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# nipype.interfaces.freesurfer.petsurfer module

Provides interfaces to various commands for running PET analyses provided by FreeSurfer

## GTMPVC

Link to code

> Bases: FSCommand

> Wrapped executable: `mri_gtmpvc`.

> Perform Partial Volume Correction (PVC) to PET Data.

> Examples

>     >>> gtmpvc = GTMPVC()
>     >>> gtmpvc.inputs.in_file = 'sub-01_ses-baseline_pet.nii.gz'
>     >>> gtmpvc.inputs.segmentation = 'gtmseg.mgz'
>     >>> gtmpvc.inputs.reg_file = 'sub-01_ses-baseline_pet_mean_reg.lta'
>     >>> gtmpvc.inputs.pvc_dir = 'pvc'
>     >>> gtmpvc.inputs.psf = 4
>     >>> gtmpvc.inputs.default_seg_merge = True
>     >>> gtmpvc.inputs.auto_mask = (1, 0.1)
>     >>> gtmpvc.inputs.km_ref = ['8 47']
>     >>> gtmpvc.inputs.km_hb = ['11 12 50 51']
>     >>> gtmpvc.inputs.no_rescale = True
>     >>> gtmpvc.inputs.save_input = True
>     >>> gtmpvc.cmdline
>     'mri_gtmpvc --auto-mask 1.000000 0.100000 --default-seg-merge     --i sub-01_ses-baseline_pet.nii.gz --km-hb 11 12 50 51 --km-ref 8 47 --no-rescale     --psf 4.000000 --o pvc --reg sub-01_ses-baseline_pet_mean_reg.lta --save-input     --seg gtmseg.mgz'

>     >>> gtmpvc = GTMPVC()
>     >>> gtmpvc.inputs.in_file = 'sub-01_ses-baseline_pet.nii.gz'
>     >>> gtmpvc.inputs.segmentation = 'gtmseg.mgz'
>     >>> gtmpvc.inputs.regheader = True
>     >>> gtmpvc.inputs.pvc_dir = 'pvc'
>     >>> gtmpvc.inputs.mg = (0.5, ["ROI1", "ROI2"])
>     >>> gtmpvc.cmdline
>     'mri_gtmpvc --i sub-01_ses-baseline_pet.nii.gz --mg 0.5 ROI1 ROI2 --o pvc --regheader --seg gtmseg.mgz'

> in_filea pathlike object or string representing an existing file

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

> reg_filea pathlike object or string representing an existing file

>   LTA registration file that maps PET to anatomical. Maps to a command-line argument: `--reg %s`. Mutually exclusive with inputs: `reg_file`, `regheader`, `reg_identity`.

> reg_identitya boolean

>   Assume that input is in anatomical space. Maps to a command-line argument: `--reg-identity`. Mutually exclusive with inputs: `reg_file`, `regheader`, `reg_identity`.

> regheadera boolean

>   Assume input and seg share scanner space. Maps to a command-line argument: `--regheader`. Mutually exclusive with inputs: `reg_file`, `regheader`, `reg_identity`.

> segmentationa pathlike object or string representing an existing file

>   Segfile : anatomical segmentation to define regions for GTM. Maps to a command-line argument: `--seg %s`.

> Xa boolean

>   Save X matrix in matlab4 format as X.mat (it will be big). Maps to a command-line argument: `--X`.

> X0a boolean

>   Save X0 matrix in matlab4 format as X0.mat (it will be big). Maps to a command-line argument: `--X0`.

> argsa string

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

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

>   FWHM thresh : automatically compute mask. Maps to a command-line argument: `--auto-mask %f %f`.

> betaa boolean

>   Save beta matrix in matlab4 format as beta.mat. Maps to a command-line argument: `--beta`.

> color_table_filea pathlike object or string representing an existing file

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

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

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

> default_color_tablea boolean

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

> default_seg_mergea boolean

>   Default schema for merging ROIs. Maps to a command-line argument: `--default-seg-merge`.

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

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

> framean integer

>   Only process 0-based frame F from inputvol. Maps to a command-line argument: `--frame %i`.

> km_hba list of items which are any value

>   RefId1 RefId2 … : compute HiBinding TAC for KM as mean of given RefIds. Maps to a command-line argument: `--km-hb %s...`.

> km_refa list of items which are any value

>   RefId1 RefId2 … : compute reference TAC for KM as mean of given RefIds. Maps to a command-line argument: `--km-ref %s...`.

> lata boolean

>   Lateralize tissue types. Maps to a command-line argument: `--lat`.

> mask_filea pathlike object or string representing an existing file

>   Ignore areas outside of the mask (in input vol space). Maps to a command-line argument: `--mask %s`.

> merge_cblum_wm_gyria boolean

>   Cerebellum WM gyri back into cerebellum WM. Maps to a command-line argument: `--merge-cblum-wm-gyri`.

> merge_hyposa boolean

>   Merge left and right hypointensites into to ROI. Maps to a command-line argument: `--merge-hypos`.

> mga tuple of the form: (a float, a list of items which are a string)

>   Gmthresh RefId1 RefId2 …: perform Mueller-Gaertner PVC, gmthresh is min gm pvf bet 0 and 1. Maps to a command-line argument: `--mg %g %s`.

> mg_ref_cerebral_wma boolean

>   > set MG RefIds to 2 and 41.

>   Maps to a command-line argument: `--mg-ref-cerebral-wm`.

> mg_ref_lobes_wma boolean

>   Set MG RefIds to those for lobes when using wm subseg. Maps to a command-line argument: `--mg-ref-lobes-wm`.

> mgxa float

>   Gmxthresh : GLM-based Mueller-Gaertner PVC, gmxthresh is min gm pvf bet 0 and 1. Maps to a command-line argument: `--mgx %f`.

> no_pvca boolean

>   Turns off PVC entirely (both PSF and TFE). Maps to a command-line argument: `--no-pvc`.

> no_reduce_fova boolean

>   Do not reduce FoV to encompass mask. Maps to a command-line argument: `--no-reduce-fov`.

> no_rescalea boolean

>   Do not global rescale such that mean of reference region is scaleref. Maps to a command-line argument: `--no-rescale`.

> no_tfea boolean

>   Do not correct for tissue fraction effect (with –psf 0 turns off PVC entirely). Maps to a command-line argument: `--no-tfe`.

> num_threadsan integer

>   Threads : number of threads to use. Maps to a command-line argument: `--threads %i`.

> opt_braina boolean

>   Apply adaptive GTM. Maps to a command-line argument: `--opt-brain`.

> opt_seg_mergea boolean

>   Optimal schema for merging ROIs when applying adaptive GTM. Maps to a command-line argument: `--opt-seg-merge`.

> opt_tola tuple of the form: (an integer, a float, a float)

>   N_iters_max ftol lin_min_tol : optimization parameters for adaptive gtm using fminsearch. Maps to a command-line argument: `--opt-tol %i %f %f`.

> optimization_schema‘3D’ or ‘2D’ or ‘1D’ or ‘3D_MB’ or ‘2D_MB’ or ‘1D_MB’ or ‘MBZ’ or ‘MB3’

>   Opt : optimization schema for applying adaptive GTM. Maps to a command-line argument: `--opt %s`.

> psfa float

>   Scanner PSF FWHM in mm. Maps to a command-line argument: `--psf %f`.

> psf_cola float

>   XFWHM : full-width-half-maximum in the x-direction. Maps to a command-line argument: `--psf-col %f`.

> psf_rowa float

>   YFWHM : full-width-half-maximum in the y-direction. Maps to a command-line argument: `--psf-row %f`.

> psf_slicea float

>   ZFWHM : full-width-half-maximum in the z-direction. Maps to a command-line argument: `--psf-slice %f`.

> pvc_dira string

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

> rbva boolean

>   Perform Region-based Voxelwise (RBV) PVC. Maps to a command-line argument: `--rbv`. Requires inputs: `subjects_dir`.

> rbv_resa float

>   Voxsize : set RBV voxel resolution (good for when standard res takes too much memory). Maps to a command-line argument: `--rbv-res %f`.

> reduce_fox_eqodda boolean

>   Reduce FoV to encompass mask but force nc=nr and ns to be odd. Maps to a command-line argument: `--reduce-fox-eqodd`.

> replacea tuple of the form: (an integer, an integer)

>   Id1 Id2 : replace seg Id1 with seg Id2. Maps to a command-line argument: `--replace %i %i`.

> rescalea list of items which are any value

>   Id1 <Id2…> : specify reference region(s) used to rescale (default is pons). Maps to a command-line argument: `--rescale %s...`.

> save_eresa boolean

>   Saves residual error. Maps to a command-line argument: `--save-eres`.

> save_inputa boolean

>   Saves rescaled input as input.rescaled.nii.gz. Maps to a command-line argument: `--save-input`.

> save_yhata boolean

>   Save signal estimate (yhat) smoothed with the PSF. Maps to a command-line argument: `--save-yhat`. Mutually exclusive with inputs: `save_yhat_with_noise`.

> save_yhat0a boolean

>   Save signal estimate (yhat). Maps to a command-line argument: `--save-yhat0`.

> save_yhat_full_fova boolean

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

> save_yhat_with_noisea tuple of the form: (an integer, an integer)

>   Seed nreps : save signal estimate (yhat) with noise. Maps to a command-line argument: `--save-yhat-with-noise %i %i`. Mutually exclusive with inputs: `save_yhat`.

> scale_refvala float

>   Refval : scale such that mean in reference region is refval. Maps to a command-line argument: `--scale-refval %f`.

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

>   Bpc scale dcf : steady-state analysis spec blood plasma concentration, unit scale and decay correction factor. You must also spec –km-ref. Turns off rescaling. Maps to a command-line argument: `--ss %f %f %f`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> tissue_fraction_resolutiona float

>   Set the tissue fraction resolution parameter (def is 0.5). Maps to a command-line argument: `--segpvfres %f`.

> tt_reducea boolean

>   Reduce segmentation to that of a tissue type. Maps to a command-line argument: `--tt-reduce`.

> tt_updatea boolean

>   Changes tissue type of VentralDC, BrainStem, and Pons to be SubcortGM. Maps to a command-line argument: `--tt-update`.

> ya boolean

>   Save y matrix in matlab4 format as y.mat. Maps to a command-line argument: `--y`.

> eresa pathlike object or string representing a file

>   4D PET file of residual error after PVC (smoothed with PSF).

> gtm_filea pathlike object or string representing a file

>   TACs for all regions with GTM PVC.

> gtm_statsa pathlike object or string representing a file

>   Statistics for the GTM PVC.

> hb_data pathlike object or string representing a file

>   High-binding TAC in .dat.

> hb_niftia pathlike object or string representing a file

>   High-binding TAC in nifti.

> input_filea pathlike object or string representing a file

>   4D PET file in native volume space.

> mgx_ctxgma pathlike object or string representing a file

>   Cortical GM voxel-wise values corrected using the extended Muller-Gartner method.

> mgx_gma pathlike object or string representing a file

>   All GM voxel-wise values corrected using the extended Muller-Gartner method.

> mgx_subctxgma pathlike object or string representing a file

>   Subcortical GM voxel-wise values corrected using the extended Muller-Gartner method.

> nopvc_filea pathlike object or string representing a file

>   TACs for all regions with no PVC.

> opt_paramsa pathlike object or string representing a file

>   Optimal parameter estimates for the FWHM using adaptive GTM.

> pvc_dira pathlike object or string representing a directory

>   Output directory.

> rbva pathlike object or string representing a file

>   All GM voxel-wise values corrected using the RBV method.

> ref_filea pathlike object or string representing a file

>   Reference TAC in .dat.

> reg_anat2peta pathlike object or string representing a file

>   Registration file to go from anat to PET.

> reg_anat2rbvpeta pathlike object or string representing a file

>   Registration file to go from anat to RBV corrected PET.

> reg_pet2anata pathlike object or string representing a file

>   Registration file to go from PET to anat.

> reg_rbvpet2anata pathlike object or string representing a file

>   Registration file to go from RBV corrected PET to anat.

> sega pathlike object or string representing a file

>   Segmentation file of regions used for PVC.

> seg_ctaba pathlike object or string representing a file

>   Color table file for segmentation file.

> tissue_fractiona pathlike object or string representing a file

>   4D PET file of tissue fraction before PVC.

> tissue_fraction_psfa pathlike object or string representing a file

>   4D PET file of tissue fraction after PVC (smoothed with PSF).

> yhata pathlike object or string representing a file

>   4D PET file of signal estimate (yhat) after PVC (smoothed with PSF).

> yhat0a pathlike object or string representing a file

>   4D PET file of signal estimate (yhat) after PVC (unsmoothed).

> yhat_full_fova pathlike object or string representing a file

>   4D PET file with full FOV of signal estimate (yhat) after PVC (smoothed with PSF).

> yhat_with_noisea pathlike object or string representing a file

>   4D PET file with full FOV of signal estimate (yhat) with noise after PVC (smoothed with PSF).

## GTMSeg

Link to code

> Bases: FSCommand

> Wrapped executable: `gtmseg`.

> create an anatomical segmentation for the geometric transfer matrix (GTM).

> Examples

>     >>> gtmseg = GTMSeg()
>     >>> gtmseg.inputs.subject_id = 'subject_id'
>     >>> gtmseg.cmdline
>     'gtmseg --o gtmseg.mgz --s subject_id'

> subject_ida string

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

> argsa string

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

> colortablea pathlike object or string representing an existing file

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

> ctx_annota tuple of the form: (a string, an integer, an integer)

>   Annot lhbase rhbase : annotation to use for cortical segmentation (default is aparc 1000 2000). Maps to a command-line argument: `--ctx-annot %s %i %i`.

> dmaxa float

>   Distance threshold to use when subsegmenting WM (default is 5). Maps to a command-line argument: `--dmax %f`.

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

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

> heada string

>   Use headseg instead of apas+head.mgz. Maps to a command-line argument: `--head %s`.

> keep_cca boolean

>   Do not relabel corpus callosum as WM. Maps to a command-line argument: `--keep-cc`.

> keep_hypoa boolean

>   Do not relabel hypointensities as WM when subsegmenting WM. Maps to a command-line argument: `--keep-hypo`.

> no_ponsa boolean

>   Do not add pons segmentation when doing —xcerseg. Maps to a command-line argument: `--no-pons`.

> no_seg_statsa boolean

>   Do not compute segmentation stats. Maps to a command-line argument: `--no-seg-stats`.

> no_vermisa boolean

>   Do not add vermis segmentation when doing —xcerseg. Maps to a command-line argument: `--no-vermis`.

> out_filea pathlike object or string representing a file

>   Output volume relative to subject/mri. Maps to a command-line argument: `--o %s`. (Nipype default value: `gtmseg.mgz`)

> output_upsampling_factoran integer

>   Set output USF different than USF, mostly for debugging. Maps to a command-line argument: `--output-usf %i`.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> subseg_cblum_wma boolean

>   Subsegment cerebellum WM into core and gyri. Maps to a command-line argument: `--subseg-cblum-wm`.

> subsegwma boolean

>   Subsegment WM into lobes (default). Maps to a command-line argument: `--subsegwm`.

> upsampling_factoran integer

>   Upsampling factor (default is 2). Maps to a command-line argument: `--usf %i`.

> wm_annota tuple of the form: (a string, an integer, an integer)

>   Annot lhbase rhbase : annotation to use for WM segmentation (with –subsegwm, default is lobes 3200 4200). Maps to a command-line argument: `--wm-annot %s %i %i`.

> xcersega boolean

>   Run xcerebralseg on this subject to create apas+head.mgz. Maps to a command-line argument: `--xcerseg`.

> out_filea pathlike object or string representing a file

>   GTM segmentation.

## Logan

Link to code

> Bases: GLMFit

> Wrapped executable: `mri_glmfit`.

> Perform Logan kinetic modeling. .. rubric:: Examples

>     >>> logan = Logan()
>     >>> logan.inputs.in_file = 'tac.nii'
>     >>> logan.inputs.logan = ('ref_tac.dat', 'timing.dat', 2600)
>     >>> logan.inputs.glm_dir = 'logan'
>     >>> logan.cmdline
>     'mri_glmfit --glmdir logan --y tac.nii --logan ref_tac.dat timing.dat 2600'

> in_filea pathlike object or string representing a file

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

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

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

> allow_ill_conda boolean

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

> allow_repeated_subjectsa boolean

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

> argsa string

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

> bp_clip_maxa float

>   Set BP voxels above max to max. Maps to a command-line argument: `--bp-clip-max %f`.

> bp_clip_nega boolean

>   Set negative BP voxels to zero. Maps to a command-line argument: `--bp-clip-neg`.

> calc_AR1a boolean

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

> check_optsa boolean

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

> compute_log_ya boolean

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

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

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

> cortexa boolean

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

> debuga boolean

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

> designa pathlike object or string representing an existing file

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

> diagan integer

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

> diag_clustera boolean

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

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

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

> fixed_fx_dofan integer

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

> fixed_fx_dof_filea pathlike object or string representing a file

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

> fixed_fx_vara pathlike object or string representing an existing file

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

> force_perma boolean

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

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

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

> fwhma floating point number >= 0.0

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

> glm_dira string

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

> hemi‘lh’ or ‘rh’

>   Surface hemisphere.

> invert_maska boolean

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

> label_filea pathlike object or string representing an existing file

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

> mask_filea pathlike object or string representing an existing file

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

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

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

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

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

> niia boolean

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

> nii_gza boolean

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

> no_contrast_oka boolean

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

> no_est_fwhma boolean

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

> no_mask_smootha boolean

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

> no_prunea boolean

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

> one_samplea boolean

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

> pcaa boolean

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

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

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

> profilean integer

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

> prunea boolean

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

> prune_thresha float

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

> resynth_testan integer

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

> save_conda boolean

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

> save_estimatea boolean

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

> save_res_corr_mtxa boolean

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

> save_residuala boolean

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

> seedan integer

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

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

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

> sim_done_filea pathlike object or string representing a file

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

> sim_sign‘abs’ or ‘pos’ or ‘neg’

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

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

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

> subject_ida string

>   Subject id for surface geometry.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surfa boolean

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

> surf_geoa string

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

> syntha boolean

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

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

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

> var_fwhma floating point number >= 0.0

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

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

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

> weight_filea pathlike object or string representing an existing file

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

> weight_inva boolean

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

> weight_sqrta boolean

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

> weighted_lsa pathlike object or string representing an existing file

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

> beta_filea pathlike object or string representing an existing file

>   Map of regression coefficients.

> bp_filea pathlike object or string representing a file

>   Binding potential estimates.

> dof_filea pathlike object or string representing a file

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

> error_filea pathlike object or string representing a file

>   Map of residual error.

> error_stddev_filea pathlike object or string representing a file

>   Map of residual error standard deviation.

> error_var_filea pathlike object or string representing a file

>   Map of residual error variance.

> estimate_filea pathlike object or string representing a file

>   Map of the estimated Y values.

> frame_eigenvectorsa pathlike object or string representing a file

>   Matrix of frame eigenvectors from residual PCA.

> ftest_filea list of items which are any value

>   Map of test statistic values.

> fwhm_filea pathlike object or string representing a file

>   Text file with estimated smoothness.

> gamma_filea list of items which are any value

>   Map of contrast of regression coefficients.

> gamma_var_filea list of items which are any value

>   Map of regression contrast variance.

> glm_dira pathlike object or string representing an existing directory

>   Output directory.

> k2p_filea pathlike object or string representing a file

>   Estimate of k2p parameter.

> mask_filea pathlike object or string representing a file

>   Map of the mask used in the analysis.

> sig_filea list of items which are any value

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

> singular_valuesa pathlike object or string representing a file

>   Matrix singular values from residual PCA.

> spatial_eigenvectorsa pathlike object or string representing a file

>   Map of spatial eigenvectors from residual PCA.

> svd_stats_filea pathlike object or string representing a file

>   Text file summarizing the residual PCA.

## MRTM1

Link to code

> Bases: GLMFit

> Wrapped executable: `mri_glmfit`.

> Perform MRTM1 kinetic modeling.

> Examples

>     >>> mrtm = MRTM1()
>     >>> mrtm.inputs.in_file = 'tac.nii'
>     >>> mrtm.inputs.mrtm1 = ('ref_tac.dat', 'timing.dat')
>     >>> mrtm.inputs.glm_dir = 'mrtm'
>     >>> mrtm.cmdline
>     'mri_glmfit --glmdir mrtm --y tac.nii --mrtm1 ref_tac.dat timing.dat'

> in_filea pathlike object or string representing a file

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

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

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

> allow_ill_conda boolean

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

> allow_repeated_subjectsa boolean

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

> argsa string

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

> bp_clip_maxa float

>   Set BP voxels above max to max. Maps to a command-line argument: `--bp-clip-max %f`.

> bp_clip_nega boolean

>   Set negative BP voxels to zero. Maps to a command-line argument: `--bp-clip-neg`.

> calc_AR1a boolean

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

> check_optsa boolean

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

> compute_log_ya boolean

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

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

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

> cortexa boolean

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

> debuga boolean

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

> designa pathlike object or string representing an existing file

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

> diagan integer

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

> diag_clustera boolean

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

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

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

> fixed_fx_dofan integer

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

> fixed_fx_dof_filea pathlike object or string representing a file

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

> fixed_fx_vara pathlike object or string representing an existing file

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

> force_perma boolean

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

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

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

> fwhma floating point number >= 0.0

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

> glm_dira string

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

> hemi‘lh’ or ‘rh’

>   Surface hemisphere.

> invert_maska boolean

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

> label_filea pathlike object or string representing an existing file

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

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

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

> mask_filea pathlike object or string representing an existing file

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

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

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

> niia boolean

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

> nii_gza boolean

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

> no_contrast_oka boolean

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

> no_est_fwhma boolean

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

> no_mask_smootha boolean

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

> no_prunea boolean

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

> one_samplea boolean

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

> pcaa boolean

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

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

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

> profilean integer

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

> prunea boolean

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

> prune_thresha float

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

> resynth_testan integer

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

> save_conda boolean

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

> save_estimatea boolean

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

> save_res_corr_mtxa boolean

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

> save_residuala boolean

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

> seedan integer

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

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

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

> sim_done_filea pathlike object or string representing a file

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

> sim_sign‘abs’ or ‘pos’ or ‘neg’

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

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

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

> subject_ida string

>   Subject id for surface geometry.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surfa boolean

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

> surf_geoa string

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

> syntha boolean

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

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

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

> var_fwhma floating point number >= 0.0

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

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

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

> weight_filea pathlike object or string representing an existing file

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

> weight_inva boolean

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

> weight_sqrta boolean

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

> weighted_lsa pathlike object or string representing an existing file

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

> beta_filea pathlike object or string representing an existing file

>   Map of regression coefficients.

> bp_filea pathlike object or string representing a file

>   Binding potential estimates.

> dof_filea pathlike object or string representing a file

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

> error_filea pathlike object or string representing a file

>   Map of residual error.

> error_stddev_filea pathlike object or string representing a file

>   Map of residual error standard deviation.

> error_var_filea pathlike object or string representing a file

>   Map of residual error variance.

> estimate_filea pathlike object or string representing a file

>   Map of the estimated Y values.

> frame_eigenvectorsa pathlike object or string representing a file

>   Matrix of frame eigenvectors from residual PCA.

> ftest_filea list of items which are any value

>   Map of test statistic values.

> fwhm_filea pathlike object or string representing a file

>   Text file with estimated smoothness.

> gamma_filea list of items which are any value

>   Map of contrast of regression coefficients.

> gamma_var_filea list of items which are any value

>   Map of regression contrast variance.

> glm_dira pathlike object or string representing an existing directory

>   Output directory.

> k2p_filea pathlike object or string representing a file

>   Estimate of k2p parameter.

> mask_filea pathlike object or string representing a file

>   Map of the mask used in the analysis.

> sig_filea list of items which are any value

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

> singular_valuesa pathlike object or string representing a file

>   Matrix singular values from residual PCA.

> spatial_eigenvectorsa pathlike object or string representing a file

>   Map of spatial eigenvectors from residual PCA.

> svd_stats_filea pathlike object or string representing a file

>   Text file summarizing the residual PCA.

## MRTM2

Link to code

> Bases: GLMFit

> Wrapped executable: `mri_glmfit`.

> Perform MRTM2 kinetic modeling. .. rubric:: Examples

>     >>> mrtm2 = MRTM2()
>     >>> mrtm2.inputs.in_file = 'tac.nii'
>     >>> mrtm2.inputs.mrtm2 = ('ref_tac.dat', 'timing.dat', 0.07872)
>     >>> mrtm2.inputs.glm_dir = 'mrtm2'
>     >>> mrtm2.cmdline
>     'mri_glmfit --glmdir mrtm2 --y tac.nii --mrtm2 ref_tac.dat timing.dat 0.078720'

> in_filea pathlike object or string representing a file

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

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

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

> allow_ill_conda boolean

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

> allow_repeated_subjectsa boolean

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

> argsa string

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

> bp_clip_maxa float

>   Set BP voxels above max to max. Maps to a command-line argument: `--bp-clip-max %f`.

> bp_clip_nega boolean

>   Set negative BP voxels to zero. Maps to a command-line argument: `--bp-clip-neg`.

> calc_AR1a boolean

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

> check_optsa boolean

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

> compute_log_ya boolean

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

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

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

> cortexa boolean

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

> debuga boolean

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

> designa pathlike object or string representing an existing file

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

> diagan integer

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

> diag_clustera boolean

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

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

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

> fixed_fx_dofan integer

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

> fixed_fx_dof_filea pathlike object or string representing a file

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

> fixed_fx_vara pathlike object or string representing an existing file

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

> force_perma boolean

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

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

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

> fwhma floating point number >= 0.0

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

> glm_dira string

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

> hemi‘lh’ or ‘rh’

>   Surface hemisphere.

> invert_maska boolean

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

> label_filea pathlike object or string representing an existing file

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

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

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

> mask_filea pathlike object or string representing an existing file

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

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

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

> niia boolean

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

> nii_gza boolean

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

> no_contrast_oka boolean

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

> no_est_fwhma boolean

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

> no_mask_smootha boolean

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

> no_prunea boolean

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

> one_samplea boolean

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

> pcaa boolean

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

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

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

> profilean integer

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

> prunea boolean

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

> prune_thresha float

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

> resynth_testan integer

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

> save_conda boolean

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

> save_estimatea boolean

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

> save_res_corr_mtxa boolean

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

> save_residuala boolean

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

> seedan integer

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

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

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

> sim_done_filea pathlike object or string representing a file

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

> sim_sign‘abs’ or ‘pos’ or ‘neg’

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

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

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

> subject_ida string

>   Subject id for surface geometry.

> subjects_dira pathlike object or string representing an existing directory

>   Subjects directory.

> surfa boolean

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

> surf_geoa string

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

> syntha boolean

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

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

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

> var_fwhma floating point number >= 0.0

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

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

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

> weight_filea pathlike object or string representing an existing file

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

> weight_inva boolean

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

> weight_sqrta boolean

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

> weighted_lsa pathlike object or string representing an existing file

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

> beta_filea pathlike object or string representing an existing file

>   Map of regression coefficients.

> bp_filea pathlike object or string representing a file

>   Binding potential estimates.

> dof_filea pathlike object or string representing a file

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

> error_filea pathlike object or string representing a file

>   Map of residual error.

> error_stddev_filea pathlike object or string representing a file

>   Map of residual error standard deviation.

> error_var_filea pathlike object or string representing a file

>   Map of residual error variance.

> estimate_filea pathlike object or string representing a file

>   Map of the estimated Y values.

> frame_eigenvectorsa pathlike object or string representing a file

>   Matrix of frame eigenvectors from residual PCA.

> ftest_filea list of items which are any value

>   Map of test statistic values.

> fwhm_filea pathlike object or string representing a file

>   Text file with estimated smoothness.

> gamma_filea list of items which are any value

>   Map of contrast of regression coefficients.

> gamma_var_filea list of items which are any value

>   Map of regression contrast variance.

> glm_dira pathlike object or string representing an existing directory

>   Output directory.

> k2p_filea pathlike object or string representing a file

>   Estimate of k2p parameter.

> mask_filea pathlike object or string representing a file

>   Map of the mask used in the analysis.

> sig_filea list of items which are any value

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

> singular_valuesa pathlike object or string representing a file

>   Matrix singular values from residual PCA.

> spatial_eigenvectorsa pathlike object or string representing a file

>   Map of spatial eigenvectors from residual PCA.

> svd_stats_filea pathlike object or string representing a file

>   Text file summarizing the residual PCA.