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# nipype.interfaces.freesurfer.model module

The freesurfer module provides basic functions for interfacing with freesurfer tools.

## Binarize

Link to code

> Bases: FSCommand

> Wrapped executable: `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'

> in_filea pathlike object or string representing an existing file

>   Input volume. Maps to a command-line argument: `--i %s`.

> absa boolean

>   Take abs of invol first (ie, make unsigned). Maps to a command-line argument: `--abs`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> bin_col_numa boolean

>   Set binarized voxel value to its column number. Maps to a command-line argument: `--bincol`.

> bin_valan integer (int or long)

>   Set vox within thresh to val (default is 1). Maps to a command-line argument: `--binval %d`.

> bin_val_notan integer (int or long)

>   Set vox outside range to val (default is 0). Maps to a command-line argument: `--binvalnot %d`.

> binary_filea pathlike object or string representing a file

>   Binary output volume. Maps to a command-line argument: `--o %s`.

> count_filea boolean or a pathlike object or string representing a file

>   Save number of hits in ascii file (hits, ntotvox, pct). Maps to a command-line argument: `--count %s`.

> dilatean integer (int or long)

>   Niters: dilate binarization in 3D. Maps to a command-line argument: `--dilate %d`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> erodean integer (int or long)

>   Nerode: erode binarization in 3D (after any dilation). Maps to a command-line argument: `--erode %d`.

> erode2dan integer (int or long)

>   Nerode2d: erode binarization in 2D (after any 3D erosion). Maps to a command-line argument: `--erode2d %d`.

> frame_noan integer (int or long)

>   Use 0-based frame of input (default is 0). Maps to a command-line argument: `--frame %s`.

> inverta boolean

>   Set binval=0, binvalnot=1. Maps to a command-line argument: `--inv`.

> mask_filea pathlike object or string representing an existing file

>   Must be within mask. Maps to a command-line argument: `--mask maskvol`.

> mask_thresha float

>   Set thresh for mask. Maps to a command-line argument: `--mask-thresh %f`.

> matcha list of items which are an integer (int or long)

>   Match instead of threshold. Maps to a command-line argument: `--match %d...`.

> maxa float

>   Max thresh. Maps to a command-line argument: `--max %f`. Mutually exclusive with inputs: `wm_ven_csf`.

> merge_filea pathlike object or string representing an existing file

>   Merge with mergevol. Maps to a command-line argument: `--merge %s`.

> mina float

>   Min thresh. Maps to a command-line argument: `--min %f`. Mutually exclusive with inputs: `wm_ven_csf`.

> out_type‘nii’ or ‘nii.gz’ or ‘mgz’

>   Output file type.

> rmaxa float

>   Compute max based on rmax*globalmean. Maps to a command-line argument: `--rmax %f`.

> rmina float

>   Compute min based on rmin*globalmean. Maps to a command-line argument: `--rmin %f`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> ventriclesa boolean

>   Set match vals those for aseg ventricles+choroid (not 4th). Maps to a command-line argument: `--ventricles`.

> wma boolean

>   Set match vals to 2 and 41 (aseg for cerebral WM). Maps to a command-line argument: `--wm`.

> wm_ven_csfa boolean

>   WM and ventricular CSF, including choroid (not 4th). Maps to a command-line argument: `--wm+vcsf`. Mutually exclusive with inputs: `min`, `max`.

> zero_edgesa boolean

>   Zero the edge voxels. Maps to a command-line argument: `--zero-edges`.

> zero_slice_edgea boolean

>   Zero the edge slice voxels. Maps to a command-line argument: `--zero-slice-edges`.

> binary_filea pathlike object or string representing an existing file

>   Binarized output volume.

> count_filea pathlike object or string representing a file

>   Ascii file containing number of hits.

## Concatenate

Link to code

> Bases: FSCommand

> Wrapped executable: `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'

> in_filesa list of items which are a pathlike object or string representing an existing file

>   Individual volumes to be concatenated. Maps to a command-line argument: `--i %s...`.

> add_vala float

>   Add some amount to the input volume. Maps to a command-line argument: `--add %f`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> combinea boolean

>   Combine non-zero values into single frame volume. Maps to a command-line argument: `--combine`.

> concatenated_filea pathlike object or string representing a file

>   Output volume. Maps to a command-line argument: `--o %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> gmeanan integer (int or long)

>   Create matrix to average Ng groups, Nper=Ntot/Ng. Maps to a command-line argument: `--gmean %d`.

> keep_dtypea boolean

>   Keep voxelwise precision type (default is float. Maps to a command-line argument: `--keep-datatype`.

> mask_filea pathlike object or string representing an existing file

>   Mask input with a volume. Maps to a command-line argument: `--mask %s`.

> max_bonfcora boolean

>   Compute max and bonferroni correct (assumes -log10(ps)). Maps to a command-line argument: `--max-bonfcor`.

> max_indexa boolean

>   Compute the index of max voxel in concatenated volumes. Maps to a command-line argument: `--max-index`.

> mean_div_na boolean

>   Compute mean/nframes (good for var). Maps to a command-line argument: `--mean-div-n`.

> multiply_bya float

>   Multiply input volume by some amount. Maps to a command-line argument: `--mul %f`.

> multiply_matrix_filea pathlike object or string representing an existing file

>   Multiply input by an ascii matrix in file. Maps to a command-line argument: `--mtx %s`.

> paired_stats‘sum’ or ‘avg’ or ‘diff’ or ‘diff-norm’ or ‘diff-norm1’ or ‘diff-norm2’

>   Compute paired sum, avg, or diff. Maps to a command-line argument: `--paired-%s`.

> sign‘abs’ or ‘pos’ or ‘neg’

>   Take only pos or neg voxles from input, or take abs. Maps to a command-line argument: `--%s`.

> sorta boolean

>   Sort each voxel by ascending frame value. Maps to a command-line argument: `--sort`.

> 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. Maps to a command-line argument: `--%s`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> votea boolean

>   Most frequent value at each voxel and fraction of occurances. Maps to a command-line argument: `--vote`.

> concatenated_filea pathlike object or string representing an existing file

>   Path/name of the output volume.

## GLMFit

Link to code

> Bases: FSCommand

> Wrapped executable: `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

> in_filea pathlike object or string representing a file

>   Input 4D file. Maps to a command-line argument: `--y %s`.

> allow_ill_conda boolean

>   Allow ill-conditioned design matrices. Maps to a command-line argument: `--illcond`.

> allow_repeated_subjectsa boolean

>   Allow subject names to repeat in the fsgd file (must appear before –fsgd. Maps to a command-line argument: `--allowsubjrep`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> calc_AR1a boolean

>   Compute and save temporal AR1 of residual. Maps to a command-line argument: `--tar1`.

> check_optsa boolean

>   Don’t run anything, just check options and exit. Maps to a command-line argument: `--checkopts`.

> compute_log_ya boolean

>   Compute natural log of y prior to analysis. Maps to a command-line argument: `--logy`.

> contrasta list of items which are a pathlike object or string representing an existing file

>   Contrast file. Maps to a command-line argument: `--C %s...`.

> cortexa boolean

>   Use subjects ?h.cortex.label as label. Maps to a command-line argument: `--cortex`. Mutually exclusive with inputs: `label_file`.

> debuga boolean

>   Turn on debugging. Maps to a command-line argument: `--debug`.

> designa pathlike object or string representing an existing file

>   Design matrix file. Maps to a command-line argument: `--X %s`. Mutually exclusive with inputs: `fsgd`, `design`, `one_sample`.

> diagan integer (int or long)

>   Gdiag_no : set diagnositc level. Maps to a command-line argument: `--diag %d`.

> diag_clustera boolean

>   Save sig volume and exit from first sim loop. Maps to a command-line argument: `--diag-cluster`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> fixed_fx_dofan integer (int or long)

>   Dof for fixed effects analysis. Maps to a command-line argument: `--ffxdof %d`. Mutually exclusive with inputs: `fixed_fx_dof_file`.

> fixed_fx_dof_filea pathlike object or string representing a file

>   Text file with dof for fixed effects analysis. Maps to a command-line argument: `--ffxdofdat %d`. Mutually exclusive with inputs: `fixed_fx_dof`.

> fixed_fx_vara pathlike object or string representing an existing file

>   For fixed effects analysis. Maps to a command-line argument: `--yffxvar %s`.

> force_perma boolean

>   Force perumtation test, even when design matrix is not orthog. Maps to a command-line argument: `--perm-force`.

> fsgda tuple of the form: (a pathlike object or string representing an existing file, ‘doss’ or ‘dods’)

>   Freesurfer descriptor file. Maps to a command-line argument: `--fsgd %s %s`. Mutually exclusive with inputs: `fsgd`, `design`, `one_sample`.

> fwhma floating point number >= 0.0

>   Smooth input by fwhm. Maps to a command-line argument: `--fwhm %f`.

> glm_dira unicode string

>   Save outputs to dir. Maps to a command-line argument: `--glmdir %s`.

> hemi‘lh’ or ‘rh’

>   Surface hemisphere.

> invert_maska boolean

>   Invert mask. Maps to a command-line argument: `--mask-inv`.

> label_filea pathlike object or string representing an existing file

>   Use label as mask, surfaces only. Maps to a command-line argument: `--label %s`. Mutually exclusive with inputs: `cortex`.

> mask_filea pathlike object or string representing an existing file

>   Binary mask. Maps to a command-line argument: `--mask %s`.

> no_contrast_oka boolean

>   Do not fail if no contrasts specified. Maps to a command-line argument: `--no-contrasts-ok`.

> no_est_fwhma boolean

>   Turn off FWHM output estimation. Maps to a command-line argument: `--no-est-fwhm`.

> no_mask_smootha boolean

>   Do not mask when smoothing. Maps to a command-line argument: `--no-mask-smooth`.

> no_prunea boolean

>   Do not prune. Maps to a command-line argument: `--no-prune`. Mutually exclusive with inputs: `prunethresh`.

> one_samplea boolean

>   Construct X and C as a one-sample group mean. Maps to a command-line argument: `--osgm`. Mutually exclusive with inputs: `one_sample`, `fsgd`, `design`, `contrast`.

> pcaa boolean

>   Perform pca/svd analysis on residual. Maps to a command-line argument: `--pca`.

> per_voxel_rega list of items which are a pathlike object or string representing an existing file

>   Per-voxel regressors. Maps to a command-line argument: `--pvr %s...`.

> profilean integer (int or long)

>   Niters : test speed. Maps to a command-line argument: `--profile %d`.

> prunea boolean

>   Remove voxels that do not have a non-zero value at each frame (def). Maps to a command-line argument: `--prune`.

> prune_thresha float

>   Prune threshold. Default is FLT_MIN. Maps to a command-line argument: `--prune_thr %f`. Mutually exclusive with inputs: `noprune`.

> resynth_testan integer (int or long)

>   Test GLM by resynthsis. Maps to a command-line argument: `--resynthtest %d`.

> save_conda boolean

>   Flag to save design matrix condition at each voxel. Maps to a command-line argument: `--save-cond`.

> save_estimatea boolean

>   Save signal estimate (yhat). Maps to a command-line argument: `--yhat-save`.

> save_res_corr_mtxa boolean

>   Save residual error spatial correlation matrix (eres.scm). Big!. Maps to a command-line argument: `--eres-scm`.

> save_residuala boolean

>   Save residual error (eres). Maps to a command-line argument: `--eres-save`.

> seedan integer (int or long)

>   Used for synthesizing noise. Maps to a command-line argument: `--seed %d`.

> self_rega tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

>   Self-regressor from index col row slice. Maps to a command-line argument: `--selfreg %d %d %d`.

> sim_done_filea pathlike object or string representing a file

>   Create file when simulation finished. Maps to a command-line argument: `--sim-done %s`.

> sim_sign‘abs’ or ‘pos’ or ‘neg’

>   Abs, pos, or neg. Maps to a command-line argument: `--sim-sign %s`.

> simulationa tuple of the form: (‘perm’ or ‘mc-full’ or ‘mc-z’, an integer (int or long), a float, a unicode string)

>   Nulltype nsim thresh csdbasename. Maps to a command-line argument: `--sim %s %d %f %s`.

> subject_ida unicode string

>   Subject id for surface geometry.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surfa boolean

>   Analysis is on a surface mesh. Maps to a command-line argument: `--surf %s %s %s`. Requires inputs: `subject_id`, `hemi`.

> surf_geoa unicode string

>   Surface geometry name (e.g. white, pial). (Nipype default value: `white`)

> syntha boolean

>   Replace input with gaussian. Maps to a command-line argument: `--synth`.

> uniforma tuple of the form: (a float, a float)

>   Use uniform distribution instead of gaussian. Maps to a command-line argument: `--uniform %f %f`.

> var_fwhma floating point number >= 0.0

>   Smooth variance by fwhm. Maps to a command-line argument: `--var-fwhm %f`.

> vox_dumpa tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

>   Dump voxel GLM and exit. Maps to a command-line argument: `--voxdump %d %d %d`.

> weight_filea pathlike object or string representing an existing file

>   Weight for each input at each voxel. Mutually exclusive with inputs: `weighted_ls`.

> weight_inva boolean

>   Invert weights. Maps to a command-line argument: `--w-inv`. Mutually exclusive with inputs: `weighted_ls`.

> weight_sqrta boolean

>   Sqrt of weights. Maps to a command-line argument: `--w-sqrt`. Mutually exclusive with inputs: `weighted_ls`.

> weighted_lsa pathlike object or string representing an existing file

>   Weighted least squares. Maps to a command-line argument: `--wls %s`. Mutually exclusive with inputs: `weight_file`, `weight_inv`, `weight_sqrt`.

> beta_filea pathlike object or string representing an existing file

>   Map of regression coefficients.

> dof_filea pathlike object or string representing a file

>   Text file with effective degrees-of-freedom for the analysis.

> error_filea pathlike object or string representing a file

>   Map of residual error.

> error_stddev_filea pathlike object or string representing a file

>   Map of residual error standard deviation.

> error_var_filea pathlike object or string representing a file

>   Map of residual error variance.

> estimate_filea pathlike object or string representing a file

>   Map of the estimated Y values.

> frame_eigenvectorsa pathlike object or string representing a file

>   Matrix of frame eigenvectors from residual PCA.

> ftest_filea list of items which are any value

>   Map of test statistic values.

> fwhm_filea pathlike object or string representing a file

>   Text file with estimated smoothness.

> gamma_filea list of items which are any value

>   Map of contrast of regression coefficients.

> gamma_var_filea list of items which are any value

>   Map of regression contrast variance.

> glm_dira pathlike object or string representing an existing directory

>   Output directory.

> mask_filea pathlike object or string representing a file

>   Map of the mask used in the analysis.

> sig_filea list of items which are any value

>   Map of F-test significance (in -log10p).

> singular_valuesa pathlike object or string representing a file

>   Matrix singular values from residual PCA.

> spatial_eigenvectorsa pathlike object or string representing a file

>   Map of spatial eigenvectors from residual PCA.

> svd_stats_filea pathlike object or string representing a file

>   Text file summarizing the residual PCA.

## Label2Annot

Link to code

> Bases: FSCommand

> Wrapped executable: `mris_label2annot`.

> Converts a set of surface labels to an annotation file

> Examples

>     >>> from nipype.interfaces.freesurfer import Label2Annot
>     >>> l2a = Label2Annot()
>     >>> l2a.inputs.hemisphere = 'lh'
>     >>> l2a.inputs.subject_id = '10335'
>     >>> l2a.inputs.in_labels = ['lh.aparc.label']
>     >>> l2a.inputs.orig = 'lh.pial'
>     >>> l2a.inputs.out_annot = 'test'
>     >>> l2a.cmdline
>     'mris_label2annot --hemi lh --l lh.aparc.label --a test --s 10335'

> hemisphere‘lh’ or ‘rh’

>   Input hemisphere. Maps to a command-line argument: `--hemi %s`.

> in_labelsa list of items which are any value

>   List of input label files. Maps to a command-line argument: `--l %s...`.

> origa pathlike object or string representing an existing file

>   Implicit {hemisphere}.orig.

> out_annota string

>   Name of the annotation to create. Maps to a command-line argument: `--a %s`.

> subject_ida string

>   Subject name/ID. Maps to a command-line argument: `--s %s`. (Nipype default value: `subject_id`)

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> color_tablea pathlike object or string representing an existing file

>   File that defines the structure names, their indices, and their color. Maps to a command-line argument: `--ctab %s`.

> copy_inputsa boolean

>   Copy implicit inputs and create a temp subjects_dir.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> keep_maxa boolean

>   Keep label with highest ‘stat’ value. Maps to a command-line argument: `--maxstatwinner`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> verbose_offa boolean

>   Turn off overlap and stat override messages. Maps to a command-line argument: `--noverbose`.

> out_filea pathlike object or string representing an existing file

>   Output annotation file.

> Label2Annot.run(**inputs)

>   Execute this interface.

>   This interface will not raise an exception if runtime.returncode is non-zero.

>   Parameters

>     - cwd (specify a folder where the interface should be run) –

>     - inputs (allows the interface settings to be updated) –

>   Returns

>     results – A copy of the instance that was executed, provenance information and, if successful, results

>   Return type

>     `nipype.interfaces.base.support.InterfaceResult`

## Label2Label

Link to code

> Bases: FSCommand

> Wrapped executable: `mri_label2label`.

> Converts a label in one subject’s space to a label in another subject’s space using either talairach or spherical as an intermediate registration space.

> If a source mask is used, then the input label must have been created from a surface (ie, the vertex numbers are valid). The format can be anything supported by mri_convert or curv or paint. Vertices in the source label that do not meet threshold in the mask will be removed from the label.

> Examples

>     >>> from nipype.interfaces.freesurfer import Label2Label
>     >>> l2l = Label2Label()
>     >>> l2l.inputs.hemisphere = 'lh'
>     >>> l2l.inputs.subject_id = '10335'
>     >>> l2l.inputs.sphere_reg = 'lh.pial'
>     >>> l2l.inputs.white = 'lh.pial'
>     >>> l2l.inputs.source_subject = 'fsaverage'
>     >>> l2l.inputs.source_label = 'lh-pial.stl'
>     >>> l2l.inputs.source_white = 'lh.pial'
>     >>> l2l.inputs.source_sphere_reg = 'lh.pial'
>     >>> l2l.cmdline
>     'mri_label2label --hemi lh --trglabel lh-pial_converted.stl --regmethod surface --srclabel lh-pial.stl --srcsubject fsaverage --trgsubject 10335'

> hemisphere‘lh’ or ‘rh’

>   Input hemisphere. Maps to a command-line argument: `--hemi %s`.

> source_labela pathlike object or string representing an existing file

>   Source label. Maps to a command-line argument: `--srclabel %s`.

> source_sphere_rega pathlike object or string representing an existing file

>   Implicit input <hemisphere>.sphere.reg.

> source_subjecta string

>   Source subject name. Maps to a command-line argument: `--srcsubject %s`.

> source_whitea pathlike object or string representing an existing file

>   Implicit input <hemisphere>.white.

> sphere_rega pathlike object or string representing an existing file

>   Implicit input <hemisphere>.sphere.reg.

> subject_ida string

>   Target subject. Maps to a command-line argument: `--trgsubject %s`. (Nipype default value: `subject_id`)

> whitea pathlike object or string representing an existing file

>   Implicit input <hemisphere>.white.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> copy_inputsa boolean

>   If running as a node, set this to True.This will copy the input files to the node directory.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> out_filea pathlike object or string representing a file

>   Target label. Maps to a command-line argument: `--trglabel %s`.

> registration_method‘surface’ or ‘volume’

>   Registration method. Maps to a command-line argument: `--regmethod %s`. (Nipype default value: `surface`)

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> out_filea pathlike object or string representing an existing file

>   Output label.

> Label2Label.run(**inputs)

>   Execute this interface.

>   This interface will not raise an exception if runtime.returncode is non-zero.

>   Parameters

>     - cwd (specify a folder where the interface should be run) –

>     - inputs (allows the interface settings to be updated) –

>   Returns

>     results – A copy of the instance that was executed, provenance information and, if successful, results

>   Return type

>     `nipype.interfaces.base.support.InterfaceResult`

## Label2Vol

Link to code

> Bases: FSCommand

> Wrapped executable: `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 0.5 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii'

> annot_filea pathlike object or string representing an existing file

>   Surface annotation file. Maps to a command-line argument: `--annot %s`. Mutually exclusive with inputs: `label_file`, `annot_file`, `seg_file`, `aparc_aseg`. Requires inputs: `subject_id`, `hemi`.

> aparc_asega boolean

>   Use aparc+aseg.mgz in subjectdir as seg. Maps to a command-line argument: `--aparc+aseg`. Mutually exclusive with inputs: `label_file`, `annot_file`, `seg_file`, `aparc_aseg`.

> label_filea list of items which are a pathlike object or string representing an existing file

>   List of label files. Maps to a command-line argument: `--label %s...`. Mutually exclusive with inputs: `label_file`, `annot_file`, `seg_file`, `aparc_aseg`.

> seg_filea pathlike object or string representing an existing file

>   Segmentation file. Maps to a command-line argument: `--seg %s`. Mutually exclusive with inputs: `label_file`, `annot_file`, `seg_file`, `aparc_aseg`.

> template_filea pathlike object or string representing an existing file

>   Output template volume. Maps to a command-line argument: `--temp %s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> fill_thresh0.0 <= a floating point number <= 1.0

>   Thresh : between 0 and 1. Maps to a command-line argument: `--fillthresh %g`.

> hemi‘lh’ or ‘rh’

>   Hemisphere to use lh or rh. Maps to a command-line argument: `--hemi %s`.

> identitya boolean

>   Set R=I. Maps to a command-line argument: `--identity`. Mutually exclusive with inputs: `reg_file`, `reg_header`, `identity`.

> invert_mtxa boolean

>   Invert the registration matrix. Maps to a command-line argument: `--invertmtx`.

> label_hit_filea pathlike object or string representing a file

>   File with each frame is nhits for a label. Maps to a command-line argument: `--hits %s`.

> label_voxel_volumea float

>   Volume of each label point (def 1mm3). Maps to a command-line argument: `--labvoxvol %f`.

> map_label_stata pathlike object or string representing a file

>   Map the label stats field into the vol. Maps to a command-line argument: `--label-stat %s`.

> native_vox2rasa boolean

>   Use native vox2ras xform instead of tkregister-style. Maps to a command-line argument: `--native-vox2ras`.

> proja tuple of the form: (‘abs’ or ‘frac’, a float, a float, a float)

>   Project along surface normal. Maps to a command-line argument: `--proj %s %f %f %f`. Requires inputs: `subject_id`, `hemi`.

> reg_filea pathlike object or string representing an existing file

>   Tkregister style matrix VolXYZ = R*LabelXYZ. Maps to a command-line argument: `--reg %s`. Mutually exclusive with inputs: `reg_file`, `reg_header`, `identity`.

> reg_headera pathlike object or string representing an existing file

>   Label template volume. Maps to a command-line argument: `--regheader %s`. Mutually exclusive with inputs: `reg_file`, `reg_header`, `identity`.

> subject_ida unicode string

>   Subject id. Maps to a command-line argument: `--subject %s`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surfacea unicode string

>   Use surface instead of white. Maps to a command-line argument: `--surf %s`.

> vol_label_filea pathlike object or string representing a file

>   Output volume. Maps to a command-line argument: `--o %s`.

> vol_label_filea pathlike object or string representing an existing file

>   Output volume.

## MRISPreproc

Link to code

> Bases: FSCommand

> Wrapped executable: `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'

> hemi‘lh’ or ‘rh’

>   Hemisphere for source and target. Maps to a command-line argument: `--hemi %s`.

> targeta unicode string

>   Target subject name. Maps to a command-line argument: `--target %s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> fsgd_filea pathlike object or string representing an existing file

>   Specify subjects using fsgd file. Maps to a command-line argument: `--fsgd %s`. Mutually exclusive with inputs: `subjects`, `fsgd_file`, `subject_file`.

> fwhma float

>   Smooth by fwhm mm on the target surface. Maps to a command-line argument: `--fwhm %f`. Mutually exclusive with inputs: `num_iters`.

> fwhm_sourcea float

>   Smooth by fwhm mm on the source surface. Maps to a command-line argument: `--fwhm-src %f`. Mutually exclusive with inputs: `num_iters_source`.

> num_itersan integer (int or long)

>   Niters : smooth by niters on the target surface. Maps to a command-line argument: `--niters %d`. Mutually exclusive with inputs: `fwhm`.

> num_iters_sourcean integer (int or long)

>   Niters : smooth by niters on the source surface. Maps to a command-line argument: `--niterssrc %d`. Mutually exclusive with inputs: `fwhm_source`.

> out_filea pathlike object or string representing a file

>   Output filename. Maps to a command-line argument: `--out %s`.

> proj_fraca float

>   Projection fraction for vol2surf. Maps to a command-line argument: `--projfrac %s`.

> smooth_cortex_onlya boolean

>   Only smooth cortex (ie, exclude medial wall). Maps to a command-line argument: `--smooth-cortex-only`.

> source_formata unicode string

>   Source format. Maps to a command-line argument: `--srcfmt %s`.

> subject_filea pathlike object or string representing an existing file

>   File specifying subjects separated by white space. Maps to a command-line argument: `--f %s`. Mutually exclusive with inputs: `subjects`, `fsgd_file`, `subject_file`.

> subjectsa list of items which are any value

>   Subjects from who measures are calculated. Maps to a command-line argument: `--s %s...`. Mutually exclusive with inputs: `subjects`, `fsgd_file`, `subject_file`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surf_areaa unicode string

>   Extract vertex area from subject/surf/hemi.surfname to use as input. Maps to a command-line argument: `--area %s`. Mutually exclusive with inputs: `surf_measure`, `surf_measure_file`, `surf_area`.

> surf_dira unicode string

>   Alternative directory (instead of surf). Maps to a command-line argument: `--surfdir %s`.

> surf_measurea unicode string

>   Use subject/surf/hemi.surf_measure as input. Maps to a command-line argument: `--meas %s`. Mutually exclusive with inputs: `surf_measure`, `surf_measure_file`, `surf_area`.

> surf_measure_filea list of items which are a pathlike object or string representing an existing file

>   File alternative to surfmeas, still requires list of subjects. Maps to a command-line argument: `--is %s...`. Mutually exclusive with inputs: `surf_measure`, `surf_measure_file`, `surf_area`.

> vol_measure_filea list of items which are a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)

>   List of volume measure and reg file tuples. Maps to a command-line argument: `--iv %s %s...`.

> out_filea pathlike object or string representing a file

>   Preprocessed output file.

## MRISPreprocReconAll

Link to code

> Bases: MRISPreproc

> Wrapped executable: `mris_preproc`.

> Extends MRISPreproc to allow it to be used in a recon-all workflow

> Examples

>     >>> preproc = MRISPreprocReconAll()
>     >>> 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 --s subject_id --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat'

> hemi‘lh’ or ‘rh’

>   Hemisphere for source and target. Maps to a command-line argument: `--hemi %s`.

> targeta unicode string

>   Target subject name. Maps to a command-line argument: `--target %s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> copy_inputsa boolean

>   If running as a node, set this to True this will copy some implicit inputs to the node directory.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> fsgd_filea pathlike object or string representing an existing file

>   Specify subjects using fsgd file. Maps to a command-line argument: `--fsgd %s`. Mutually exclusive with inputs: `subjects`, `fsgd_file`, `subject_file`.

> fwhma float

>   Smooth by fwhm mm on the target surface. Maps to a command-line argument: `--fwhm %f`. Mutually exclusive with inputs: `num_iters`.

> fwhm_sourcea float

>   Smooth by fwhm mm on the source surface. Maps to a command-line argument: `--fwhm-src %f`. Mutually exclusive with inputs: `num_iters_source`.

> lh_surfreg_targeta pathlike object or string representing a file

>   Implicit target surface registration file. Requires inputs: `surfreg_files`.

> num_itersan integer (int or long)

>   Niters : smooth by niters on the target surface. Maps to a command-line argument: `--niters %d`. Mutually exclusive with inputs: `fwhm`.

> num_iters_sourcean integer (int or long)

>   Niters : smooth by niters on the source surface. Maps to a command-line argument: `--niterssrc %d`. Mutually exclusive with inputs: `fwhm_source`.

> out_filea pathlike object or string representing a file

>   Output filename. Maps to a command-line argument: `--out %s`.

> proj_fraca float

>   Projection fraction for vol2surf. Maps to a command-line argument: `--projfrac %s`.

> rh_surfreg_targeta pathlike object or string representing a file

>   Implicit target surface registration file. Requires inputs: `surfreg_files`.

> smooth_cortex_onlya boolean

>   Only smooth cortex (ie, exclude medial wall). Maps to a command-line argument: `--smooth-cortex-only`.

> source_formata unicode string

>   Source format. Maps to a command-line argument: `--srcfmt %s`.

> subject_filea pathlike object or string representing an existing file

>   File specifying subjects separated by white space. Maps to a command-line argument: `--f %s`. Mutually exclusive with inputs: `subjects`, `fsgd_file`, `subject_file`.

> subject_ida string

>   Subject from whom measures are calculated. Maps to a command-line argument: `--s %s`. Mutually exclusive with inputs: `subjects`, `fsgd_file`, `subject_file`, `subject_id`. (Nipype default value: `subject_id`)

> subjectsa list of items which are any value

>   Subjects from who measures are calculated. Maps to a command-line argument: `--s %s...`. Mutually exclusive with inputs: `subjects`, `fsgd_file`, `subject_file`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surf_areaa unicode string

>   Extract vertex area from subject/surf/hemi.surfname to use as input. Maps to a command-line argument: `--area %s`. Mutually exclusive with inputs: `surf_measure`, `surf_measure_file`, `surf_area`.

> surf_dira unicode string

>   Alternative directory (instead of surf). Maps to a command-line argument: `--surfdir %s`.

> surf_measurea unicode string

>   Use subject/surf/hemi.surf_measure as input. Maps to a command-line argument: `--meas %s`. Mutually exclusive with inputs: `surf_measure`, `surf_measure_file`, `surf_area`.

> surf_measure_filea pathlike object or string representing an existing file

>   File necessary for surfmeas. Maps to a command-line argument: `--meas %s`. Mutually exclusive with inputs: `surf_measure`, `surf_measure_file`, `surf_area`.

> surfreg_filesa list of items which are a pathlike object or string representing an existing file

>   Lh and rh input surface registration files. Maps to a command-line argument: `--surfreg %s`. Requires inputs: `lh_surfreg_target`, `rh_surfreg_target`.

> vol_measure_filea list of items which are a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)

>   List of volume measure and reg file tuples. Maps to a command-line argument: `--iv %s %s...`.

> out_filea pathlike object or string representing a file

>   Preprocessed output file.

> MRISPreprocReconAll.run(**inputs)

>   Execute this interface.

>   This interface will not raise an exception if runtime.returncode is non-zero.

>   Parameters

>     - cwd (specify a folder where the interface should be run) –

>     - inputs (allows the interface settings to be updated) –

>   Returns

>     results – A copy of the instance that was executed, provenance information and, if successful, results

>   Return type

>     `nipype.interfaces.base.support.InterfaceResult`

## MS_LDA

Link to code

> Bases: FSCommand

> Wrapped executable: `mri_ms_LDA`.

> Perform LDA reduction on the intensity space of an arbitrary # of FLASH images

> Examples

>     >>> grey_label = 2
>     >>> white_label = 3
>     >>> zero_value = 1
>     >>> optimalWeights = MS_LDA(lda_labels=[grey_label, white_label],                                 label_file='label.mgz', weight_file='weights.txt',                                 shift=zero_value, vol_synth_file='synth_out.mgz',                                 conform=True, use_weights=True,                                 images=['FLASH1.mgz', 'FLASH2.mgz', 'FLASH3.mgz'])
>     >>> optimalWeights.cmdline
>     'mri_ms_LDA -conform -label label.mgz -lda 2 3 -shift 1 -W -synth synth_out.mgz -weight weights.txt FLASH1.mgz FLASH2.mgz FLASH3.mgz'

> imagesa list of items which are a pathlike object or string representing an existing file

>   List of input FLASH images. Maps to a command-line argument: `%s` (position: -1).

> lda_labelsa list of from 2 to 2 items which are an integer (int or long)

>   Pair of class labels to optimize. Maps to a command-line argument: `-lda %s`.

> vol_synth_filea pathlike object or string representing a file

>   Filename for the synthesized output volume. Maps to a command-line argument: `-synth %s`.

> weight_filea pathlike object or string representing a file

>   Filename for the LDA weights (input or output). Maps to a command-line argument: `-weight %s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> conforma boolean

>   Conform the input volumes (brain mask typically already conformed). Maps to a command-line argument: `-conform`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> label_filea pathlike object or string representing an existing file

>   Filename of the label volume. Maps to a command-line argument: `-label %s`.

> mask_filea pathlike object or string representing an existing file

>   Filename of the brain mask volume. Maps to a command-line argument: `-mask %s`.

> shiftan integer (int or long)

>   Shift all values equal to the given value to zero. Maps to a command-line argument: `-shift %d`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> use_weightsa boolean

>   Use the weights from a previously generated weight file. Maps to a command-line argument: `-W`.

> vol_synth_file : a pathlike object or string representing an existing file weight_file : a pathlike object or string representing an existing file

## OneSampleTTest

Link to code

> Bases: GLMFit

> Wrapped executable: `mri_glmfit`.

> in_filea pathlike object or string representing a file

>   Input 4D file. Maps to a command-line argument: `--y %s`.

> allow_ill_conda boolean

>   Allow ill-conditioned design matrices. Maps to a command-line argument: `--illcond`.

> allow_repeated_subjectsa boolean

>   Allow subject names to repeat in the fsgd file (must appear before –fsgd. Maps to a command-line argument: `--allowsubjrep`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> calc_AR1a boolean

>   Compute and save temporal AR1 of residual. Maps to a command-line argument: `--tar1`.

> check_optsa boolean

>   Don’t run anything, just check options and exit. Maps to a command-line argument: `--checkopts`.

> compute_log_ya boolean

>   Compute natural log of y prior to analysis. Maps to a command-line argument: `--logy`.

> contrasta list of items which are a pathlike object or string representing an existing file

>   Contrast file. Maps to a command-line argument: `--C %s...`.

> cortexa boolean

>   Use subjects ?h.cortex.label as label. Maps to a command-line argument: `--cortex`. Mutually exclusive with inputs: `label_file`.

> debuga boolean

>   Turn on debugging. Maps to a command-line argument: `--debug`.

> designa pathlike object or string representing an existing file

>   Design matrix file. Maps to a command-line argument: `--X %s`. Mutually exclusive with inputs: `fsgd`, `design`, `one_sample`.

> diagan integer (int or long)

>   Gdiag_no : set diagnositc level. Maps to a command-line argument: `--diag %d`.

> diag_clustera boolean

>   Save sig volume and exit from first sim loop. Maps to a command-line argument: `--diag-cluster`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> fixed_fx_dofan integer (int or long)

>   Dof for fixed effects analysis. Maps to a command-line argument: `--ffxdof %d`. Mutually exclusive with inputs: `fixed_fx_dof_file`.

> fixed_fx_dof_filea pathlike object or string representing a file

>   Text file with dof for fixed effects analysis. Maps to a command-line argument: `--ffxdofdat %d`. Mutually exclusive with inputs: `fixed_fx_dof`.

> fixed_fx_vara pathlike object or string representing an existing file

>   For fixed effects analysis. Maps to a command-line argument: `--yffxvar %s`.

> force_perma boolean

>   Force perumtation test, even when design matrix is not orthog. Maps to a command-line argument: `--perm-force`.

> fsgda tuple of the form: (a pathlike object or string representing an existing file, ‘doss’ or ‘dods’)

>   Freesurfer descriptor file. Maps to a command-line argument: `--fsgd %s %s`. Mutually exclusive with inputs: `fsgd`, `design`, `one_sample`.

> fwhma floating point number >= 0.0

>   Smooth input by fwhm. Maps to a command-line argument: `--fwhm %f`.

> glm_dira unicode string

>   Save outputs to dir. Maps to a command-line argument: `--glmdir %s`.

> hemi‘lh’ or ‘rh’

>   Surface hemisphere.

> invert_maska boolean

>   Invert mask. Maps to a command-line argument: `--mask-inv`.

> label_filea pathlike object or string representing an existing file

>   Use label as mask, surfaces only. Maps to a command-line argument: `--label %s`. Mutually exclusive with inputs: `cortex`.

> mask_filea pathlike object or string representing an existing file

>   Binary mask. Maps to a command-line argument: `--mask %s`.

> no_contrast_oka boolean

>   Do not fail if no contrasts specified. Maps to a command-line argument: `--no-contrasts-ok`.

> no_est_fwhma boolean

>   Turn off FWHM output estimation. Maps to a command-line argument: `--no-est-fwhm`.

> no_mask_smootha boolean

>   Do not mask when smoothing. Maps to a command-line argument: `--no-mask-smooth`.

> no_prunea boolean

>   Do not prune. Maps to a command-line argument: `--no-prune`. Mutually exclusive with inputs: `prunethresh`.

> one_samplea boolean

>   Construct X and C as a one-sample group mean. Maps to a command-line argument: `--osgm`. Mutually exclusive with inputs: `one_sample`, `fsgd`, `design`, `contrast`.

> pcaa boolean

>   Perform pca/svd analysis on residual. Maps to a command-line argument: `--pca`.

> per_voxel_rega list of items which are a pathlike object or string representing an existing file

>   Per-voxel regressors. Maps to a command-line argument: `--pvr %s...`.

> profilean integer (int or long)

>   Niters : test speed. Maps to a command-line argument: `--profile %d`.

> prunea boolean

>   Remove voxels that do not have a non-zero value at each frame (def). Maps to a command-line argument: `--prune`.

> prune_thresha float

>   Prune threshold. Default is FLT_MIN. Maps to a command-line argument: `--prune_thr %f`. Mutually exclusive with inputs: `noprune`.

> resynth_testan integer (int or long)

>   Test GLM by resynthsis. Maps to a command-line argument: `--resynthtest %d`.

> save_conda boolean

>   Flag to save design matrix condition at each voxel. Maps to a command-line argument: `--save-cond`.

> save_estimatea boolean

>   Save signal estimate (yhat). Maps to a command-line argument: `--yhat-save`.

> save_res_corr_mtxa boolean

>   Save residual error spatial correlation matrix (eres.scm). Big!. Maps to a command-line argument: `--eres-scm`.

> save_residuala boolean

>   Save residual error (eres). Maps to a command-line argument: `--eres-save`.

> seedan integer (int or long)

>   Used for synthesizing noise. Maps to a command-line argument: `--seed %d`.

> self_rega tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

>   Self-regressor from index col row slice. Maps to a command-line argument: `--selfreg %d %d %d`.

> sim_done_filea pathlike object or string representing a file

>   Create file when simulation finished. Maps to a command-line argument: `--sim-done %s`.

> sim_sign‘abs’ or ‘pos’ or ‘neg’

>   Abs, pos, or neg. Maps to a command-line argument: `--sim-sign %s`.

> simulationa tuple of the form: (‘perm’ or ‘mc-full’ or ‘mc-z’, an integer (int or long), a float, a unicode string)

>   Nulltype nsim thresh csdbasename. Maps to a command-line argument: `--sim %s %d %f %s`.

> subject_ida unicode string

>   Subject id for surface geometry.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surfa boolean

>   Analysis is on a surface mesh. Maps to a command-line argument: `--surf %s %s %s`. Requires inputs: `subject_id`, `hemi`.

> surf_geoa unicode string

>   Surface geometry name (e.g. white, pial). (Nipype default value: `white`)

> syntha boolean

>   Replace input with gaussian. Maps to a command-line argument: `--synth`.

> uniforma tuple of the form: (a float, a float)

>   Use uniform distribution instead of gaussian. Maps to a command-line argument: `--uniform %f %f`.

> var_fwhma floating point number >= 0.0

>   Smooth variance by fwhm. Maps to a command-line argument: `--var-fwhm %f`.

> vox_dumpa tuple of the form: (an integer (int or long), an integer (int or long), an integer (int or long))

>   Dump voxel GLM and exit. Maps to a command-line argument: `--voxdump %d %d %d`.

> weight_filea pathlike object or string representing an existing file

>   Weight for each input at each voxel. Mutually exclusive with inputs: `weighted_ls`.

> weight_inva boolean

>   Invert weights. Maps to a command-line argument: `--w-inv`. Mutually exclusive with inputs: `weighted_ls`.

> weight_sqrta boolean

>   Sqrt of weights. Maps to a command-line argument: `--w-sqrt`. Mutually exclusive with inputs: `weighted_ls`.

> weighted_lsa pathlike object or string representing an existing file

>   Weighted least squares. Maps to a command-line argument: `--wls %s`. Mutually exclusive with inputs: `weight_file`, `weight_inv`, `weight_sqrt`.

> beta_filea pathlike object or string representing an existing file

>   Map of regression coefficients.

> dof_filea pathlike object or string representing a file

>   Text file with effective degrees-of-freedom for the analysis.

> error_filea pathlike object or string representing a file

>   Map of residual error.

> error_stddev_filea pathlike object or string representing a file

>   Map of residual error standard deviation.

> error_var_filea pathlike object or string representing a file

>   Map of residual error variance.

> estimate_filea pathlike object or string representing a file

>   Map of the estimated Y values.

> frame_eigenvectorsa pathlike object or string representing a file

>   Matrix of frame eigenvectors from residual PCA.

> ftest_filea list of items which are any value

>   Map of test statistic values.

> fwhm_filea pathlike object or string representing a file

>   Text file with estimated smoothness.

> gamma_filea list of items which are any value

>   Map of contrast of regression coefficients.

> gamma_var_filea list of items which are any value

>   Map of regression contrast variance.

> glm_dira pathlike object or string representing an existing directory

>   Output directory.

> mask_filea pathlike object or string representing a file

>   Map of the mask used in the analysis.

> sig_filea list of items which are any value

>   Map of F-test significance (in -log10p).

> singular_valuesa pathlike object or string representing a file

>   Matrix singular values from residual PCA.

> spatial_eigenvectorsa pathlike object or string representing a file

>   Map of spatial eigenvectors from residual PCA.

> svd_stats_filea pathlike object or string representing a file

>   Text file summarizing the residual PCA.

## SegStats

Link to code

> Bases: FSCommand

> Wrapped executable: `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'

> annota tuple of the form: (a unicode string, ‘lh’ or ‘rh’, a unicode string)

>   Subject hemi parc : use surface parcellation. Maps to a command-line argument: `--annot %s %s %s`. Mutually exclusive with inputs: `segmentation_file`, `annot`, `surf_label`.

> segmentation_filea pathlike object or string representing an existing file

>   Segmentation volume path. Maps to a command-line argument: `--seg %s`. Mutually exclusive with inputs: `segmentation_file`, `annot`, `surf_label`.

> surf_labela tuple of the form: (a unicode string, ‘lh’ or ‘rh’, a unicode string)

>   Subject hemi label : use surface label. Maps to a command-line argument: `--slabel %s %s %s`. Mutually exclusive with inputs: `segmentation_file`, `annot`, `surf_label`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> avgwf_filea boolean or a pathlike object or string representing a file

>   Save as binary volume (bool or filename). Maps to a command-line argument: `--avgwfvol %s`.

> avgwf_txt_filea boolean or a pathlike object or string representing a file

>   Save average waveform into file (bool or filename). Maps to a command-line argument: `--avgwf %s`.

> brain_vol‘brain-vol-from-seg’ or ‘brainmask’

>   Compute brain volume either with `brainmask` or `brain-vol-from-seg`. Maps to a command-line argument: `--%s`.

> brainmask_filea pathlike object or string representing an existing file

>   Load brain mask and compute the volume of the brain as the non-zero voxels in this volume. Maps to a command-line argument: `--brainmask %s`.

> calc_power‘sqr’ or ‘sqrt’

>   Compute either the sqr or the sqrt of the input. Maps to a command-line argument: `--%s`.

> calc_snra boolean

>   Save mean/std as extra column in output table. Maps to a command-line argument: `--snr`.

> color_table_filea pathlike object or string representing an existing file

>   Color table file with seg id names. Maps to a command-line argument: `--ctab %s`. Mutually exclusive with inputs: `color_table_file`, `default_color_table`, `gca_color_table`.

> cortex_vol_from_surfa boolean

>   Compute cortex volume from surf. Maps to a command-line argument: `--surf-ctx-vol`.

> default_color_tablea boolean

>   Use $FREESURFER_HOME/FreeSurferColorLUT.txt. Maps to a command-line argument: `--ctab-default`. Mutually exclusive with inputs: `color_table_file`, `default_color_table`, `gca_color_table`.

> emptya boolean

>   Report on segmentations listed in the color table. Maps to a command-line argument: `--empty`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> etiva boolean

>   Compute ICV from talairach transform. Maps to a command-line argument: `--etiv`.

> etiv_only‘etiv’ or ‘old-etiv’ or ‘–%s-only’

>   Compute etiv and exit. Use `etiv` or `old-etiv`.

> eulera boolean

>   Write out number of defect holes in orig.nofix based on the euler number. Maps to a command-line argument: `--euler`.

> exclude_ctx_gm_wma boolean

>   Exclude cortical gray and white matter. Maps to a command-line argument: `--excl-ctxgmwm`.

> exclude_idan integer (int or long)

>   Exclude seg id from report. Maps to a command-line argument: `--excludeid %d`.

> framean integer (int or long)

>   Report stats on nth frame of input volume. Maps to a command-line argument: `--frame %d`.

> gca_color_tablea pathlike object or string representing an existing file

>   Get color table from GCA (CMA). Maps to a command-line argument: `--ctab-gca %s`. Mutually exclusive with inputs: `color_table_file`, `default_color_table`, `gca_color_table`.

> in_filea pathlike object or string representing an existing file

>   Use the segmentation to report stats on this volume. Maps to a command-line argument: `--i %s`.

> in_intensitya pathlike object or string representing a file

>   Undocumented input norm.mgz file. Maps to a command-line argument: `--in %s --in-intensity-name %s`.

> intensity_units‘MR’

>   Intensity units. Maps to a command-line argument: `--in-intensity-units %s`. Requires inputs: `in_intensity`.

> mask_erodean integer (int or long)

>   Erode mask by some amount. Maps to a command-line argument: `--maskerode %d`.

> mask_filea pathlike object or string representing an existing file

>   Mask volume (same size as seg. Maps to a command-line argument: `--mask %s`.

> mask_framean integer (int or long)

>   Mask with this (0 based) frame of the mask volume. Requires inputs: `mask_file`.

> mask_inverta boolean

>   Invert binarized mask volume. Maps to a command-line argument: `--maskinvert`.

> mask_sign‘abs’ or ‘pos’ or ‘neg’ or ‘–masksign %s’

>   Sign for mask threshold: pos, neg, or abs.

> mask_thresha float

>   Binarize mask with this threshold <0.5>. Maps to a command-line argument: `--maskthresh %f`.

> multiplya float

>   Multiply input by val. Maps to a command-line argument: `--mul %f`.

> non_empty_onlya boolean

>   Only report nonempty segmentations. Maps to a command-line argument: `--nonempty`.

> partial_volume_filea pathlike object or string representing an existing file

>   Compensate for partial voluming. Maps to a command-line argument: `--pv %s`.

> segment_ida list of items which are any value

>   Manually specify segmentation ids. Maps to a command-line argument: `--id %s...`.

> sf_avg_filea boolean or a pathlike object or string representing a file

>   Save mean across space and time. Maps to a command-line argument: `--sfavg %s`.

> subcort_gma boolean

>   Compute volume of subcortical gray matter. Maps to a command-line argument: `--subcortgray`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> summary_filea pathlike object or string representing a file

>   Segmentation stats summary table file. Maps to a command-line argument: `--sum %s` (position: -1).

> supratenta boolean

>   Undocumented input flag. Maps to a command-line argument: `--supratent`.

> total_graya boolean

>   Compute volume of total gray matter. Maps to a command-line argument: `--totalgray`.

> voxa list of items which are an integer (int or long)

>   Replace seg with all 0s except at C R S (three int inputs). Maps to a command-line argument: `--vox %s`.

> wm_vol_from_surfa boolean

>   Compute wm volume from surf. Maps to a command-line argument: `--surf-wm-vol`.

> avgwf_filea pathlike object or string representing a file

>   Volume with functional statistics averaged over segs.

> avgwf_txt_filea pathlike object or string representing a file

>   Text file with functional statistics averaged over segs.

> sf_avg_filea pathlike object or string representing a file

>   Text file with func statistics averaged over segs and framss.

> summary_filea pathlike object or string representing an existing file

>   Segmentation summary statistics table.

## SegStatsReconAll

Link to code

> Bases: SegStats

> Wrapped executable: `mri_segstats`.

> This class inherits SegStats and modifies it for use in a recon-all workflow. This implementation mandates implicit inputs that SegStats. To ensure backwards compatability of SegStats, this class was created.

> Examples

>     >>> from nipype.interfaces.freesurfer import SegStatsReconAll
>     >>> segstatsreconall = SegStatsReconAll()
>     >>> segstatsreconall.inputs.annot = ('PWS04', 'lh', 'aparc')
>     >>> segstatsreconall.inputs.avgwf_txt_file = 'avgwf.txt'
>     >>> segstatsreconall.inputs.summary_file = 'summary.stats'
>     >>> segstatsreconall.inputs.subject_id = '10335'
>     >>> segstatsreconall.inputs.ribbon = 'wm.mgz'
>     >>> segstatsreconall.inputs.transform = 'trans.mat'
>     >>> segstatsreconall.inputs.presurf_seg = 'wm.mgz'
>     >>> segstatsreconall.inputs.lh_orig_nofix = 'lh.pial'
>     >>> segstatsreconall.inputs.rh_orig_nofix = 'lh.pial'
>     >>> segstatsreconall.inputs.lh_pial = 'lh.pial'
>     >>> segstatsreconall.inputs.rh_pial = 'lh.pial'
>     >>> segstatsreconall.inputs.lh_white = 'lh.pial'
>     >>> segstatsreconall.inputs.rh_white = 'lh.pial'
>     >>> segstatsreconall.inputs.empty = True
>     >>> segstatsreconall.inputs.brain_vol = 'brain-vol-from-seg'
>     >>> segstatsreconall.inputs.exclude_ctx_gm_wm = True
>     >>> segstatsreconall.inputs.supratent = True
>     >>> segstatsreconall.inputs.subcort_gm = True
>     >>> segstatsreconall.inputs.etiv = True
>     >>> segstatsreconall.inputs.wm_vol_from_surf = True
>     >>> segstatsreconall.inputs.cortex_vol_from_surf = True
>     >>> segstatsreconall.inputs.total_gray = True
>     >>> segstatsreconall.inputs.euler = True
>     >>> segstatsreconall.inputs.exclude_id = 0
>     >>> segstatsreconall.cmdline
>     'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --brain-vol-from-seg --surf-ctx-vol --empty --etiv --euler --excl-ctxgmwm --excludeid 0 --subcortgray --subject 10335 --supratent --totalgray --surf-wm-vol --sum ./summary.stats'

> annota tuple of the form: (a unicode string, ‘lh’ or ‘rh’, a unicode string)

>   Subject hemi parc : use surface parcellation. Maps to a command-line argument: `--annot %s %s %s`. Mutually exclusive with inputs: `segmentation_file`, `annot`, `surf_label`.

> lh_orig_nofixa pathlike object or string representing an existing file

>   Input lh.orig.nofix.

> lh_piala pathlike object or string representing an existing file

>   Input file must be <subject_id>/surf/lh.pial.

> lh_whitea pathlike object or string representing an existing file

>   Input file must be <subject_id>/surf/lh.white.

> rh_orig_nofixa pathlike object or string representing an existing file

>   Input rh.orig.nofix.

> rh_piala pathlike object or string representing an existing file

>   Input file must be <subject_id>/surf/rh.pial.

> rh_whitea pathlike object or string representing an existing file

>   Input file must be <subject_id>/surf/rh.white.

> ribbona pathlike object or string representing an existing file

>   Input file mri/ribbon.mgz.

> segmentation_filea pathlike object or string representing an existing file

>   Segmentation volume path. Maps to a command-line argument: `--seg %s`. Mutually exclusive with inputs: `segmentation_file`, `annot`, `surf_label`.

> subject_ida string

>   Subject id being processed. Maps to a command-line argument: `--subject %s`. (Nipype default value: `subject_id`)

> surf_labela tuple of the form: (a unicode string, ‘lh’ or ‘rh’, a unicode string)

>   Subject hemi label : use surface label. Maps to a command-line argument: `--slabel %s %s %s`. Mutually exclusive with inputs: `segmentation_file`, `annot`, `surf_label`.

> transforma pathlike object or string representing an existing file

>   Input transform file.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> asega pathlike object or string representing an existing file

>   Mandatory implicit input in 5.3.

> avgwf_filea boolean or a pathlike object or string representing a file

>   Save as binary volume (bool or filename). Maps to a command-line argument: `--avgwfvol %s`.

> avgwf_txt_filea boolean or a pathlike object or string representing a file

>   Save average waveform into file (bool or filename). Maps to a command-line argument: `--avgwf %s`.

> brain_vol‘brain-vol-from-seg’ or ‘brainmask’

>   Compute brain volume either with `brainmask` or `brain-vol-from-seg`. Maps to a command-line argument: `--%s`.

> brainmask_filea pathlike object or string representing an existing file

>   Load brain mask and compute the volume of the brain as the non-zero voxels in this volume. Maps to a command-line argument: `--brainmask %s`.

> calc_power‘sqr’ or ‘sqrt’

>   Compute either the sqr or the sqrt of the input. Maps to a command-line argument: `--%s`.

> calc_snra boolean

>   Save mean/std as extra column in output table. Maps to a command-line argument: `--snr`.

> color_table_filea pathlike object or string representing an existing file

>   Color table file with seg id names. Maps to a command-line argument: `--ctab %s`. Mutually exclusive with inputs: `color_table_file`, `default_color_table`, `gca_color_table`.

> copy_inputsa boolean

>   If running as a node, set this to True otherwise, this will copy the implicit inputs to the node directory.

> cortex_vol_from_surfa boolean

>   Compute cortex volume from surf. Maps to a command-line argument: `--surf-ctx-vol`.

> default_color_tablea boolean

>   Use $FREESURFER_HOME/FreeSurferColorLUT.txt. Maps to a command-line argument: `--ctab-default`. Mutually exclusive with inputs: `color_table_file`, `default_color_table`, `gca_color_table`.

> emptya boolean

>   Report on segmentations listed in the color table. Maps to a command-line argument: `--empty`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> etiva boolean

>   Compute ICV from talairach transform. Maps to a command-line argument: `--etiv`.

> etiv_only‘etiv’ or ‘old-etiv’ or ‘–%s-only’

>   Compute etiv and exit. Use `etiv` or `old-etiv`.

> eulera boolean

>   Write out number of defect holes in orig.nofix based on the euler number. Maps to a command-line argument: `--euler`.

> exclude_ctx_gm_wma boolean

>   Exclude cortical gray and white matter. Maps to a command-line argument: `--excl-ctxgmwm`.

> exclude_idan integer (int or long)

>   Exclude seg id from report. Maps to a command-line argument: `--excludeid %d`.

> framean integer (int or long)

>   Report stats on nth frame of input volume. Maps to a command-line argument: `--frame %d`.

> gca_color_tablea pathlike object or string representing an existing file

>   Get color table from GCA (CMA). Maps to a command-line argument: `--ctab-gca %s`. Mutually exclusive with inputs: `color_table_file`, `default_color_table`, `gca_color_table`.

> in_filea pathlike object or string representing an existing file

>   Use the segmentation to report stats on this volume. Maps to a command-line argument: `--i %s`.

> in_intensitya pathlike object or string representing a file

>   Undocumented input norm.mgz file. Maps to a command-line argument: `--in %s --in-intensity-name %s`.

> intensity_units‘MR’

>   Intensity units. Maps to a command-line argument: `--in-intensity-units %s`. Requires inputs: `in_intensity`.

> mask_erodean integer (int or long)

>   Erode mask by some amount. Maps to a command-line argument: `--maskerode %d`.

> mask_filea pathlike object or string representing an existing file

>   Mask volume (same size as seg. Maps to a command-line argument: `--mask %s`.

> mask_framean integer (int or long)

>   Mask with this (0 based) frame of the mask volume. Requires inputs: `mask_file`.

> mask_inverta boolean

>   Invert binarized mask volume. Maps to a command-line argument: `--maskinvert`.

> mask_sign‘abs’ or ‘pos’ or ‘neg’ or ‘–masksign %s’

>   Sign for mask threshold: pos, neg, or abs.

> mask_thresha float

>   Binarize mask with this threshold <0.5>. Maps to a command-line argument: `--maskthresh %f`.

> multiplya float

>   Multiply input by val. Maps to a command-line argument: `--mul %f`.

> non_empty_onlya boolean

>   Only report nonempty segmentations. Maps to a command-line argument: `--nonempty`.

> partial_volume_filea pathlike object or string representing an existing file

>   Compensate for partial voluming. Maps to a command-line argument: `--pv %s`.

> presurf_sega pathlike object or string representing an existing file

>   Input segmentation volume.

> segment_ida list of items which are any value

>   Manually specify segmentation ids. Maps to a command-line argument: `--id %s...`.

> sf_avg_filea boolean or a pathlike object or string representing a file

>   Save mean across space and time. Maps to a command-line argument: `--sfavg %s`.

> subcort_gma boolean

>   Compute volume of subcortical gray matter. Maps to a command-line argument: `--subcortgray`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> summary_filea pathlike object or string representing a file

>   Segmentation stats summary table file. Maps to a command-line argument: `--sum %s` (position: -1).

> supratenta boolean

>   Undocumented input flag. Maps to a command-line argument: `--supratent`.

> total_graya boolean

>   Compute volume of total gray matter. Maps to a command-line argument: `--totalgray`.

> voxa list of items which are an integer (int or long)

>   Replace seg with all 0s except at C R S (three int inputs). Maps to a command-line argument: `--vox %s`.

> wm_vol_from_surfa boolean

>   Compute wm volume from surf. Maps to a command-line argument: `--surf-wm-vol`.

> avgwf_filea pathlike object or string representing a file

>   Volume with functional statistics averaged over segs.

> avgwf_txt_filea pathlike object or string representing a file

>   Text file with functional statistics averaged over segs.

> sf_avg_filea pathlike object or string representing a file

>   Text file with func statistics averaged over segs and framss.

> summary_filea pathlike object or string representing an existing file

>   Segmentation summary statistics table.

> SegStatsReconAll.run(**inputs)

>   Execute this interface.

>   This interface will not raise an exception if runtime.returncode is non-zero.

>   Parameters

>     - cwd (specify a folder where the interface should be run) –

>     - inputs (allows the interface settings to be updated) –

>   Returns

>     results – A copy of the instance that was executed, provenance information and, if successful, results

>   Return type

>     `nipype.interfaces.base.support.InterfaceResult`

## SphericalAverage

Link to code

> Bases: FSCommand

> Wrapped executable: `mris_spherical_average`.

> This program will add a template into an average surface.

> Examples

>     >>> from nipype.interfaces.freesurfer import SphericalAverage
>     >>> sphericalavg = SphericalAverage()
>     >>> sphericalavg.inputs.out_file = 'test.out'
>     >>> sphericalavg.inputs.in_average = '.'
>     >>> sphericalavg.inputs.in_surf = 'lh.pial'
>     >>> sphericalavg.inputs.hemisphere = 'lh'
>     >>> sphericalavg.inputs.fname = 'lh.entorhinal'
>     >>> sphericalavg.inputs.which = 'label'
>     >>> sphericalavg.inputs.subject_id = '10335'
>     >>> sphericalavg.inputs.erode = 2
>     >>> sphericalavg.inputs.threshold = 5
>     >>> sphericalavg.cmdline
>     'mris_spherical_average -erode 2 -o 10335 -t 5.0 label lh.entorhinal lh pial . test.out'

> fnamea string

>   Filename from the average subject directory. Example: to use rh.entorhinal.label as the input label filename, set fname to ‘rh.entorhinal’ and which to ‘label’. The program will then search for `<in_average>/label/rh.entorhinal.label`. Maps to a command-line argument: `%s` (position: -5).

> hemisphere‘lh’ or ‘rh’

>   Input hemisphere. Maps to a command-line argument: `%s` (position: -4).

> in_surfa pathlike object or string representing an existing file

>   Input surface file. Maps to a command-line argument: `%s` (position: -3).

> subject_ida string

>   Output subject id. Maps to a command-line argument: `-o %s`.

> which‘coords’ or ‘label’ or ‘vals’ or ‘curv’ or ‘area’

>   No documentation. Maps to a command-line argument: `%s` (position: -6).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> erodean integer (int or long)

>   Undocumented. Maps to a command-line argument: `-erode %d`.

> in_averagea pathlike object or string representing an existing directory

>   Average subject. Maps to a command-line argument: `%s` (position: -2).

> in_origa pathlike object or string representing an existing file

>   Original surface filename. Maps to a command-line argument: `-orig %s`.

> out_filea pathlike object or string representing a file

>   Output filename. Maps to a command-line argument: `%s` (position: -1).

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> thresholda float

>   Undocumented. Maps to a command-line argument: `-t %.1f`.

> out_filea pathlike object or string representing a file

>   Output label.