Perform Logan kinetic modeling.
Usage
ni_freesurfer_logan(
in_file,
logan,
allow_ill_cond = NULL,
allow_repeated_subjects = NULL,
args = NULL,
bp_clip_max = NULL,
bp_clip_neg = NULL,
calc_AR1 = NULL,
check_opts = NULL,
compute_log_y = NULL,
contrast = NULL,
cortex = NULL,
debug = NULL,
design = NULL,
diag = NULL,
diag_cluster = NULL,
fixed_fx_dof = NULL,
fixed_fx_dof_file = NULL,
fixed_fx_var = NULL,
force_perm = NULL,
fsgd = NULL,
fwhm = NULL,
glm_dir = NULL,
invert_mask = NULL,
label_file = NULL,
mask_file = NULL,
mrtm1 = NULL,
mrtm2 = NULL,
nii = NULL,
nii_gz = NULL,
no_contrast_ok = NULL,
no_est_fwhm = NULL,
no_mask_smooth = NULL,
no_prune = NULL,
one_sample = NULL,
pca = NULL,
per_voxel_reg = NULL,
profile = NULL,
prune = NULL,
prune_thresh = NULL,
resynth_test = NULL,
save_cond = NULL,
save_estimate = NULL,
save_res_corr_mtx = NULL,
save_residual = NULL,
seed = NULL,
self_reg = NULL,
sim_done_file = NULL,
sim_sign = NULL,
simulation = NULL,
surf = NULL,
synth = NULL,
uniform = NULL,
var_fwhm = NULL,
vox_dump = NULL,
weight_inv = NULL,
weight_sqrt = NULL,
weighted_ls = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. input 4D file Required.
- logan
Character or numeric vector. RefTac TimeSec tstar : perform Logan kinetic modeling Required.
- allow_ill_cond
Logical. allow ill-conditioned design matrices
- allow_repeated_subjects
Logical. allow subject names to repeat in the fsgd file (must appear before –fsgd
- args
Character. Additional parameters to the command
- bp_clip_max
Numeric. set BP voxels above max to max
- bp_clip_neg
Logical. set negative BP voxels to zero
- calc_AR1
Logical. compute and save temporal AR1 of residual
- check_opts
Logical. don't run anything, just check options and exit
- compute_log_y
Logical. compute natural log of y prior to analysis
- contrast
Character or numeric vector. contrast file
- cortex
Logical. use subjects ?h.cortex.label as label
- debug
Logical. turn on debugging
- design
Character; file path. design matrix file
- diag
Integer. Gdiag_no : set diagnostic level
- diag_cluster
Logical. save sig volume and exit from first sim loop
- fixed_fx_dof
Integer. dof for fixed effects analysis
- fixed_fx_dof_file
Character; file path. text file with dof for fixed effects analysis
- fixed_fx_var
Character; file path. for fixed effects analysis
- force_perm
Logical. force perumtation test, even when design matrix is not orthog
- fsgd
Character or numeric vector. freesurfer descriptor file
- fwhm
Character. smooth input by fwhm
- glm_dir
Character. save outputs to dir
- invert_mask
Logical. invert mask
- label_file
Character; file path. use label as mask, surfaces only
- mask_file
Character; file path. binary mask
- mrtm1
Character or numeric vector. RefTac TimeSec : perform MRTM1 kinetic modeling
- mrtm2
Character or numeric vector. RefTac TimeSec k2prime : perform MRTM2 kinetic modeling
- nii
Logical. save outputs as nii
- nii_gz
Logical. save outputs as nii.gz
- no_contrast_ok
Logical. do not fail if no contrasts specified
- no_est_fwhm
Logical. turn off FWHM output estimation
- no_mask_smooth
Logical. do not mask when smoothing
- no_prune
Logical. do not prune
- one_sample
Logical. construct X and C as a one-sample group mean
- pca
Logical. perform pca/svd analysis on residual
- per_voxel_reg
Character or numeric vector. per-voxel regressors
- profile
Integer. niters : test speed
- prune
Logical. remove voxels that do not have a non-zero value at each frame (def)
- prune_thresh
Numeric. prune threshold. Default is FLT_MIN
- resynth_test
Integer. test GLM by resynthsis
- save_cond
Logical. flag to save design matrix condition at each voxel
- save_estimate
Logical. save signal estimate (yhat)
- save_res_corr_mtx
Logical. save residual error spatial correlation matrix (eres.scm). Big!
- save_residual
Logical. save residual error (eres)
- seed
Integer. used for synthesizing noise
- self_reg
Character or numeric vector. self-regressor from index col row slice
- sim_done_file
Character; file path. create file when simulation finished
- sim_sign
Character; one of: "abs", "pos", "neg". abs, pos, or neg
- simulation
Character or numeric vector. nulltype nsim thresh csdbasename
- surf
Logical. analysis is on a surface mesh
- synth
Logical. replace input with gaussian
- uniform
Character or numeric vector. use uniform distribution instead of gaussian
- var_fwhm
Character. smooth variance by fwhm
- vox_dump
Character or numeric vector. dump voxel GLM and exit
- weight_inv
Logical. invert weights
- weight_sqrt
Logical. sqrt of weights
- weighted_ls
Character; file path. weighted least squares
- .cwd
Working directory override.
- .env
Named character vector of environment variables.
- .engine
Execution engine override.
- .profile
Runtime profile override.
- dry_run
Logical; preview command without executing.
- echo
Logical; echo stdout/stderr in real time.