civet.computeTissueVolumes: Compute GM, WM, and CSF Tissue Volumes

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

Compute GM, WM, and CSF Tissue Volumes

Description

Returns a named vector of tissue volumes.

Usage

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

civet.computeNativeTissueVolumes(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

Actually, this function really returns the number of voxels of each tissue type contained within the final discrete Civet-produced classification volume. Now, given that Civet volumes are currently sampled using 1-mm isotropic voxels, the voxel count value should also reflect the volume in cubic millimeters. If this ever changes, we're going to have to make a minor change in this function. Please let me know if this ever happens. The native volume measurements are created by taking the stereotactic volumes and dividing each of them by the xfm-derived rescaling factor.

Value

A named vector containing a value for each of the 3 tissue types.

Functions

• civet.computeStxTissueVolumes: standard space

• civet.computeNativeTissueVolumes: native space

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"

# print gray matter volume in stereotactic space
stx_cls_vec <- civet.computeStxTissueVolumes(scanID, baseDir)
print(stx_cls_vec["gm"])

# print csf volume in native space
native_cls_vec <- civet.computeNativeTissueVolumes(scanID, baseDir)
print(native_cls_vec["csf"])

## End(Not run)

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