nipype.interfaces.freesurfer.model module¶
The freesurfer module provides basic functions for interfacing with freesurfer tools.
Binarize¶
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'
- Mandatory Inputs:
in_file (a pathlike object or string representing an existing file) – Input volume. Maps to a command-line argument:
--i %s.- Optional Inputs:
abs (a boolean) – Take abs of invol first (ie, make unsigned). Maps to a command-line argument:
--abs.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.bin_col_num (a boolean) – Set binarized voxel value to its column number. Maps to a command-line argument:
--bincol.bin_val (an integer) – Set vox within thresh to val (default is 1). Maps to a command-line argument:
--binval %d.bin_val_not (an integer) – Set vox outside range to val (default is 0). Maps to a command-line argument:
--binvalnot %d.binary_file (a pathlike object or string representing a file) – Binary output volume. Maps to a command-line argument:
--o %s.count_file (a 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.dilate (an integer) – Niters: dilate binarization in 3D. Maps to a command-line argument:
--dilate %d.environ (a 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:
{})erode (an integer) – Nerode: erode binarization in 3D (after any dilation). Maps to a command-line argument:
--erode %d.erode2d (an integer) – Nerode2d: erode binarization in 2D (after any 3D erosion). Maps to a command-line argument:
--erode2d %d.frame_no (an integer) – Use 0-based frame of input (default is 0). Maps to a command-line argument:
--frame %s.invert (a boolean) – Set binval=0, binvalnot=1. Maps to a command-line argument:
--inv.mask_file (a pathlike object or string representing an existing file) – Must be within mask. Maps to a command-line argument:
--mask maskvol.mask_thresh (a float) – Set thresh for mask. Maps to a command-line argument:
--mask-thresh %f.match (a list of items which are an integer) – Match instead of threshold. Maps to a command-line argument:
--match %d....max (a float) – Max thresh. Maps to a command-line argument:
--max %f. Mutually exclusive with inputs:wm_ven_csf.merge_file (a pathlike object or string representing an existing file) – Merge with mergevol. Maps to a command-line argument:
--merge %s.min (a 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.
rmax (a float) – Compute max based on rmax*globalmean. Maps to a command-line argument:
--rmax %f.rmin (a float) – Compute min based on rmin*globalmean. Maps to a command-line argument:
--rmin %f.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
ventricles (a boolean) – Set match vals those for aseg ventricles+choroid (not 4th). Maps to a command-line argument:
--ventricles.wm (a boolean) – Set match vals to 2 and 41 (aseg for cerebral WM). Maps to a command-line argument:
--wm.wm_ven_csf (a boolean) – WM and ventricular CSF, including choroid (not 4th). Maps to a command-line argument:
--wm+vcsf. Mutually exclusive with inputs:min,max.zero_edges (a boolean) – Zero the edge voxels. Maps to a command-line argument:
--zero-edges.zero_slice_edge (a boolean) – Zero the edge slice voxels. Maps to a command-line argument:
--zero-slice-edges.- Outputs:
binary_file (a pathlike object or string representing an existing file) – Binarized output volume.
count_file (a pathlike object or string representing a file) – Ascii file containing number of hits.
Concatenate¶
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'
- Mandatory Inputs:
in_files (a 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....- Optional Inputs:
add_val (a float) – Add some amount to the input volume. Maps to a command-line argument:
--add %f.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.combine (a boolean) – Combine non-zero values into single frame volume. Maps to a command-line argument:
--combine.concatenated_file (a pathlike object or string representing a file) – Output volume. Maps to a command-line argument:
--o %s.environ (a 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:
{})gmean (an integer) – Create matrix to average Ng groups, Nper=Ntot/Ng. Maps to a command-line argument:
--gmean %d.keep_dtype (a boolean) – Keep voxelwise precision type (default is float. Maps to a command-line argument:
--keep-datatype.mask_file (a pathlike object or string representing an existing file) – Mask input with a volume. Maps to a command-line argument:
--mask %s.max_bonfcor (a boolean) – Compute max and bonferroni correct (assumes -log10(ps)). Maps to a command-line argument:
--max-bonfcor.max_index (a boolean) – Compute the index of max voxel in concatenated volumes. Maps to a command-line argument:
--max-index.mean_div_n (a boolean) – Compute mean/nframes (good for var). Maps to a command-line argument:
--mean-div-n.multiply_by (a float) – Multiply input volume by some amount. Maps to a command-line argument:
--mul %f.multiply_matrix_file (a 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.sort (a 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_dir (a pathlike object or string representing an existing directory) – Subjects directory.
vote (a boolean) – Most frequent value at each voxel and fraction of occurrences. Maps to a command-line argument:
--vote.- Outputs:
concatenated_file (a pathlike object or string representing an existing file) – Path/name of the output volume.
GLMFit¶
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
- Mandatory Inputs:
in_file (a pathlike object or string representing a file) – Input 4D file. Maps to a command-line argument:
--y %s.- Optional Inputs:
allow_ill_cond (a boolean) – Allow ill-conditioned design matrices. Maps to a command-line argument:
--illcond.allow_repeated_subjects (a boolean) – Allow subject names to repeat in the fsgd file (must appear before –fsgd. Maps to a command-line argument:
--allowsubjrep.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.calc_AR1 (a boolean) – Compute and save temporal AR1 of residual. Maps to a command-line argument:
--tar1.check_opts (a boolean) – Don’t run anything, just check options and exit. Maps to a command-line argument:
--checkopts.compute_log_y (a boolean) – Compute natural log of y prior to analysis. Maps to a command-line argument:
--logy.contrast (a list of items which are a pathlike object or string representing an existing file) – Contrast file. Maps to a command-line argument:
--C %s....cortex (a boolean) – Use subjects ?h.cortex.label as label. Maps to a command-line argument:
--cortex. Mutually exclusive with inputs:label_file.debug (a boolean) – Turn on debugging. Maps to a command-line argument:
--debug.design (a 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.diag (an integer) – Gdiag_no : set diagnostic level. Maps to a command-line argument:
--diag %d.diag_cluster (a boolean) – Save sig volume and exit from first sim loop. Maps to a command-line argument:
--diag-cluster.environ (a 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_dof (an 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_file (a 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_var (a pathlike object or string representing an existing file) – For fixed effects analysis. Maps to a command-line argument:
--yffxvar %s.force_perm (a boolean) – Force perumtation test, even when design matrix is not orthog. Maps to a command-line argument:
--perm-force.fsgd (a 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.fwhm (a floating point number >= 0.0) – Smooth input by fwhm. Maps to a command-line argument:
--fwhm %f.glm_dir (a string) – Save outputs to dir. Maps to a command-line argument:
--glmdir %s.hemi (‘lh’ or ‘rh’) – Surface hemisphere.
invert_mask (a boolean) – Invert mask. Maps to a command-line argument:
--mask-inv.label_file (a 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.logan (a 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_file (a pathlike object or string representing an existing file) – Binary mask. Maps to a command-line argument:
--mask %s.mrtm1 (a 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.mrtm2 (a 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.nii (a boolean) – Save outputs as nii. Maps to a command-line argument:
--nii. Mutually exclusive with inputs:nii,nii_gz.nii_gz (a boolean) – Save outputs as nii.gz. Maps to a command-line argument:
--nii.gz. Mutually exclusive with inputs:nii,nii_gz.no_contrast_ok (a boolean) – Do not fail if no contrasts specified. Maps to a command-line argument:
--no-contrasts-ok.no_est_fwhm (a boolean) – Turn off FWHM output estimation. Maps to a command-line argument:
--no-est-fwhm.no_mask_smooth (a boolean) – Do not mask when smoothing. Maps to a command-line argument:
--no-mask-smooth.no_prune (a boolean) – Do not prune. Maps to a command-line argument:
--no-prune. Mutually exclusive with inputs:prunethresh.one_sample (a 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.pca (a boolean) – Perform pca/svd analysis on residual. Maps to a command-line argument:
--pca.per_voxel_reg (a 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....profile (an integer) – Niters : test speed. Maps to a command-line argument:
--profile %d.prune (a boolean) – Remove voxels that do not have a non-zero value at each frame (def). Maps to a command-line argument:
--prune.prune_thresh (a float) – Prune threshold. Default is FLT_MIN. Maps to a command-line argument:
--prune_thr %f. Mutually exclusive with inputs:noprune.resynth_test (an integer) – Test GLM by resynthsis. Maps to a command-line argument:
--resynthtest %d.save_cond (a boolean) – Flag to save design matrix condition at each voxel. Maps to a command-line argument:
--save-cond.save_estimate (a boolean) – Save signal estimate (yhat). Maps to a command-line argument:
--yhat-save.save_res_corr_mtx (a boolean) – Save residual error spatial correlation matrix (eres.scm). Big!. Maps to a command-line argument:
--eres-scm.save_residual (a boolean) – Save residual error (eres). Maps to a command-line argument:
--eres-save.seed (an integer) – Used for synthesizing noise. Maps to a command-line argument:
--seed %d.self_reg (a 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_file (a 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.simulation (a 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_id (a string) – Subject id for surface geometry.
subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
surf (a boolean) – Analysis is on a surface mesh. Maps to a command-line argument:
--surf %s %s %s. Requires inputs:subject_id,hemi.surf_geo (a string) – Surface geometry name (e.g. white, pial). (Nipype default value:
white)synth (a boolean) – Replace input with gaussian. Maps to a command-line argument:
--synth.uniform (a tuple of the form: (a float, a float)) – Use uniform distribution instead of gaussian. Maps to a command-line argument:
--uniform %f %f.var_fwhm (a floating point number >= 0.0) – Smooth variance by fwhm. Maps to a command-line argument:
--var-fwhm %f.vox_dump (a 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_file (a pathlike object or string representing an existing file) – Weight for each input at each voxel. Mutually exclusive with inputs:
weighted_ls.weight_inv (a boolean) – Invert weights. Maps to a command-line argument:
--w-inv. Mutually exclusive with inputs:weighted_ls.weight_sqrt (a boolean) – Sqrt of weights. Maps to a command-line argument:
--w-sqrt. Mutually exclusive with inputs:weighted_ls.weighted_ls (a 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.- Outputs:
beta_file (a pathlike object or string representing an existing file) – Map of regression coefficients.
bp_file (a pathlike object or string representing a file) – Binding potential estimates.
dof_file (a pathlike object or string representing a file) – Text file with effective degrees-of-freedom for the analysis.
error_file (a pathlike object or string representing a file) – Map of residual error.
error_stddev_file (a pathlike object or string representing a file) – Map of residual error standard deviation.
error_var_file (a pathlike object or string representing a file) – Map of residual error variance.
estimate_file (a pathlike object or string representing a file) – Map of the estimated Y values.
frame_eigenvectors (a pathlike object or string representing a file) – Matrix of frame eigenvectors from residual PCA.
ftest_file (a list of items which are any value) – Map of test statistic values.
fwhm_file (a pathlike object or string representing a file) – Text file with estimated smoothness.
gamma_file (a list of items which are any value) – Map of contrast of regression coefficients.
gamma_var_file (a list of items which are any value) – Map of regression contrast variance.
glm_dir (a pathlike object or string representing an existing directory) – Output directory.
k2p_file (a pathlike object or string representing a file) – Estimate of k2p parameter.
mask_file (a pathlike object or string representing a file) – Map of the mask used in the analysis.
sig_file (a list of items which are any value) – Map of F-test significance (in -log10p).
singular_values (a pathlike object or string representing a file) – Matrix singular values from residual PCA.
spatial_eigenvectors (a pathlike object or string representing a file) – Map of spatial eigenvectors from residual PCA.
svd_stats_file (a pathlike object or string representing a file) – Text file summarizing the residual PCA.
Label2Annot¶
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'
- Mandatory Inputs:
hemisphere (‘lh’ or ‘rh’) – Input hemisphere. Maps to a command-line argument:
--hemi %s.in_labels (a list of items which are any value) – List of input label files. Maps to a command-line argument:
--l %s....orig (a pathlike object or string representing an existing file) – Implicit {hemisphere}.orig.
out_annot (a string) – Name of the annotation to create. Maps to a command-line argument:
--a %s.subject_id (a string) – Subject name/ID. Maps to a command-line argument:
--s %s. (Nipype default value:subject_id)- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.color_table (a 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_inputs (a boolean) – Copy implicit inputs and create a temp subjects_dir.
environ (a 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_max (a boolean) – Keep label with highest ‘stat’ value. Maps to a command-line argument:
--maxstatwinner.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
verbose_off (a boolean) – Turn off overlap and stat override messages. Maps to a command-line argument:
--noverbose.- Outputs:
out_file (a 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:
Label2Label¶
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'
- Mandatory Inputs:
hemisphere (‘lh’ or ‘rh’) – Input hemisphere. Maps to a command-line argument:
--hemi %s.source_label (a pathlike object or string representing an existing file) – Source label. Maps to a command-line argument:
--srclabel %s.source_sphere_reg (a pathlike object or string representing an existing file) – Implicit input <hemisphere>.sphere.reg.
source_subject (a string) – Source subject name. Maps to a command-line argument:
--srcsubject %s.source_white (a pathlike object or string representing an existing file) – Implicit input <hemisphere>.white.
sphere_reg (a pathlike object or string representing an existing file) – Implicit input <hemisphere>.sphere.reg.
subject_id (a string) – Target subject. Maps to a command-line argument:
--trgsubject %s. (Nipype default value:subject_id)white (a pathlike object or string representing an existing file) – Implicit input <hemisphere>.white.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.copy_inputs (a boolean) – If running as a node, set this to True.This will copy the input files to the node directory.
environ (a 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_file (a 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_dir (a pathlike object or string representing an existing directory) – Subjects directory.
- Outputs:
out_file (a 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:
Label2Vol¶
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'
- Mandatory Inputs:
annot_file (a 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_aseg (a 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_file (a 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_file (a 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_file (a pathlike object or string representing an existing file) – Output template volume. Maps to a command-line argument:
--temp %s.- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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_thresh (0.0 <= 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.identity (a boolean) – Set R=I. Maps to a command-line argument:
--identity. Mutually exclusive with inputs:reg_file,reg_header,identity.invert_mtx (a boolean) – Invert the registration matrix. Maps to a command-line argument:
--invertmtx.label_hit_file (a 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_volume (a float) – Volume of each label point (def 1mm3). Maps to a command-line argument:
--labvoxvol %f.map_label_stat (a 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_vox2ras (a boolean) – Use native vox2ras xform instead of tkregister-style. Maps to a command-line argument:
--native-vox2ras.proj (a 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_file (a 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_header (a 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_id (a string) – Subject id. Maps to a command-line argument:
--subject %s.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
surface (a string) – Use surface instead of white. Maps to a command-line argument:
--surf %s.vol_label_file (a pathlike object or string representing a file) – Output volume. Maps to a command-line argument:
--o %s.- Outputs:
vol_label_file (a pathlike object or string representing an existing file) – Output volume.
MRISPreproc¶
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'
- Mandatory Inputs:
hemi (‘lh’ or ‘rh’) – Hemisphere for source and target. Maps to a command-line argument:
--hemi %s.target (a string) – Target subject name. Maps to a command-line argument:
--target %s.- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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_file (a 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.fwhm (a float) – Smooth by fwhm mm on the target surface. Maps to a command-line argument:
--fwhm %f. Mutually exclusive with inputs:num_iters.fwhm_source (a 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_iters (an integer) – Niters : smooth by niters on the target surface. Maps to a command-line argument:
--niters %d. Mutually exclusive with inputs:fwhm.num_iters_source (an integer) – Niters : smooth by niters on the source surface. Maps to a command-line argument:
--niterssrc %d. Mutually exclusive with inputs:fwhm_source.out_file (a pathlike object or string representing a file) – Output filename. Maps to a command-line argument:
--out %s.proj_frac (a float) – Projection fraction for vol2surf. Maps to a command-line argument:
--projfrac %s.smooth_cortex_only (a boolean) – Only smooth cortex (ie, exclude medial wall). Maps to a command-line argument:
--smooth-cortex-only.source_format (a string) – Source format. Maps to a command-line argument:
--srcfmt %s.subject_file (a 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.subjects (a 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_dir (a pathlike object or string representing an existing directory) – Subjects directory.
surf_area (a 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_dir (a string) – Alternative directory (instead of surf). Maps to a command-line argument:
--surfdir %s.surf_measure (a 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_file (a 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_file (a 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....- Outputs:
out_file (a pathlike object or string representing a file) – Preprocessed output file.
MRISPreprocReconAll¶
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'
- Mandatory Inputs:
hemi (‘lh’ or ‘rh’) – Hemisphere for source and target. Maps to a command-line argument:
--hemi %s.target (a string) – Target subject name. Maps to a command-line argument:
--target %s.- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.copy_inputs (a boolean) – If running as a node, set this to True this will copy some implicit inputs to the node directory.
environ (a 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_file (a 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.fwhm (a float) – Smooth by fwhm mm on the target surface. Maps to a command-line argument:
--fwhm %f. Mutually exclusive with inputs:num_iters.fwhm_source (a 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_target (a pathlike object or string representing a file) – Implicit target surface registration file. Requires inputs:
surfreg_files.num_iters (an integer) – Niters : smooth by niters on the target surface. Maps to a command-line argument:
--niters %d. Mutually exclusive with inputs:fwhm.num_iters_source (an integer) – Niters : smooth by niters on the source surface. Maps to a command-line argument:
--niterssrc %d. Mutually exclusive with inputs:fwhm_source.out_file (a pathlike object or string representing a file) – Output filename. Maps to a command-line argument:
--out %s.proj_frac (a float) – Projection fraction for vol2surf. Maps to a command-line argument:
--projfrac %s.rh_surfreg_target (a pathlike object or string representing a file) – Implicit target surface registration file. Requires inputs:
surfreg_files.smooth_cortex_only (a boolean) – Only smooth cortex (ie, exclude medial wall). Maps to a command-line argument:
--smooth-cortex-only.source_format (a string) – Source format. Maps to a command-line argument:
--srcfmt %s.subject_file (a 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_id (a 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)subjects (a 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_dir (a pathlike object or string representing an existing directory) – Subjects directory.
surf_area (a 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_dir (a string) – Alternative directory (instead of surf). Maps to a command-line argument:
--surfdir %s.surf_measure (a 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_file (a 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_files (a 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_file (a 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....- Outputs:
out_file (a 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:
MS_LDA¶
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'
- Mandatory Inputs:
images (a 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_labels (a 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_file (a pathlike object or string representing a file) – Filename for the synthesized output volume. Maps to a command-line argument:
-synth %s.weight_file (a pathlike object or string representing a file) – Filename for the LDA weights (input or output). Maps to a command-line argument:
-weight %s.- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.conform (a boolean) – Conform the input volumes (brain mask typically already conformed). Maps to a command-line argument:
-conform.environ (a 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_file (a pathlike object or string representing an existing file) – Filename of the label volume. Maps to a command-line argument:
-label %s.mask_file (a pathlike object or string representing an existing file) – Filename of the brain mask volume. Maps to a command-line argument:
-mask %s.shift (an integer) – Shift all values equal to the given value to zero. Maps to a command-line argument:
-shift %d.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
use_weights (a boolean) – Use the weights from a previously generated weight file. Maps to a command-line argument:
-W.- Outputs:
vol_synth_file (a pathlike object or string representing an existing file)
weight_file (a pathlike object or string representing an existing file)
OneSampleTTest¶
Bases: GLMFit
Wrapped executable:
mri_glmfit.
- Mandatory Inputs:
in_file (a pathlike object or string representing a file) – Input 4D file. Maps to a command-line argument:
--y %s.- Optional Inputs:
allow_ill_cond (a boolean) – Allow ill-conditioned design matrices. Maps to a command-line argument:
--illcond.allow_repeated_subjects (a boolean) – Allow subject names to repeat in the fsgd file (must appear before –fsgd. Maps to a command-line argument:
--allowsubjrep.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.calc_AR1 (a boolean) – Compute and save temporal AR1 of residual. Maps to a command-line argument:
--tar1.check_opts (a boolean) – Don’t run anything, just check options and exit. Maps to a command-line argument:
--checkopts.compute_log_y (a boolean) – Compute natural log of y prior to analysis. Maps to a command-line argument:
--logy.contrast (a list of items which are a pathlike object or string representing an existing file) – Contrast file. Maps to a command-line argument:
--C %s....cortex (a boolean) – Use subjects ?h.cortex.label as label. Maps to a command-line argument:
--cortex. Mutually exclusive with inputs:label_file.debug (a boolean) – Turn on debugging. Maps to a command-line argument:
--debug.design (a 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.diag (an integer) – Gdiag_no : set diagnostic level. Maps to a command-line argument:
--diag %d.diag_cluster (a boolean) – Save sig volume and exit from first sim loop. Maps to a command-line argument:
--diag-cluster.environ (a 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_dof (an 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_file (a 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_var (a pathlike object or string representing an existing file) – For fixed effects analysis. Maps to a command-line argument:
--yffxvar %s.force_perm (a boolean) – Force perumtation test, even when design matrix is not orthog. Maps to a command-line argument:
--perm-force.fsgd (a 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.fwhm (a floating point number >= 0.0) – Smooth input by fwhm. Maps to a command-line argument:
--fwhm %f.glm_dir (a string) – Save outputs to dir. Maps to a command-line argument:
--glmdir %s.hemi (‘lh’ or ‘rh’) – Surface hemisphere.
invert_mask (a boolean) – Invert mask. Maps to a command-line argument:
--mask-inv.label_file (a 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.logan (a 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_file (a pathlike object or string representing an existing file) – Binary mask. Maps to a command-line argument:
--mask %s.mrtm1 (a 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.mrtm2 (a 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.nii (a boolean) – Save outputs as nii. Maps to a command-line argument:
--nii. Mutually exclusive with inputs:nii,nii_gz.nii_gz (a boolean) – Save outputs as nii.gz. Maps to a command-line argument:
--nii.gz. Mutually exclusive with inputs:nii,nii_gz.no_contrast_ok (a boolean) – Do not fail if no contrasts specified. Maps to a command-line argument:
--no-contrasts-ok.no_est_fwhm (a boolean) – Turn off FWHM output estimation. Maps to a command-line argument:
--no-est-fwhm.no_mask_smooth (a boolean) – Do not mask when smoothing. Maps to a command-line argument:
--no-mask-smooth.no_prune (a boolean) – Do not prune. Maps to a command-line argument:
--no-prune. Mutually exclusive with inputs:prunethresh.one_sample (a 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.pca (a boolean) – Perform pca/svd analysis on residual. Maps to a command-line argument:
--pca.per_voxel_reg (a 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....profile (an integer) – Niters : test speed. Maps to a command-line argument:
--profile %d.prune (a boolean) – Remove voxels that do not have a non-zero value at each frame (def). Maps to a command-line argument:
--prune.prune_thresh (a float) – Prune threshold. Default is FLT_MIN. Maps to a command-line argument:
--prune_thr %f. Mutually exclusive with inputs:noprune.resynth_test (an integer) – Test GLM by resynthsis. Maps to a command-line argument:
--resynthtest %d.save_cond (a boolean) – Flag to save design matrix condition at each voxel. Maps to a command-line argument:
--save-cond.save_estimate (a boolean) – Save signal estimate (yhat). Maps to a command-line argument:
--yhat-save.save_res_corr_mtx (a boolean) – Save residual error spatial correlation matrix (eres.scm). Big!. Maps to a command-line argument:
--eres-scm.save_residual (a boolean) – Save residual error (eres). Maps to a command-line argument:
--eres-save.seed (an integer) – Used for synthesizing noise. Maps to a command-line argument:
--seed %d.self_reg (a 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_file (a 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.simulation (a 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_id (a string) – Subject id for surface geometry.
subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
surf (a boolean) – Analysis is on a surface mesh. Maps to a command-line argument:
--surf %s %s %s. Requires inputs:subject_id,hemi.surf_geo (a string) – Surface geometry name (e.g. white, pial). (Nipype default value:
white)synth (a boolean) – Replace input with gaussian. Maps to a command-line argument:
--synth.uniform (a tuple of the form: (a float, a float)) – Use uniform distribution instead of gaussian. Maps to a command-line argument:
--uniform %f %f.var_fwhm (a floating point number >= 0.0) – Smooth variance by fwhm. Maps to a command-line argument:
--var-fwhm %f.vox_dump (a 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_file (a pathlike object or string representing an existing file) – Weight for each input at each voxel. Mutually exclusive with inputs:
weighted_ls.weight_inv (a boolean) – Invert weights. Maps to a command-line argument:
--w-inv. Mutually exclusive with inputs:weighted_ls.weight_sqrt (a boolean) – Sqrt of weights. Maps to a command-line argument:
--w-sqrt. Mutually exclusive with inputs:weighted_ls.weighted_ls (a 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.- Outputs:
beta_file (a pathlike object or string representing an existing file) – Map of regression coefficients.
bp_file (a pathlike object or string representing a file) – Binding potential estimates.
dof_file (a pathlike object or string representing a file) – Text file with effective degrees-of-freedom for the analysis.
error_file (a pathlike object or string representing a file) – Map of residual error.
error_stddev_file (a pathlike object or string representing a file) – Map of residual error standard deviation.
error_var_file (a pathlike object or string representing a file) – Map of residual error variance.
estimate_file (a pathlike object or string representing a file) – Map of the estimated Y values.
frame_eigenvectors (a pathlike object or string representing a file) – Matrix of frame eigenvectors from residual PCA.
ftest_file (a list of items which are any value) – Map of test statistic values.
fwhm_file (a pathlike object or string representing a file) – Text file with estimated smoothness.
gamma_file (a list of items which are any value) – Map of contrast of regression coefficients.
gamma_var_file (a list of items which are any value) – Map of regression contrast variance.
glm_dir (a pathlike object or string representing an existing directory) – Output directory.
k2p_file (a pathlike object or string representing a file) – Estimate of k2p parameter.
mask_file (a pathlike object or string representing a file) – Map of the mask used in the analysis.
sig_file (a list of items which are any value) – Map of F-test significance (in -log10p).
singular_values (a pathlike object or string representing a file) – Matrix singular values from residual PCA.
spatial_eigenvectors (a pathlike object or string representing a file) – Map of spatial eigenvectors from residual PCA.
svd_stats_file (a pathlike object or string representing a file) – Text file summarizing the residual PCA.
SegStats¶
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'
- Mandatory Inputs:
annot (a 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_file (a 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_label (a 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.- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.avgwf_file (a 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_file (a 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
brainmaskorbrain-vol-from-seg. Maps to a command-line argument:--%s.brainmask_file (a 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_snr (a boolean) – Save mean/std as extra column in output table. Maps to a command-line argument:
--snr.color_table_file (a 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_surf (a boolean) – Compute cortex volume from surf. Maps to a command-line argument:
--surf-ctx-vol.default_color_table (a 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.empty (a boolean) – Report on segmentations listed in the color table. Maps to a command-line argument:
--empty.environ (a 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:
{})etiv (a 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
etivorold-etiv.euler (a 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_wm (a boolean) – Exclude cortical gray and white matter. Maps to a command-line argument:
--excl-ctxgmwm.exclude_id (an integer) – Exclude seg id from report. Maps to a command-line argument:
--excludeid %d.frame (an integer) – Report stats on nth frame of input volume. Maps to a command-line argument:
--frame %d.gca_color_table (a 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_file (a 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_intensity (a 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_erode (an integer) – Erode mask by some amount. Maps to a command-line argument:
--maskerode %d.mask_file (a pathlike object or string representing an existing file) – Mask volume (same size as seg. Maps to a command-line argument:
--mask %s.mask_frame (an integer) – Mask with this (0 based) frame of the mask volume. Requires inputs:
mask_file.mask_invert (a 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_thresh (a float) – Binarize mask with this threshold <0.5>. Maps to a command-line argument:
--maskthresh %f.multiply (a float) – Multiply input by val. Maps to a command-line argument:
--mul %f.non_empty_only (a boolean) – Only report nonempty segmentations. Maps to a command-line argument:
--nonempty.partial_volume_file (a pathlike object or string representing an existing file) – Compensate for partial voluming. Maps to a command-line argument:
--pv %s.segment_id (a list of items which are any value) – Manually specify segmentation ids. Maps to a command-line argument:
--id %s....sf_avg_file (a 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_gm (a boolean) – Compute volume of subcortical gray matter. Maps to a command-line argument:
--subcortgray.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
summary_file (a pathlike object or string representing a file) – Segmentation stats summary table file. Maps to a command-line argument:
--sum %s(position: -1).supratent (a boolean) – Undocumented input flag. Maps to a command-line argument:
--supratent.total_gray (a boolean) – Compute volume of total gray matter. Maps to a command-line argument:
--totalgray.vox (a 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_surf (a boolean) – Compute wm volume from surf. Maps to a command-line argument:
--surf-wm-vol.- Outputs:
avgwf_file (a pathlike object or string representing a file) – Volume with functional statistics averaged over segs.
avgwf_txt_file (a pathlike object or string representing a file) – Text file with functional statistics averaged over segs.
sf_avg_file (a pathlike object or string representing a file) – Text file with func statistics averaged over segs and framss.
summary_file (a pathlike object or string representing an existing file) – Segmentation summary statistics table.
SegStatsReconAll¶
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'
- Mandatory Inputs:
annot (a 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_nofix (a pathlike object or string representing an existing file) – Input lh.orig.nofix.
lh_pial (a pathlike object or string representing an existing file) – Input file must be <subject_id>/surf/lh.pial.
lh_white (a pathlike object or string representing an existing file) – Input file must be <subject_id>/surf/lh.white.
rh_orig_nofix (a pathlike object or string representing an existing file) – Input rh.orig.nofix.
rh_pial (a pathlike object or string representing an existing file) – Input file must be <subject_id>/surf/rh.pial.
rh_white (a pathlike object or string representing an existing file) – Input file must be <subject_id>/surf/rh.white.
ribbon (a pathlike object or string representing an existing file) – Input file mri/ribbon.mgz.
segmentation_file (a 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_id (a string) – Subject id being processed. Maps to a command-line argument:
--subject %s. (Nipype default value:subject_id)surf_label (a 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.transform (a pathlike object or string representing an existing file) – Input transform file.
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.aseg (a pathlike object or string representing an existing file) – Mandatory implicit input in 5.3.
avgwf_file (a 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_file (a 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
brainmaskorbrain-vol-from-seg. Maps to a command-line argument:--%s.brainmask_file (a 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_snr (a boolean) – Save mean/std as extra column in output table. Maps to a command-line argument:
--snr.color_table_file (a 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_inputs (a boolean) – If running as a node, set this to True otherwise, this will copy the implicit inputs to the node directory.
cortex_vol_from_surf (a boolean) – Compute cortex volume from surf. Maps to a command-line argument:
--surf-ctx-vol.default_color_table (a 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.empty (a boolean) – Report on segmentations listed in the color table. Maps to a command-line argument:
--empty.environ (a 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:
{})etiv (a 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
etivorold-etiv.euler (a 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_wm (a boolean) – Exclude cortical gray and white matter. Maps to a command-line argument:
--excl-ctxgmwm.exclude_id (an integer) – Exclude seg id from report. Maps to a command-line argument:
--excludeid %d.frame (an integer) – Report stats on nth frame of input volume. Maps to a command-line argument:
--frame %d.gca_color_table (a 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_file (a 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_intensity (a 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_erode (an integer) – Erode mask by some amount. Maps to a command-line argument:
--maskerode %d.mask_file (a pathlike object or string representing an existing file) – Mask volume (same size as seg. Maps to a command-line argument:
--mask %s.mask_frame (an integer) – Mask with this (0 based) frame of the mask volume. Requires inputs:
mask_file.mask_invert (a 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_thresh (a float) – Binarize mask with this threshold <0.5>. Maps to a command-line argument:
--maskthresh %f.multiply (a float) – Multiply input by val. Maps to a command-line argument:
--mul %f.non_empty_only (a boolean) – Only report nonempty segmentations. Maps to a command-line argument:
--nonempty.partial_volume_file (a pathlike object or string representing an existing file) – Compensate for partial voluming. Maps to a command-line argument:
--pv %s.presurf_seg (a pathlike object or string representing an existing file) – Input segmentation volume.
segment_id (a list of items which are any value) – Manually specify segmentation ids. Maps to a command-line argument:
--id %s....sf_avg_file (a 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_gm (a boolean) – Compute volume of subcortical gray matter. Maps to a command-line argument:
--subcortgray.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
summary_file (a pathlike object or string representing a file) – Segmentation stats summary table file. Maps to a command-line argument:
--sum %s(position: -1).supratent (a boolean) – Undocumented input flag. Maps to a command-line argument:
--supratent.total_gray (a boolean) – Compute volume of total gray matter. Maps to a command-line argument:
--totalgray.vox (a 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_surf (a boolean) – Compute wm volume from surf. Maps to a command-line argument:
--surf-wm-vol.- Outputs:
avgwf_file (a pathlike object or string representing a file) – Volume with functional statistics averaged over segs.
avgwf_txt_file (a pathlike object or string representing a file) – Text file with functional statistics averaged over segs.
sf_avg_file (a pathlike object or string representing a file) – Text file with func statistics averaged over segs and framss.
summary_file (a 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:
SphericalAverage¶
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'
- Mandatory Inputs:
fname (a 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_surf (a pathlike object or string representing an existing file) – Input surface file. Maps to a command-line argument:
%s(position: -3).subject_id (a 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).- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a 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:
{})erode (an integer) – Undocumented. Maps to a command-line argument:
-erode %d.in_average (a pathlike object or string representing an existing directory) – Average subject. Maps to a command-line argument:
%s(position: -2).in_orig (a pathlike object or string representing an existing file) – Original surface filename. Maps to a command-line argument:
-orig %s.out_file (a pathlike object or string representing a file) – Output filename. Maps to a command-line argument:
%s(position: -1).subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
threshold (a float) – Undocumented. Maps to a command-line argument:
-t %.1f.- Outputs:
out_file (a pathlike object or string representing a file) – Output label.