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 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

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

bin_val_notan integer

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

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

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

erode2dan integer

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

frame_noan integer

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

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 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

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 occurrences. 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 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

Gdiag_no : set diagnostic 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

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 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.

logana tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file, a float)

RefTac TimeSec tstar : perform Logan kinetic modeling. Maps to a command-line argument: --logan %s %s %f.

mask_filea pathlike object or string representing an existing file

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

mrtm1a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)

RefTac TimeSec : perform MRTM1 kinetic modeling. Maps to a command-line argument: --mrtm1 %s %s.

mrtm2a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file, a float)

RefTac TimeSec k2prime : perform MRTM2 kinetic modeling. Maps to a command-line argument: --mrtm2 %s %s %f.

niia boolean

Save outputs as nii. Maps to a command-line argument: --nii. Mutually exclusive with inputs: nii, nii_gz.

nii_gza boolean

Save outputs as nii.gz. Maps to a command-line argument: --nii.gz. Mutually exclusive with inputs: nii, nii_gz.

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

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

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

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

self_rega tuple of the form: (an integer, an integer, an integer)

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, a float, a string)

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

subject_ida 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 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, an integer, an integer)

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.

bp_filea pathlike object or string representing a file

Binding potential estimates.

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.

k2p_filea pathlike object or string representing a file

Estimate of k2p parameter.

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 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 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 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 string

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

subjects_dira pathlike object or string representing an existing directory

Subjects directory.

surfacea 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 string

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

argsa 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

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

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 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 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 string

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

surf_measurea 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 string

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

argsa 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

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

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 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 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 string

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

surf_measurea 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

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 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

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 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

Gdiag_no : set diagnostic 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

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 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.

logana tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file, a float)

RefTac TimeSec tstar : perform Logan kinetic modeling. Maps to a command-line argument: --logan %s %s %f.

mask_filea pathlike object or string representing an existing file

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

mrtm1a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)

RefTac TimeSec : perform MRTM1 kinetic modeling. Maps to a command-line argument: --mrtm1 %s %s.

mrtm2a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file, a float)

RefTac TimeSec k2prime : perform MRTM2 kinetic modeling. Maps to a command-line argument: --mrtm2 %s %s %f.

niia boolean

Save outputs as nii. Maps to a command-line argument: --nii. Mutually exclusive with inputs: nii, nii_gz.

nii_gza boolean

Save outputs as nii.gz. Maps to a command-line argument: --nii.gz. Mutually exclusive with inputs: nii, nii_gz.

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

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

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

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

self_rega tuple of the form: (an integer, an integer, an integer)

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, a float, a string)

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

subject_ida 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 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, an integer, an integer)

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.

bp_filea pathlike object or string representing a file

Binding potential estimates.

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.

k2p_filea pathlike object or string representing a file

Estimate of k2p parameter.

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 string, ‘lh’ or ‘rh’, a 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 string, ‘lh’ or ‘rh’, a 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 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

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

framean integer

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

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

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

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 compatibility 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 string, ‘lh’ or ‘rh’, a 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 string, ‘lh’ or ‘rh’, a 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 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

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

framean integer

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

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

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

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 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

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.