nipype.interfaces.freesurfer.petsurfer module

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

GTMPVC

Link to code

Bases: FSCommand

Wrapped executable: mri_gtmpvc.

Perform Partial Volume Correction (PVC) to PET Data.

Examples

>>> gtmpvc = GTMPVC()
>>> gtmpvc.inputs.in_file = 'sub-01_ses-baseline_pet.nii.gz'
>>> gtmpvc.inputs.segmentation = 'gtmseg.mgz'
>>> gtmpvc.inputs.reg_file = 'sub-01_ses-baseline_pet_mean_reg.lta'
>>> gtmpvc.inputs.pvc_dir = 'pvc'
>>> gtmpvc.inputs.psf = 4
>>> gtmpvc.inputs.default_seg_merge = True
>>> gtmpvc.inputs.auto_mask = (1, 0.1)
>>> gtmpvc.inputs.km_ref = ['8 47']
>>> gtmpvc.inputs.km_hb = ['11 12 50 51']
>>> gtmpvc.inputs.no_rescale = True
>>> gtmpvc.inputs.save_input = True
>>> gtmpvc.cmdline
'mri_gtmpvc --auto-mask 1.000000 0.100000 --default-seg-merge     --i sub-01_ses-baseline_pet.nii.gz --km-hb 11 12 50 51 --km-ref 8 47 --no-rescale     --psf 4.000000 --o pvc --reg sub-01_ses-baseline_pet_mean_reg.lta --save-input     --seg gtmseg.mgz'
>>> gtmpvc = GTMPVC()
>>> gtmpvc.inputs.in_file = 'sub-01_ses-baseline_pet.nii.gz'
>>> gtmpvc.inputs.segmentation = 'gtmseg.mgz'
>>> gtmpvc.inputs.regheader = True
>>> gtmpvc.inputs.pvc_dir = 'pvc'
>>> gtmpvc.inputs.mg = (0.5, ["ROI1", "ROI2"])
>>> gtmpvc.cmdline
'mri_gtmpvc --i sub-01_ses-baseline_pet.nii.gz --mg 0.5 ROI1 ROI2 --o pvc --regheader --seg gtmseg.mgz'
in_filea pathlike object or string representing an existing file

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

reg_filea pathlike object or string representing an existing file

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

reg_identitya boolean

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

regheadera boolean

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

segmentationa pathlike object or string representing an existing file

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

Xa boolean

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

X0a boolean

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

argsa string

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

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

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

betaa boolean

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

color_table_filea pathlike object or string representing an existing file

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

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

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

default_color_tablea boolean

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

default_seg_mergea boolean

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

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

Environment variables. (Nipype default value: {})

framean integer

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

km_hba list of items which are any value

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

km_refa list of items which are any value

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

lata boolean

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

mask_filea pathlike object or string representing an existing file

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

merge_cblum_wm_gyria boolean

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

merge_hyposa boolean

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

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

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

mg_ref_cerebral_wma boolean

set MG RefIds to 2 and 41.

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

mg_ref_lobes_wma boolean

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

mgxa float

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

no_pvca boolean

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

no_reduce_fova boolean

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

no_rescalea boolean

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

no_tfea boolean

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

num_threadsan integer

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

opt_braina boolean

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

opt_seg_mergea boolean

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

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

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

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

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

psfa float

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

psf_cola float

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

psf_rowa float

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

psf_slicea float

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

pvc_dira string

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

rbva boolean

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

rbv_resa float

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

reduce_fox_eqodda boolean

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

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

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

rescalea list of items which are any value

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

save_eresa boolean

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

save_inputa boolean

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

save_yhata boolean

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

save_yhat0a boolean

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

save_yhat_full_fova boolean

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

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

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

scale_refvala float

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

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

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

subjects_dira pathlike object or string representing an existing directory

Subjects directory.

tissue_fraction_resolutiona float

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

tt_reducea boolean

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

tt_updatea boolean

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

ya boolean

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

eresa pathlike object or string representing a file

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

gtm_filea pathlike object or string representing a file

TACs for all regions with GTM PVC.

gtm_statsa pathlike object or string representing a file

Statistics for the GTM PVC.

hb_data pathlike object or string representing a file

High-binding TAC in .dat.

hb_niftia pathlike object or string representing a file

High-binding TAC in nifti.

input_filea pathlike object or string representing a file

4D PET file in native volume space.

mgx_ctxgma pathlike object or string representing a file

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

mgx_gma pathlike object or string representing a file

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

mgx_subctxgma pathlike object or string representing a file

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

nopvc_filea pathlike object or string representing a file

TACs for all regions with no PVC.

opt_paramsa pathlike object or string representing a file

Optimal parameter estimates for the FWHM using adaptive GTM.

pvc_dira pathlike object or string representing a directory

Output directory.

rbva pathlike object or string representing a file

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

ref_filea pathlike object or string representing a file

Reference TAC in .dat.

reg_anat2peta pathlike object or string representing a file

Registration file to go from anat to PET.

reg_anat2rbvpeta pathlike object or string representing a file

Registration file to go from anat to RBV corrected PET.

reg_pet2anata pathlike object or string representing a file

Registration file to go from PET to anat.

reg_rbvpet2anata pathlike object or string representing a file

Registration file to go from RBV corrected PET to anat.

sega pathlike object or string representing a file

Segmentation file of regions used for PVC.

seg_ctaba pathlike object or string representing a file

Color table file for segmentation file.

tissue_fractiona pathlike object or string representing a file

4D PET file of tissue fraction before PVC.

tissue_fraction_psfa pathlike object or string representing a file

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

yhata pathlike object or string representing a file

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

yhat0a pathlike object or string representing a file

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

yhat_full_fova pathlike object or string representing a file

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

yhat_with_noisea pathlike object or string representing a file

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

GTMSeg

Link to code

Bases: FSCommand

Wrapped executable: gtmseg.

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

Examples

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

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

argsa string

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

colortablea pathlike object or string representing an existing file

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

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

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

dmaxa float

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

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

Environment variables. (Nipype default value: {})

heada string

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

keep_cca boolean

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

keep_hypoa boolean

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

no_ponsa boolean

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

no_seg_statsa boolean

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

no_vermisa boolean

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

out_filea pathlike object or string representing a file

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

output_upsampling_factoran integer

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

subjects_dira pathlike object or string representing an existing directory

Subjects directory.

subseg_cblum_wma boolean

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

subsegwma boolean

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

upsampling_factoran integer

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

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

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

xcersega boolean

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

out_filea pathlike object or string representing a file

GTM segmentation.

Logan

Link to code

Bases: GLMFit

Wrapped executable: mri_glmfit.

Perform Logan kinetic modeling. .. rubric:: Examples

>>> logan = Logan()
>>> logan.inputs.in_file = 'tac.nii'
>>> logan.inputs.logan = ('ref_tac.dat', 'timing.dat', 2600)
>>> logan.inputs.glm_dir = 'logan'
>>> logan.cmdline
'mri_glmfit --glmdir logan --y tac.nii --logan ref_tac.dat timing.dat 2600'
in_filea pathlike object or string representing a file

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

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

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

allow_ill_conda boolean

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

allow_repeated_subjectsa boolean

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

argsa string

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

bp_clip_maxa float

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

bp_clip_nega boolean

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

calc_AR1a boolean

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

check_optsa boolean

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

compute_log_ya boolean

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

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

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

cortexa boolean

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

debuga boolean

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

designa pathlike object or string representing an existing file

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

diagan integer

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

diag_clustera boolean

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

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

Environment variables. (Nipype default value: {})

fixed_fx_dofan integer

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

fixed_fx_dof_filea pathlike object or string representing a file

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

fixed_fx_vara pathlike object or string representing an existing file

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

force_perma boolean

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

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

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

fwhma floating point number >= 0.0

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

glm_dira string

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

hemi‘lh’ or ‘rh’

Surface hemisphere.

invert_maska boolean

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

label_filea pathlike object or string representing an existing file

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

mask_filea pathlike object or string representing an existing file

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

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

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

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

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

niia boolean

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

nii_gza boolean

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

no_contrast_oka boolean

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

no_est_fwhma boolean

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

no_mask_smootha boolean

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

no_prunea boolean

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

one_samplea boolean

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

pcaa boolean

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

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

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

profilean integer

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

prunea boolean

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

prune_thresha float

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

resynth_testan integer

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

save_conda boolean

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

save_estimatea boolean

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

save_res_corr_mtxa boolean

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

save_residuala boolean

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

seedan integer

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

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

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

sim_done_filea pathlike object or string representing a file

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

sim_sign‘abs’ or ‘pos’ or ‘neg’

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

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

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

subject_ida string

Subject id for surface geometry.

subjects_dira pathlike object or string representing an existing directory

Subjects directory.

surfa boolean

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

surf_geoa string

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

syntha boolean

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

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

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

var_fwhma floating point number >= 0.0

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

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

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

weight_filea pathlike object or string representing an existing file

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

weight_inva boolean

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

weight_sqrta boolean

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

weighted_lsa pathlike object or string representing an existing file

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

beta_filea pathlike object or string representing an existing file

Map of regression coefficients.

bp_filea pathlike object or string representing a file

Binding potential estimates.

dof_filea pathlike object or string representing a file

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

error_filea pathlike object or string representing a file

Map of residual error.

error_stddev_filea pathlike object or string representing a file

Map of residual error standard deviation.

error_var_filea pathlike object or string representing a file

Map of residual error variance.

estimate_filea pathlike object or string representing a file

Map of the estimated Y values.

frame_eigenvectorsa pathlike object or string representing a file

Matrix of frame eigenvectors from residual PCA.

ftest_filea list of items which are any value

Map of test statistic values.

fwhm_filea pathlike object or string representing a file

Text file with estimated smoothness.

gamma_filea list of items which are any value

Map of contrast of regression coefficients.

gamma_var_filea list of items which are any value

Map of regression contrast variance.

glm_dira pathlike object or string representing an existing directory

Output directory.

k2p_filea pathlike object or string representing a file

Estimate of k2p parameter.

mask_filea pathlike object or string representing a file

Map of the mask used in the analysis.

sig_filea list of items which are any value

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

singular_valuesa pathlike object or string representing a file

Matrix singular values from residual PCA.

spatial_eigenvectorsa pathlike object or string representing a file

Map of spatial eigenvectors from residual PCA.

svd_stats_filea pathlike object or string representing a file

Text file summarizing the residual PCA.

MRTM1

Link to code

Bases: GLMFit

Wrapped executable: mri_glmfit.

Perform MRTM1 kinetic modeling.

Examples

>>> mrtm = MRTM1()
>>> mrtm.inputs.in_file = 'tac.nii'
>>> mrtm.inputs.mrtm1 = ('ref_tac.dat', 'timing.dat')
>>> mrtm.inputs.glm_dir = 'mrtm'
>>> mrtm.cmdline
'mri_glmfit --glmdir mrtm --y tac.nii --mrtm1 ref_tac.dat timing.dat'
in_filea pathlike object or string representing a file

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

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

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

allow_ill_conda boolean

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

allow_repeated_subjectsa boolean

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

argsa string

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

bp_clip_maxa float

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

bp_clip_nega boolean

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

calc_AR1a boolean

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

check_optsa boolean

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

compute_log_ya boolean

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

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

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

cortexa boolean

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

debuga boolean

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

designa pathlike object or string representing an existing file

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

diagan integer

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

diag_clustera boolean

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

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

Environment variables. (Nipype default value: {})

fixed_fx_dofan integer

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

fixed_fx_dof_filea pathlike object or string representing a file

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

fixed_fx_vara pathlike object or string representing an existing file

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

force_perma boolean

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

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

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

fwhma floating point number >= 0.0

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

glm_dira string

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

hemi‘lh’ or ‘rh’

Surface hemisphere.

invert_maska boolean

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

label_filea pathlike object or string representing an existing file

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

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

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

mask_filea pathlike object or string representing an existing file

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

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

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

niia boolean

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

nii_gza boolean

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

no_contrast_oka boolean

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

no_est_fwhma boolean

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

no_mask_smootha boolean

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

no_prunea boolean

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

one_samplea boolean

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

pcaa boolean

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

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

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

profilean integer

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

prunea boolean

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

prune_thresha float

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

resynth_testan integer

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

save_conda boolean

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

save_estimatea boolean

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

save_res_corr_mtxa boolean

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

save_residuala boolean

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

seedan integer

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

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

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

sim_done_filea pathlike object or string representing a file

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

sim_sign‘abs’ or ‘pos’ or ‘neg’

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

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

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

subject_ida string

Subject id for surface geometry.

subjects_dira pathlike object or string representing an existing directory

Subjects directory.

surfa boolean

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

surf_geoa string

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

syntha boolean

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

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

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

var_fwhma floating point number >= 0.0

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

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

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

weight_filea pathlike object or string representing an existing file

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

weight_inva boolean

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

weight_sqrta boolean

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

weighted_lsa pathlike object or string representing an existing file

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

beta_filea pathlike object or string representing an existing file

Map of regression coefficients.

bp_filea pathlike object or string representing a file

Binding potential estimates.

dof_filea pathlike object or string representing a file

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

error_filea pathlike object or string representing a file

Map of residual error.

error_stddev_filea pathlike object or string representing a file

Map of residual error standard deviation.

error_var_filea pathlike object or string representing a file

Map of residual error variance.

estimate_filea pathlike object or string representing a file

Map of the estimated Y values.

frame_eigenvectorsa pathlike object or string representing a file

Matrix of frame eigenvectors from residual PCA.

ftest_filea list of items which are any value

Map of test statistic values.

fwhm_filea pathlike object or string representing a file

Text file with estimated smoothness.

gamma_filea list of items which are any value

Map of contrast of regression coefficients.

gamma_var_filea list of items which are any value

Map of regression contrast variance.

glm_dira pathlike object or string representing an existing directory

Output directory.

k2p_filea pathlike object or string representing a file

Estimate of k2p parameter.

mask_filea pathlike object or string representing a file

Map of the mask used in the analysis.

sig_filea list of items which are any value

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

singular_valuesa pathlike object or string representing a file

Matrix singular values from residual PCA.

spatial_eigenvectorsa pathlike object or string representing a file

Map of spatial eigenvectors from residual PCA.

svd_stats_filea pathlike object or string representing a file

Text file summarizing the residual PCA.

MRTM2

Link to code

Bases: GLMFit

Wrapped executable: mri_glmfit.

Perform MRTM2 kinetic modeling. .. rubric:: Examples

>>> mrtm2 = MRTM2()
>>> mrtm2.inputs.in_file = 'tac.nii'
>>> mrtm2.inputs.mrtm2 = ('ref_tac.dat', 'timing.dat', 0.07872)
>>> mrtm2.inputs.glm_dir = 'mrtm2'
>>> mrtm2.cmdline
'mri_glmfit --glmdir mrtm2 --y tac.nii --mrtm2 ref_tac.dat timing.dat 0.078720'
in_filea pathlike object or string representing a file

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

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

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

allow_ill_conda boolean

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

allow_repeated_subjectsa boolean

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

argsa string

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

bp_clip_maxa float

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

bp_clip_nega boolean

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

calc_AR1a boolean

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

check_optsa boolean

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

compute_log_ya boolean

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

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

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

cortexa boolean

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

debuga boolean

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

designa pathlike object or string representing an existing file

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

diagan integer

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

diag_clustera boolean

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

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

Environment variables. (Nipype default value: {})

fixed_fx_dofan integer

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

fixed_fx_dof_filea pathlike object or string representing a file

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

fixed_fx_vara pathlike object or string representing an existing file

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

force_perma boolean

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

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

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

fwhma floating point number >= 0.0

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

glm_dira string

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

hemi‘lh’ or ‘rh’

Surface hemisphere.

invert_maska boolean

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

label_filea pathlike object or string representing an existing file

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

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

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

mask_filea pathlike object or string representing an existing file

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

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

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

niia boolean

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

nii_gza boolean

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

no_contrast_oka boolean

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

no_est_fwhma boolean

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

no_mask_smootha boolean

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

no_prunea boolean

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

one_samplea boolean

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

pcaa boolean

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

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

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

profilean integer

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

prunea boolean

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

prune_thresha float

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

resynth_testan integer

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

save_conda boolean

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

save_estimatea boolean

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

save_res_corr_mtxa boolean

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

save_residuala boolean

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

seedan integer

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

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

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

sim_done_filea pathlike object or string representing a file

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

sim_sign‘abs’ or ‘pos’ or ‘neg’

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

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

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

subject_ida string

Subject id for surface geometry.

subjects_dira pathlike object or string representing an existing directory

Subjects directory.

surfa boolean

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

surf_geoa string

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

syntha boolean

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

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

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

var_fwhma floating point number >= 0.0

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

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

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

weight_filea pathlike object or string representing an existing file

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

weight_inva boolean

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

weight_sqrta boolean

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

weighted_lsa pathlike object or string representing an existing file

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

beta_filea pathlike object or string representing an existing file

Map of regression coefficients.

bp_filea pathlike object or string representing a file

Binding potential estimates.

dof_filea pathlike object or string representing a file

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

error_filea pathlike object or string representing a file

Map of residual error.

error_stddev_filea pathlike object or string representing a file

Map of residual error standard deviation.

error_var_filea pathlike object or string representing a file

Map of residual error variance.

estimate_filea pathlike object or string representing a file

Map of the estimated Y values.

frame_eigenvectorsa pathlike object or string representing a file

Matrix of frame eigenvectors from residual PCA.

ftest_filea list of items which are any value

Map of test statistic values.

fwhm_filea pathlike object or string representing a file

Text file with estimated smoothness.

gamma_filea list of items which are any value

Map of contrast of regression coefficients.

gamma_var_filea list of items which are any value

Map of regression contrast variance.

glm_dira pathlike object or string representing an existing directory

Output directory.

k2p_filea pathlike object or string representing a file

Estimate of k2p parameter.

mask_filea pathlike object or string representing a file

Map of the mask used in the analysis.

sig_filea list of items which are any value

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

singular_valuesa pathlike object or string representing a file

Matrix singular values from residual PCA.

spatial_eigenvectorsa pathlike object or string representing a file

Map of spatial eigenvectors from residual PCA.

svd_stats_filea pathlike object or string representing a file

Text file summarizing the residual PCA.