Runs FSL epi_reg script for simultaneous coregistration and fieldmap
Usage
ni_fsl_epi_reg(
epi,
t1_brain,
t1_head,
args = NULL,
echospacing = NULL,
fmap = NULL,
fmapmag = NULL,
fmapmagbrain = NULL,
no_clean = TRUE,
no_fmapreg = NULL,
out_base = "epi2struct",
pedir = NULL,
weight_image = NULL,
wmseg = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- epi
Character; file path. EPI image Required.
- t1_brain
Character; file path. brain extracted T1 image Required.
- t1_head
Character; file path. wholehead T1 image Required.
- args
Character. Additional parameters to the command
- echospacing
Numeric. Effective EPI echo spacing (sometimes called dwell time) - in seconds
- fmap
Character; file path. fieldmap image (in rad/s)
- fmapmag
Character; file path. fieldmap magnitude image - wholehead
- fmapmagbrain
Character; file path. fieldmap magnitude image - brain extracted
- no_clean
Logical. do not clean up intermediate files
- no_fmapreg
Logical. do not perform registration of fmap to T1 (use if fmap already registered)
- out_base
Character. output base name
- pedir
Character; one of: "x", "y", "z", "-x", "-y", "-z". phase encoding direction, dir = x/y/z/-x/-y/-z
- weight_image
Character; file path. weighting image (in T1 space)
- wmseg
Character; file path. white matter segmentation of T1 image, has to be named like the t1brain and end on _wmseg
- .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.