mincIO.getSliceFromSliceArray-methods: Methods to Get a Slice from a MincSliceIO Object
In jnikelski/rmincIO: Package for reading and writing MINC2 files

Description Usage Arguments Details Value Methods Author(s) See Also Examples

This method retrieves a specific slice from a MincSliceIO object, and uses it to instantiate a MincSlice object.

1 2	## S4 method for signature 'MincSliceIO' mincIO.getSliceFromSliceArray(mincSliceMatrix, sliceIndex)

mincSliceMatrix

The name of a MincSliceIO object, most likely created via a call to mincIO.readBySlice.

sliceIndex

The column number within the MincSliceIO object data matrix used to create the Slice object. If the MincSliceIO object was initialized from a single 4D volume, then each column will represent a specific slice across all frames of the dynamic volume. Thus, in this case, the sliceIndex would refer to a specific slice at a specific frame. Similarly, if the MincSliceIO object was initialized from a list of 3D volumes, then the sliceIndex would refer to a specific slice within a specific volume.

MincSliceIO objects contain their data within a M x N matrix, in which each of the N columns store data from a specific slice, obtained from either (1) all frames of a single 4D volume, or (2) a collection of 3D volumes. This method can be used to convert one of these matrix columns into a MincSlice object for visualization or manipulation.

A MincSlice object.

mincSliceMatrix = "MincSliceIO": Only one method/signature.

Jim Nikelski nikelski@bic.mni.mcgill.ca

mincIO.readBySlice MincSlice MincSliceIO

## Not run: 
\dontshow{
# clear debug flag and get full volume pathname
# ... dunno why zzz.R debug setting is not passed
    R_DEBUG_rmincIO <- 0      
    volDir <- system.file("packageData/volumes", package="rmincIO")
}

# read a slice from a dynamic volume
v4d <- file.path(volDir, "functional_4D.mnc")
s080_SA <- mincIO.readBySlice(v4d, 80)                 # read slice 80 across all frames
s080f006 <- mincIO.getSliceFromSliceArray(s080_SA,6)   # get the slice from the 6th frame
print(s080f006)
plot(s080f006)

# read a slice from a series of 3D volumes
v305 <- file.path(volDir, "average305_PET_t1_tal_lin.mnc")
s020_SA <- mincIO.readBySlice(c(v305, v305), 20)       # read slice 20 for all volumes
s020v002 <- mincIO.getSliceFromSliceArray(s020_SA,2)   # get the slice for the 2nd volume
print(s020v002)
plot(s020v002)

## End(Not run)