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'
- 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
.
- 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.
- 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¶
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.
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'
- 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
.- 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.
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'
- 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
.- 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¶
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
.- 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.