inputs.subjects_dir = '.'
>>> ss.inputs.avgwf_txt_file = './avgwf.txt'
>>> ss.inputs.summary_file = './summary.stats'
>>> ss.cmdline
'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --i functional.nii --sum ./summary.stats'

Inputs:: 

	[Mandatory]
	annot : (a tuple of the form: (a string, 'lh' or 'rh', a string))
		subject hemi parc : use surface parcellation
		exclusive: segmentation_file,annot,surf_label
	segmentation_file : (an existing file name)
		segmentation volume path
		exclusive: segmentation_file,annot,surf_label
	surf_label : (a tuple of the form: (a string, 'lh' or 'rh', a string))
		subject hemi label : use surface label
		exclusive: segmentation_file,annot,surf_label

	[Optional]
	args : (a string)
		Additional parameters to the command
	avgwf_file : (a boolean or a file name)
		Save as binary volume (bool or filename)
	avgwf_txt_file : (a boolean or a file name)
		Save average waveform into file (bool or filename)
	brain_vol : ('brain-vol-from-seg' or 'brainmask' or '--%s')
		Compute brain volume either with ``brainmask`` or ``brain-vol-from-seg``
	calc_power : ('sqr' or 'sqrt')
		Compute either the sqr or the sqrt of the input
	calc_snr : (a boolean)
		save mean/std as extra column in output table
	color_table_file : (an existing file name)
		color table file with seg id names
		exclusive: color_table_file,default_color_table,gca_color_table
	cortex_vol_from_surf : (a boolean)
		Compute cortex volume from surf
	default_color_table : (a boolean)
		use $FREESURFER_HOME/FreeSurferColorLUT.txt
		exclusive: color_table_file,default_color_table,gca_color_table
	environ : (a dictionary with keys which are a value of type 'str' and with values which are a value of type 'str')
		Environment variables
	etiv : (a boolean)
		Compute ICV from talairach transform
	etiv_only : ('etiv' or 'old-etiv' or '--%s-only')
		Compute etiv and exit.  Use ``etiv`` or ``old-etiv``
	exclude_ctx_gm_wm : (a boolean)
		exclude cortical gray and white matter
	exclude_id : (an integer)
		Exclude seg id from report
	frame : (an integer)
		Report stats on nth frame of input volume
	gca_color_table : (an existing file name)
		get color table from GCA (CMA)
		exclusive: color_table_file,default_color_table,gca_color_table
	ignore_exception : (a boolean)
		Print an error message instead of throwing an exception in case the interface fails to run
	in_file : (an existing file name)
		Use the segmentation to report stats on this volume
	mask_erode : (an integer)
		Erode mask by some amount
	mask_file : (an existing file name)
		Mask volume (same size as seg
	mask_frame : (an integer)
		Mask with this (0 based) frame of the mask volume
		requires: mask_file
	mask_invert : (a boolean)
		Invert binarized mask volume
	mask_sign : ('abs' or 'pos' or 'neg' or '--masksign %s')
		Sign for mask threshold: pos, neg, or abs
	mask_thresh : (a float)
		binarize mask with this threshold <0.5>
	multiply : (a float)
		multiply input by val
	non_empty_only : (a boolean)
		Only report nonempty segmentations
	partial_volume_file : (an existing file name)
		Compensate for partial voluming
	segment_id : (a list of items which are any value)
		Manually specify segmentation ids
	sf_avg_file : (a boolean or a file name)
		Save mean across space and time
	subjects_dir : (an existing directory name)
		subjects directory
	summary_file : (a file name)
		Segmentation stats summary table file
	vox : (a list of items which are an integer)
		Replace seg with all 0s except at C R S (three int inputs)
	wm_vol_from_surf : (a boolean)
		Compute wm volume from surf


Outputs:: 

	avgwf_file : (a file name)
		Volume with functional statistics averaged over segs
	avgwf_txt_file : (a file name)
		Text file with functional statistics averaged over segs
	sf_avg_file : (a file name)
		Text file with func statistics averaged over segs and framss
	summary_file : (an existing file name)
		Segmentation summary statistics table
