nipype.interfaces.freesurfer.petsurfer module¶
Provides interfaces to various commands for running PET analyses provided by FreeSurfer
GTMPVC¶
Bases: FSCommand
Wrapped executable:
mri_gtmpvc.create an anatomical segmentation for the geometric transfer matrix (GTM).
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'
- Mandatory Inputs:
in_file (a pathlike object or string representing an existing file) – Input volume - source data to pvc. Maps to a command-line argument:
--i %s.reg_file (a 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_identity (a 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.regheader (a boolean) – Assume input and seg share scanner space. Maps to a command-line argument:
--regheader. Mutually exclusive with inputs:reg_file,regheader,reg_identity.segmentation (a pathlike object or string representing an existing file) – Segfile : anatomical segmentation to define regions for GTM. Maps to a command-line argument:
--seg %s.- Optional Inputs:
X (a boolean) – Save X matrix in matlab4 format as X.mat (it will be big). Maps to a command-line argument:
--X.X0 (a boolean) – Save X0 matrix in matlab4 format as X0.mat (it will be big). Maps to a command-line argument:
--X0.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.auto_mask (a tuple of the form: (a float, a float)) – FWHM thresh : automatically compute mask. Maps to a command-line argument:
--auto-mask %f %f.beta (a boolean) – Save beta matrix in matlab4 format as beta.mat. Maps to a command-line argument:
--beta.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.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....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.default_seg_merge (a boolean) – Default schema for merging ROIs. Maps to a command-line argument:
--default-seg-merge.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:
{})frame (an integer) – Only process 0-based frame F from inputvol. Maps to a command-line argument:
--frame %i.km_hb (a 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_ref (a 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....lat (a boolean) – Lateralize tissue types. Maps to a command-line argument:
--lat.mask_file (a 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_gyri (a boolean) – Cerebellum WM gyri back into cerebellum WM. Maps to a command-line argument:
--merge-cblum-wm-gyri.merge_hypos (a boolean) – Merge left and right hypointensites into to ROI. Maps to a command-line argument:
--merge-hypos.mg (a 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_wm (a boolean) – set MG RefIds to 2 and 41. Maps to a command-line argument:
--mg-ref-cerebral-wm.mg_ref_lobes_wm (a boolean) – Set MG RefIds to those for lobes when using wm subseg. Maps to a command-line argument:
--mg-ref-lobes-wm.mgx (a 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_pvc (a boolean) – Turns off PVC entirely (both PSF and TFE). Maps to a command-line argument:
--no-pvc.no_reduce_fov (a boolean) – Do not reduce FoV to encompass mask. Maps to a command-line argument:
--no-reduce-fov.no_rescale (a boolean) – Do not global rescale such that mean of reference region is scaleref. Maps to a command-line argument:
--no-rescale.no_tfe (a boolean) – Do not correct for tissue fraction effect (with –psf 0 turns off PVC entirely). Maps to a command-line argument:
--no-tfe.num_threads (an integer) – Threads : number of threads to use. Maps to a command-line argument:
--threads %i.opt_brain (a boolean) – Apply adaptive GTM. Maps to a command-line argument:
--opt-brain.opt_seg_merge (a boolean) – Optimal schema for merging ROIs when applying adaptive GTM. Maps to a command-line argument:
--opt-seg-merge.opt_tol (a 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.psf (a float) – Scanner PSF FWHM in mm. Maps to a command-line argument:
--psf %f.psf_col (a float) – XFWHM : full-width-half-maximum in the x-direction. Maps to a command-line argument:
--psf-col %f.psf_row (a float) – YFWHM : full-width-half-maximum in the y-direction. Maps to a command-line argument:
--psf-row %f.psf_slice (a float) – ZFWHM : full-width-half-maximum in the z-direction. Maps to a command-line argument:
--psf-slice %f.pvc_dir (a string) – Save outputs to dir. Maps to a command-line argument:
--o %s.rbv (a boolean) – Perform Region-based Voxelwise (RBV) PVC. Maps to a command-line argument:
--rbv. Requires inputs:subjects_dir.rbv_res (a 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_eqodd (a boolean) – Reduce FoV to encompass mask but force nc=nr and ns to be odd. Maps to a command-line argument:
--reduce-fox-eqodd.replace (a 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.rescale (a 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_eres (a boolean) – Saves residual error. Maps to a command-line argument:
--save-eres.save_input (a boolean) – Saves rescaled input as input.rescaled.nii.gz. Maps to a command-line argument:
--save-input.save_yhat (a 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_yhat0 (a boolean) – Save signal estimate (yhat). Maps to a command-line argument:
--save-yhat0.save_yhat_full_fov (a boolean) – Save signal estimate (yhat). Maps to a command-line argument:
--save-yhat-full-fov.save_yhat_with_noise (a 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_refval (a float) – Refval : scale such that mean in reference region is refval. Maps to a command-line argument:
--scale-refval %f.steady_state_params (a 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_dir (a pathlike object or string representing an existing directory) – Subjects directory.
tissue_fraction_resolution (a float) – Set the tissue fraction resolution parameter (def is 0.5). Maps to a command-line argument:
--segpvfres %f.tt_reduce (a boolean) – Reduce segmentation to that of a tissue type. Maps to a command-line argument:
--tt-reduce.tt_update (a boolean) – Changes tissue type of VentralDC, BrainStem, and Pons to be SubcortGM. Maps to a command-line argument:
--tt-update.y (a boolean) – Save y matrix in matlab4 format as y.mat. Maps to a command-line argument:
--y.- Outputs:
gtm_file (a pathlike object or string representing a file) – TACs for all regions with GTM PVC.
gtm_stats (a pathlike object or string representing a file) – Statistics for the GTM PVC.
hb_dat (a pathlike object or string representing a file) – High-binding TAC in .dat.
hb_nifti (a pathlike object or string representing a file) – High-binding TAC in nifti.
input_file (a pathlike object or string representing a file) – 4D PET file in native volume space.
mgx_ctxgm (a pathlike object or string representing a file) – Cortical GM voxel-wise values corrected using the extended Muller-Gartner method.
mgx_gm (a pathlike object or string representing a file) – All GM voxel-wise values corrected using the extended Muller-Gartner method.
mgx_subctxgm (a pathlike object or string representing a file) – Subcortical GM voxel-wise values corrected using the extended Muller-Gartner method.
nopvc_file (a pathlike object or string representing a file) – TACs for all regions with no PVC.
opt_params (a pathlike object or string representing a file) – Optimal parameter estimates for the FWHM using adaptive GTM.
pvc_dir (a pathlike object or string representing a directory) – Output directory.
rbv (a pathlike object or string representing a file) – All GM voxel-wise values corrected using the RBV method.
ref_file (a pathlike object or string representing a file) – Reference TAC in .dat.
reg_anat2pet (a pathlike object or string representing a file) – Registration file to go from anat to PET.
reg_anat2rbvpet (a pathlike object or string representing a file) – Registration file to go from anat to RBV corrected PET.
reg_pet2anat (a pathlike object or string representing a file) – Registration file to go from PET to anat.
reg_rbvpet2anat (a pathlike object or string representing a file) – Registration file to go from RBV corrected PET to anat.
yhat (a pathlike object or string representing a file) – 4D PET file of signal estimate (yhat) after PVC (smoothed with PSF).
yhat0 (a pathlike object or string representing a file) – 4D PET file of signal estimate (yhat) after PVC (unsmoothed).
yhat_full_fov (a pathlike object or string representing a file) – 4D PET file with full FOV of signal estimate (yhat) after PVC (smoothed with PSF).
yhat_with_noise (a 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¶
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'
- Mandatory Inputs:
subject_id (a string) – Subject id. Maps to a command-line argument:
--s %s.- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.colortable (a pathlike object or string representing an existing file) – Colortable. Maps to a command-line argument:
--ctab %s.ctx_annot (a 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.dmax (a float) – Distance threshold to use when subsegmenting WM (default is 5). Maps to a command-line argument:
--dmax %f.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:
{})head (a string) – Use headseg instead of apas+head.mgz. Maps to a command-line argument:
--head %s.keep_cc (a boolean) – Do not relabel corpus callosum as WM. Maps to a command-line argument:
--keep-cc.keep_hypo (a boolean) – Do not relabel hypointensities as WM when subsegmenting WM. Maps to a command-line argument:
--keep-hypo.no_pons (a boolean) – Do not add pons segmentation when doing —xcerseg. Maps to a command-line argument:
--no-pons.no_seg_stats (a boolean) – Do not compute segmentation stats. Maps to a command-line argument:
--no-seg-stats.no_vermis (a boolean) – Do not add vermis segmentation when doing —xcerseg. Maps to a command-line argument:
--no-vermis.out_file (a 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_factor (an integer) – Set output USF different than USF, mostly for debugging. Maps to a command-line argument:
--output-usf %i.subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.
subseg_cblum_wm (a boolean) – Subsegment cerebellum WM into core and gyri. Maps to a command-line argument:
--subseg-cblum-wm.subsegwm (a boolean) – Subsegment WM into lobes (default). Maps to a command-line argument:
--subsegwm.upsampling_factor (an integer) – Upsampling factor (default is 2). Maps to a command-line argument:
--usf %i.wm_annot (a 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.xcerseg (a boolean) – Run xcerebralseg on this subject to create apas+head.mgz. Maps to a command-line argument:
--xcerseg.- Outputs:
out_file (a pathlike object or string representing a file) – GTM segmentation.
LoganRef¶
Bases: GLMFit
Wrapped executable:
mri_glmfit.Perform Logan reference kinetic modeling. .. rubric:: Examples
>>> logan = LoganRef() >>> 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'
- Mandatory Inputs:
in_file (a pathlike object or string representing a file) – Input 4D file. Maps to a command-line argument:
--y %s.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 %g.- 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.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.
MRTM¶
Bases: GLMFit
Wrapped executable:
mri_glmfit.Perform MRTM1 kinetic modeling.
Examples
>>> mrtm = MRTM() >>> 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'
- Mandatory Inputs:
in_file (a pathlike object or string representing a file) – Input 4D file. Maps to a command-line argument:
--y %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.- 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.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.
MRTM2¶
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'
- Mandatory Inputs:
in_file (a pathlike object or string representing a file) – Input 4D file. Maps to a command-line argument:
--y %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.- 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.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.