civet.computeNativeToStxRescalingFactor: Compute Native to Stereotactic Rescaling Factor

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

Compute Native to Stereotactic Rescaling Factor

Description

Returns a single float scalar reflecting a global rescaling factor needed to transform the native image to stereotactic space.

Usage

civet.computeNativeToStxRescalingFactor(
  scanID,
  baseDir,
  civetVersion = "1.1.9"
)

Arguments

scanID	A string specifying the unique scan-id (and thus sub-directory) within the Civet root output directory.
baseDir	A string specifying the Civet root output directory. This directory will, in turn, contain all of the scanIDs.
civetVersion	An optional string specifying the version of Civet used to create the output. This is significant since filenames and directory structures may change across difference versions of Civet.

Details

XFM files contain information to transform a given volume to a model. In the case of Civet and rescaling, the XFM contains the rescaling factors (x,y,z) needed to transform the Native volume to the model, which currently, is usually the symmetrical icbm-152 model.

This functuon serves to compute a global rescaling factor by reading the individual x,y,z rescales from the linear XFM, and returning the product.

Interpretation of rescaling factors:

• rescale > 1.0 The native brain is expanded to fit model

• rescale < 1.0 The native brain is reduced to fit model

Value

A scalar float reflecting the rescaling factor is returned.

Author(s)

Jim Nikelski [e-mail]

Examples

## Not run: 
library(RMINC)

# set Civet root path and scan-identifier
basePath <- "~/tmp/ADNI/civet/pipeOut"
scanID = "0221-M-AD"

# compute the global rescaling factor
rescale <- civet.computeNativeToStxRescalingFactor(scanID, basePath)
print(rescale)

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.