Description Usage Arguments Details Value Methods Author(s) See Also Examples
This method retrieves slice 1 from a MincVolumeIO object, and uses it to instantiate an axial MincSlice object. If an initialization vector is provided, it will be used to initialize the slice values, else the slice will be initialized to zeros.
1 2 | ## S4 method for signature 'MincVolumeIO'
mincIO.makeNewSliceZ(mincVolume,initVector)
|
mincVolume |
The name of a MincVolumeIO object. |
initVector |
An initialization vector that must contain the same number of elements as are in the slice. |
This method fills a very particular need. Specifically, let's say that we have loaded
a bunch of slices into a MincSliceIO
matrix object, and we do a computation at every
voxel. This computation will result in a vector having a length reflecting the number
of voxels in the slice. Obviously, we would want to store this result somewhere, so this
method permits us to create an empty Z-slice to act as a container for the result. Once
the result is in a MincSlice
object, it can then be easily moved into a
MincVolumeIO
object for subsequent writing.
Note that the reason for having a mincIO.makeNewSliceZ
method and no mincIO.newSliceX
or
mincIO.newSliceY
methods is because the MincSliceIO
objects currently
only store axial slices. If a need arises for these other methods, they shall be
written.
A MincSlice object.
Only one method/signature.
Jim Nikelski nikelski@bic.mni.mcgill.ca
mincIO.putSlice
MincSlice
MincVolumeIO
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## 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")
}
# create an empty volume and axial slice
vol <- mincIO.makeNewVolume("myResultsVolume.mnc", likeTemplate="mni305PET")
# load slice 20 from 2 3D volumes into a MincSliceIO object
v305 <- file.path(volDir, "average305_PET_t1_tal_lin.mnc")
slicesMatrix <- mincIO.readBySlice(c(v305, v305), 20)
# compute the mean at each voxel
sliceMean <- apply(slicesMatrix,1,mean)
# create an axial slice and init with the mean() result
zSlice <- mincIO.makeNewSliceZ(vol, sliceMean)
# display/visualize the slice
print(zSlice)
plot(zSlice)
# move the results slice into the output volume
# ... as slice 20
vol <- mincIO.putSlice(zSlice, vol, 20)
## End(Not run)
|
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