camino_fsl2scheme: Wrapper for Camino 'fsl2scheme' function

Description Usage Arguments Value

View source: R/camino_fsl2scheme.R

Description

Performs the Camino fsl2scheme function

Usage

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camino_fsl2scheme(bvecs, bvals, outfile = NULL, diffusiontime = NULL,
  bscale = NULL, flipx = FALSE, flipy = FALSE, flipz = FALSE,
  interleave = FALSE, zerobval = NULL, numscans = NULL,
  usegradmod = FALSE, verbose = TRUE)

Arguments

bvecs

The file containing the b-vectors.

bvals

The file containing the b-values.

outfile

output filename for fsl scheme file

diffusiontime

Diffusion time in seconds

bscale

Scaling factor to convert the b-values into different units. Default is 10^6.

flipx

Negate the x component of all the vectors.

flipy

Negate the y component of all the vectors.

flipz

Negate the z component of all the vectors.

interleave

Interleave repeated scans. Only used with -numscans. If this is selected, the output will be interleaved, so you will have mea- surement 0 repeated numScans times, then measurement 1, etc.

zerobval

Set an effective zero b-value, input b-values less than or equal to this are set to zero in the output. This is needed for some Camino programs that normalize the input data by dividing each measurement by the mean b=0 measurement. This value is tested after any applicable scaling is applied to the bvals.

numscans

Output all measurements number times, used when combining multiple scans from the same imaging session. The default behaviour is to repeat the entire block of measurements, like you'd get from copying and pasting the scheme number times. If -interleave is specified, then identical measurements are grouped together.

usegradmod

Use the gradient magnitude to scale b. This option has no effect if your gradient directions have unit magnitude. It should only be used if your scanner does not normalize the gradient directions.

verbose

Print diagnostic messages

Value

Output filename


muschellij2/caminor documentation built on Nov. 9, 2019, 2:48 a.m.