niworkflows.interfaces.reportlets.segmentation module

ReportCapableInterfaces for segmentation tools.

class niworkflows.interfaces.reportlets.segmentation.FASTRPT(generate_report=False, **kwargs)

Bases: SegmentationRC, FAST

Wrapped executable: fast.

Mandatory Inputs:

in_files (a list of items which are a pathlike object or string representing an existing file) – Image, or multi-channel set of images, to be segmented. Maps to a command-line argument: %s (position: -1).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bias_iters (1 <= an integer <= 10) – Number of main-loop iterations during bias-field removal. Maps to a command-line argument: -I %d.

• bias_lowpass (4 <= an integer <= 40) – Bias field smoothing extent (FWHM) in mm. Maps to a command-line argument: -l %d.

• compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)

• 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: {})

• hyper (0.0 <= a floating point number <= 1.0) – Segmentation spatial smoothness. Maps to a command-line argument: -H %.2f.

• img_type (1 or 2 or 3) – Int specifying type of image: (1 = T1, 2 = T2, 3 = PD). Maps to a command-line argument: -t %d.

• init_seg_smooth (0.0001 <= a floating point number <= 0.1) – Initial segmentation spatial smoothness (during bias field estimation). Maps to a command-line argument: -f %.3f.

• init_transform (a pathlike object or string representing an existing file) – <standard2input.mat> initialise using priors. Maps to a command-line argument: -a %s.

• iters_afterbias (1 <= an integer <= 20) – Number of main-loop iterations after bias-field removal. Maps to a command-line argument: -O %d.

• manual_seg (a pathlike object or string representing an existing file) – Filename containing intensities. Maps to a command-line argument: -s %s.

• mixel_smooth (0.0 <= a floating point number <= 1.0) – Spatial smoothness for mixeltype. Maps to a command-line argument: -R %.2f.

• no_bias (a boolean) – Do not remove bias field. Maps to a command-line argument: -N.

• no_pve (a boolean) – Turn off PVE (partial volume estimation). Maps to a command-line argument: --nopve.

• number_classes (1 <= an integer <= 10) – Number of tissue-type classes. Maps to a command-line argument: -n %d.

• other_priors (a list of from 3 to 3 items which are a pathlike object or string representing a file) – Alternative prior images. Maps to a command-line argument: -A %s.

• out_basename (a pathlike object or string representing a file) – Base name of output files. Maps to a command-line argument: -o %s.

• out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)

• output_biascorrected (a boolean) – Output restored image (bias-corrected image). Maps to a command-line argument: -B.

• output_biasfield (a boolean) – Output estimated bias field. Maps to a command-line argument: -b.

• output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

• probability_maps (a boolean) – Outputs individual probability maps. Maps to a command-line argument: -p.

• segment_iters (1 <= an integer <= 50) – Number of segmentation-initialisation iterations. Maps to a command-line argument: -W %d.

• segments (a boolean) – Outputs a separate binary image for each tissue type. Maps to a command-line argument: -g.

• use_priors (a boolean) – Use priors throughout. Maps to a command-line argument: -P.

• verbose (a boolean) – Switch on diagnostic messages. Maps to a command-line argument: -v.

Outputs:

• bias_field (a list of items which are a pathlike object or string representing a file)

• mixeltype (a pathlike object or string representing a file) – Path/name of mixeltype volume file _mixeltype.

• out_report (a pathlike object or string representing a file) – Filename for the visual report.

• partial_volume_files (a list of items which are a pathlike object or string representing a file)

• partial_volume_map (a pathlike object or string representing a file) – Path/name of partial volume file _pveseg.

• probability_maps (a list of items which are a pathlike object or string representing a file)

• restored_image (a list of items which are a pathlike object or string representing a file)

• tissue_class_files (a list of items which are a pathlike object or string representing a file)

• tissue_class_map (a pathlike object or string representing an existing file) – Path/name of binary segmented volume file one val for each class _seg.

class niworkflows.interfaces.reportlets.segmentation.ICA_AROMARPT(generate_report=False, **kwargs)

Bases: ReportCapableInterface, ICA_AROMA

Wrapped executable: ICA_AROMA.py.

Mandatory Inputs:

• denoise_type (‘nonaggr’ or ‘aggr’ or ‘both’ or ‘no’) – Type of denoising strategy: -no: only classification, no denoising -nonaggr (default): non-aggresssive denoising, i.e. partial component regression -aggr: aggressive denoising, i.e. full component regression -both: both aggressive and non-aggressive denoising (two outputs). Maps to a command-line argument: -den %s. (Nipype default value: nonaggr)

• feat_dir (a pathlike object or string representing an existing directory) – If a feat directory exists and temporal filtering has not been run yet, ICA_AROMA can use the files in this directory. Maps to a command-line argument: -feat %s. Mutually exclusive with inputs: in_file, mat_file, fnirt_warp_file, motion_parameters.

• in_file (a pathlike object or string representing an existing file) – Volume to be denoised. Maps to a command-line argument: -i %s. Mutually exclusive with inputs: feat_dir.

• motion_parameters (a pathlike object or string representing an existing file) – Motion parameters file. Maps to a command-line argument: -mc %s. Mutually exclusive with inputs: feat_dir.

• out_dir (a pathlike object or string representing a directory) – Output directory. Maps to a command-line argument: -o %s. (Nipype default value: out)

Optional Inputs:

• TR (a float) – TR in seconds. If this is not specified the TR will be extracted from the header of the fMRI nifti file. Maps to a command-line argument: -tr %.3f.

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)

• dim (an integer) – Dimensionality reduction when running MELODIC (default is automatic estimation). Maps to a command-line argument: -dim %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: {})

• fnirt_warp_file (a pathlike object or string representing an existing file) – File name of the warp-file describing the non-linear registration (e.g. FSL FNIRT) of the structural data to MNI152 space (.nii.gz). Maps to a command-line argument: -warp %s. Mutually exclusive with inputs: feat_dir.

• mask (a pathlike object or string representing an existing file) – Path/name volume mask. Maps to a command-line argument: -m %s. Mutually exclusive with inputs: feat_dir.

• mat_file (a pathlike object or string representing an existing file) – Path/name of the mat-file describing the affine registration (e.g. FSL FLIRT) of the functional data to structural space (.mat file). Maps to a command-line argument: -affmat %s. Mutually exclusive with inputs: feat_dir.

• melodic_dir (a pathlike object or string representing an existing directory) – Path to MELODIC directory if MELODIC has already been run. Maps to a command-line argument: -meldir %s.

• out_report (a pathlike object or string representing a file) – Filename for the visual report generated by Nipype. (Nipype default value: ica_aroma_reportlet.svg)

• report_mask (a pathlike object or string representing a file) – Mask used to draw the outline on the reportlet. If not set the mask will be derived from the data.

Outputs:

• aggr_denoised_file (a pathlike object or string representing an existing file) – If generated: aggressively denoised volume.

• nonaggr_denoised_file (a pathlike object or string representing an existing file) – If generated: non aggressively denoised volume.

• out_dir (a pathlike object or string representing an existing directory) – Directory contains (in addition to the denoised files): melodic.ica + classified_motion_components + classification_overview + feature_scores + melodic_ic_mni).

• out_report (a pathlike object or string representing a file) – Filename for the visual report.

class niworkflows.interfaces.reportlets.segmentation.MELODICRPT(generate_report=False, **kwargs)

Bases: MELODIC

Wrapped executable: melodic.

Mandatory Inputs:

in_files (a list of items which are a pathlike object or string representing an existing file) – Input file names (either single file name or a list). Maps to a command-line argument: -i %s (position: 0).

Optional Inputs:

• ICs (a pathlike object or string representing an existing file) – Filename of the IC components file for mixture modelling. Maps to a command-line argument: --ICs=%s.

• approach (a string) – Approach for decomposition, 2D: defl, symm (default), 3D: tica (default), concat. Maps to a command-line argument: -a %s.

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bg_image (a pathlike object or string representing an existing file) – Specify background image for report (default: mean image). Maps to a command-line argument: --bgimage=%s.

• bg_threshold (a float) – Brain/non-brain threshold used to mask non-brain voxels, as a percentage (only if –nobet selected). Maps to a command-line argument: --bgthreshold=%f.

• compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)

• cov_weight (a float) – Voxel-wise weights for the covariance matrix (e.g. segmentation information). Maps to a command-line argument: --covarweight=%f.

• dim (an integer) – Dimensionality reduction into #num dimensions (default: automatic estimation). Maps to a command-line argument: -d %d.

• dim_est (a string) – Use specific dim. estimation technique: lap, bic, mdl, aic, mean (default: lap). Maps to a command-line argument: --dimest=%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: {})

• epsilon (a float) – Minimum error change. Maps to a command-line argument: --eps=%f.

• epsilonS (a float) – Minimum error change for rank-1 approximation in TICA. Maps to a command-line argument: --epsS=%f.

• log_power (a boolean) – Calculate log of power for frequency spectrum. Maps to a command-line argument: --logPower.

• mask (a pathlike object or string representing an existing file) – File name of mask for thresholding. Maps to a command-line argument: -m %s.

• max_restart (an integer) – Maximum number of restarts. Maps to a command-line argument: --maxrestart=%d.

• maxit (an integer) – Maximum number of iterations before restart. Maps to a command-line argument: --maxit=%d.

• migp (a boolean) – Switch on MIGP data reduction. Maps to a command-line argument: --migp.

• migpN (an integer) – Number of internal Eigenmaps. Maps to a command-line argument: --migpN %d.

• migp_factor (an integer) – Internal Factor of mem-threshold relative to number of Eigenmaps (default: 2). Maps to a command-line argument: --migp_factor %d.

• migp_shuffle (a boolean) – Randomise MIGP file order (default: TRUE). Maps to a command-line argument: --migp_shuffle.

• mix (a pathlike object or string representing an existing file) – Mixing matrix for mixture modelling / filtering. Maps to a command-line argument: --mix=%s.

• mm_thresh (a float) – Threshold for Mixture Model based inference. Maps to a command-line argument: --mmthresh=%f.

• no_bet (a boolean) – Switch off BET. Maps to a command-line argument: --nobet.

• no_mask (a boolean) – Switch off masking. Maps to a command-line argument: --nomask.

• no_mm (a boolean) – Switch off mixture modelling on IC maps. Maps to a command-line argument: --no_mm.

• non_linearity (a string) – Nonlinearity: gauss, tanh, pow3, pow4. Maps to a command-line argument: --nl=%s.

• num_ICs (an integer) – Number of IC’s to extract (for deflation approach). Maps to a command-line argument: -n %d.

• out_all (a boolean) – Output everything. Maps to a command-line argument: --Oall.

• out_dir (a pathlike object or string representing a directory) – Output directory name. Maps to a command-line argument: -o %s.

• out_mean (a boolean) – Output mean volume. Maps to a command-line argument: --Omean.

• out_orig (a boolean) – Output the original ICs. Maps to a command-line argument: --Oorig.

• out_pca (a boolean) – Output PCA results. Maps to a command-line argument: --Opca.

• out_report (a pathlike object or string representing a file) – Filename for the visual report generated by Nipype. (Nipype default value: melodic_reportlet.svg)

• out_stats (a boolean) – Output thresholded maps and probability maps. Maps to a command-line argument: --Ostats.

• out_unmix (a boolean) – Output unmixing matrix. Maps to a command-line argument: --Ounmix.

• out_white (a boolean) – Output whitening/dewhitening matrices. Maps to a command-line argument: --Owhite.

• output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’ or ‘GIFTI’) – FSL output type.

• pbsc (a boolean) – Switch off conversion to percent BOLD signal change. Maps to a command-line argument: --pbsc.

• rem_cmp (a list of items which are an integer) – Component numbers to remove. Maps to a command-line argument: -f %d.

• remove_deriv (a boolean) – Removes every second entry in paradigm file (EV derivatives). Maps to a command-line argument: --remove_deriv.

• report (a boolean) – Generate Melodic web report. Maps to a command-line argument: --report.

• report_maps (a string) – Control string for spatial map images (see slicer). Maps to a command-line argument: --report_maps=%s.

• report_mask (a pathlike object or string representing a file) – Mask used to draw the outline on the reportlet. If not set the mask will be derived from the data.

• s_con (a pathlike object or string representing an existing file) – T-contrast matrix across subject-domain. Maps to a command-line argument: --Scon=%s.

• s_des (a pathlike object or string representing an existing file) – Design matrix across subject-domain. Maps to a command-line argument: --Sdes=%s.

• sep_vn (a boolean) – Switch off joined variance normalization. Maps to a command-line argument: --sep_vn.

• sep_whiten (a boolean) – Switch on separate whitening. Maps to a command-line argument: --sep_whiten.

• smode (a pathlike object or string representing an existing file) – Matrix of session modes for report generation. Maps to a command-line argument: --smode=%s.

• t_con (a pathlike object or string representing an existing file) – T-contrast matrix across time-domain. Maps to a command-line argument: --Tcon=%s.

• t_des (a pathlike object or string representing an existing file) – Design matrix across time-domain. Maps to a command-line argument: --Tdes=%s.

• tr_sec (a float) – TR in seconds. Maps to a command-line argument: --tr=%f.

• update_mask (a boolean) – Switch off mask updating. Maps to a command-line argument: --update_mask.

• var_norm (a boolean) – Switch off variance normalization. Maps to a command-line argument: --vn.

Outputs:

• out_dir (a pathlike object or string representing an existing directory)

• out_report (a pathlike object or string representing a file) – Filename for the visual report.

• report_dir (a pathlike object or string representing an existing directory)

class niworkflows.interfaces.reportlets.segmentation.ReconAllRPT(generate_report=False, **kwargs)

Bases: SurfaceSegmentationRC, ReconAll

Wrapped executable: recon-all.

Optional Inputs:

• FLAIR_file (a pathlike object or string representing an existing file) – Convert FLAIR image to orig directory. Maps to a command-line argument: -FLAIR %s. Requires inputs: subject_id.

• T1_files (a list of items which are a pathlike object or string representing an existing file) – Name of T1 file to process. Maps to a command-line argument: -i %s.... Requires inputs: subject_id.

• T2_file (a pathlike object or string representing an existing file) – Convert T2 image to orig directory. Maps to a command-line argument: -T2 %s. Requires inputs: subject_id.

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• base_template_id (a string) – Base template id. Maps to a command-line argument: -base %s. Mutually exclusive with inputs: subject_id, longitudinal_timepoint_id. Requires inputs: base_timepoint_ids.

• base_timepoint_ids (a list of items which are a string) – Processed timepoint to use in template. Maps to a command-line argument: -base-tp %s....

• big_ventricles (a boolean) – For use in subjects with enlarged ventricles. Maps to a command-line argument: -bigventricles.

• brainstem (a boolean) – Segment brainstem structures. Maps to a command-line argument: -brainstem-structures. Requires inputs: subject_id.

• compress_report (‘auto’ or True or False) – Compress the reportlet using SVGO orWEBP. ‘auto’ - compress if relevant software is installed, True = force,False - don’t attempt to compress. (Nipype default value: auto)

• directive (‘all’ or ‘autorecon1’ or ‘autorecon2’ or ‘autorecon2-volonly’ or ‘autorecon2-perhemi’ or ‘autorecon2-inflate1’ or ‘autorecon2-cp’ or ‘autorecon2-wm’ or ‘autorecon3’ or ‘autorecon3-T2pial’ or ‘autorecon-pial’ or ‘autorecon-hemi’ or ‘localGI’ or ‘qcache’) – Process directive. Maps to a command-line argument: -%s (position: 0). (Nipype default value: all)

• 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: {})

• expert (a pathlike object or string representing an existing file) – Set parameters using expert file. Maps to a command-line argument: -expert %s.

• flags (a list of items which are a string) – Additional parameters. Maps to a command-line argument: %s.

• hemi (‘lh’ or ‘rh’) – Hemisphere to process. Maps to a command-line argument: -hemi %s. Requires inputs: subject_id.

• hippocampal_subfields_T1 (a boolean) – Segment hippocampal subfields using input T1 scan. Maps to a command-line argument: -hippocampal-subfields-T1. Requires inputs: subject_id.

• hippocampal_subfields_T2 (a tuple of the form: (a pathlike object or string representing an existing file, a string)) – Segment hippocampal subfields using T2 scan, identified by ID (may be combined with hippocampal_subfields_T1). Maps to a command-line argument: -hippocampal-subfields-T2 %s %s. Requires inputs: subject_id.

• hires (a boolean) – Conform to minimum voxel size (for voxels < 1mm). Maps to a command-line argument: -hires.

• longitudinal_template_id (a string) – Longitudinal base template id. Maps to a command-line argument: %s (position: 2).

• longitudinal_timepoint_id (a string) – Longitudinal session/timepoint id. Maps to a command-line argument: -long %s (position: 1). Mutually exclusive with inputs: subject_id, base_template_id. Requires inputs: longitudinal_template_id.

• mprage (a boolean) – Assume scan parameters are MGH MP-RAGE protocol, which produces darker gray matter. Maps to a command-line argument: -mprage. Requires inputs: subject_id.

• mri_aparc2aseg (a string) – Flags to pass to mri_aparc2aseg commands. Mutually exclusive with inputs: expert.

• mri_ca_label (a string) – Flags to pass to mri_ca_label commands. Mutually exclusive with inputs: expert.

• mri_ca_normalize (a string) – Flags to pass to mri_ca_normalize commands. Mutually exclusive with inputs: expert.

• mri_ca_register (a string) – Flags to pass to mri_ca_register commands. Mutually exclusive with inputs: expert.

• mri_edit_wm_with_aseg (a string) – Flags to pass to mri_edit_wm_with_aseg commands. Mutually exclusive with inputs: expert.

• mri_em_register (a string) – Flags to pass to mri_em_register commands. Mutually exclusive with inputs: expert.

• mri_fill (a string) – Flags to pass to mri_fill commands. Mutually exclusive with inputs: expert.

• mri_mask (a string) – Flags to pass to mri_mask commands. Mutually exclusive with inputs: expert.

• mri_normalize (a string) – Flags to pass to mri_normalize commands. Mutually exclusive with inputs: expert.

• mri_pretess (a string) – Flags to pass to mri_pretess commands. Mutually exclusive with inputs: expert.

• mri_remove_neck (a string) – Flags to pass to mri_remove_neck commands. Mutually exclusive with inputs: expert.

• mri_segment (a string) – Flags to pass to mri_segment commands. Mutually exclusive with inputs: expert.

• mri_segstats (a string) – Flags to pass to mri_segstats commands. Mutually exclusive with inputs: expert.

• mri_tessellate (a string) – Flags to pass to mri_tessellate commands. Mutually exclusive with inputs: expert.

• mri_watershed (a string) – Flags to pass to mri_watershed commands. Mutually exclusive with inputs: expert.

• mris_anatomical_stats (a string) – Flags to pass to mris_anatomical_stats commands. Mutually exclusive with inputs: expert.

• mris_ca_label (a string) – Flags to pass to mris_ca_label commands. Mutually exclusive with inputs: expert.

• mris_fix_topology (a string) – Flags to pass to mris_fix_topology commands. Mutually exclusive with inputs: expert.

• mris_inflate (a string) – Flags to pass to mri_inflate commands. Mutually exclusive with inputs: expert.

• mris_make_surfaces (a string) – Flags to pass to mris_make_surfaces commands. Mutually exclusive with inputs: expert.

• mris_register (a string) – Flags to pass to mris_register commands. Mutually exclusive with inputs: expert.

• mris_smooth (a string) – Flags to pass to mri_smooth commands. Mutually exclusive with inputs: expert.

• mris_sphere (a string) – Flags to pass to mris_sphere commands. Mutually exclusive with inputs: expert.

• mris_surf2vol (a string) – Flags to pass to mris_surf2vol commands. Mutually exclusive with inputs: expert.

• mrisp_paint (a string) – Flags to pass to mrisp_paint commands. Mutually exclusive with inputs: expert.

• openmp (an integer) – Number of processors to use in parallel. Maps to a command-line argument: -openmp %d.

• out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value: report.svg)

• parallel (a boolean) – Enable parallel execution. Maps to a command-line argument: -parallel.

• subject_id (a string) – Subject name. Maps to a command-line argument: -subjid %s. Mutually exclusive with inputs: base_template_id, longitudinal_timepoint_id.

• subjects_dir (a pathlike object or string representing an existing directory) – Path to subjects directory. Maps to a command-line argument: -sd %s.

• talairach (a string) – Flags to pass to talairach commands. Mutually exclusive with inputs: expert.

• use_FLAIR (a boolean) – Use FLAIR image to refine the pial surface. Maps to a command-line argument: -FLAIRpial. Mutually exclusive with inputs: use_T2.

• use_T2 (a boolean) – Use T2 image to refine the pial surface. Maps to a command-line argument: -T2pial. Mutually exclusive with inputs: use_FLAIR.

• xopts (‘use’ or ‘clean’ or ‘overwrite’) – Use, delete or overwrite existing expert options file. Maps to a command-line argument: -xopts-%s.

Outputs:

• BA_stats (a list of items which are a pathlike object or string representing an existing file) – Brodmann Area statistics files.

• T1 (a pathlike object or string representing an existing file) – Intensity normalized whole-head volume.

• annot (a list of items which are a pathlike object or string representing an existing file) – Surface annotation files.

• aparc_a2009s_stats (a list of items which are a pathlike object or string representing an existing file) – Aparc a2009s parcellation statistics files.

• aparc_aseg (a list of items which are a pathlike object or string representing an existing file) – Aparc parcellation projected into aseg volume.

• aparc_stats (a list of items which are a pathlike object or string representing an existing file) – Aparc parcellation statistics files.

• area_pial (a list of items which are a pathlike object or string representing an existing file) – Mean area of triangles each vertex on the pial surface is associated with.

• aseg (a pathlike object or string representing an existing file) – Volumetric map of regions from automatic segmentation.

• aseg_stats (a list of items which are a pathlike object or string representing an existing file) – Automated segmentation statistics file.

• avg_curv (a list of items which are a pathlike object or string representing an existing file) – Average atlas curvature, sampled to subject.

• brain (a pathlike object or string representing an existing file) – Intensity normalized brain-only volume.

• brainmask (a pathlike object or string representing an existing file) – Skull-stripped (brain-only) volume.

• curv (a list of items which are a pathlike object or string representing an existing file) – Maps of surface curvature.

• curv_pial (a list of items which are a pathlike object or string representing an existing file) – Curvature of pial surface.

• curv_stats (a list of items which are a pathlike object or string representing an existing file) – Curvature statistics files.

• entorhinal_exvivo_stats (a list of items which are a pathlike object or string representing an existing file) – Entorhinal exvivo statistics files.

• filled (a pathlike object or string representing an existing file) – Subcortical mass volume.

• graymid (a list of items which are a pathlike object or string representing an existing file) – Graymid/midthickness surface meshes.

• inflated (a list of items which are a pathlike object or string representing an existing file) – Inflated surface meshes.

• jacobian_white (a list of items which are a pathlike object or string representing an existing file) – Distortion required to register to spherical atlas.

• label (a list of items which are a pathlike object or string representing an existing file) – Volume and surface label files.

• norm (a pathlike object or string representing an existing file) – Normalized skull-stripped volume.

• nu (a pathlike object or string representing an existing file) – Non-uniformity corrected whole-head volume.

• orig (a pathlike object or string representing an existing file) – Base image conformed to Freesurfer space.

• out_report (a pathlike object or string representing a file) – Filename for the visual report.

• pial (a list of items which are a pathlike object or string representing an existing file) – Gray matter/pia matter surface meshes.

• rawavg (a pathlike object or string representing an existing file) – Volume formed by averaging input images.

• ribbon (a list of items which are a pathlike object or string representing an existing file) – Volumetric maps of cortical ribbons.

• smoothwm (a list of items which are a pathlike object or string representing an existing file) – Smoothed original surface meshes.

• sphere (a list of items which are a pathlike object or string representing an existing file) – Spherical surface meshes.

• sphere_reg (a list of items which are a pathlike object or string representing an existing file) – Spherical registration file.

• subject_id (a string) – Subject name for whom to retrieve data.

• subjects_dir (a pathlike object or string representing an existing directory) – Freesurfer subjects directory.

• sulc (a list of items which are a pathlike object or string representing an existing file) – Surface maps of sulcal depth.

• thickness (a list of items which are a pathlike object or string representing an existing file) – Surface maps of cortical thickness.

• volume (a list of items which are a pathlike object or string representing an existing file) – Surface maps of cortical volume.

• white (a list of items which are a pathlike object or string representing an existing file) – White/gray matter surface meshes.

• wm (a pathlike object or string representing an existing file) – Segmented white-matter volume.

• wmparc (a pathlike object or string representing an existing file) – Aparc parcellation projected into subcortical white matter.

• wmparc_stats (a list of items which are a pathlike object or string representing an existing file) – White matter parcellation statistics file.