Description Usage Arguments Value Author(s) Examples
View source: R/getUniqueLesionPatches.R
Compute uniqe patches of voxels with the same pattern of lesions in all subjects. Useful to understand the number of patterns that will be analyzed in a lesion dataset. A patch is a group of voxels, not necessarily close to each other, which have the same identical lesion pattern.
1 2 3 | getUniqueLesionPatches(lesions.list, mask = NA,
returnPatchMatrix = FALSE, thresholdPercent = 0.1,
binaryCheck = FALSE, showInfo = TRUE)
|
lesions.list |
list of antsImages (faster) or filenames (slower) |
mask |
(default=NA) a mask image to restrict the search for patches. Will be
automatically calculated if not provided. Normally the mask restricts
the search only to voxels lesioned in >10% of subejcts. To set this proportion
use |
returnPatchMatrix |
(default=FALSE) logical, should the matrix of patches
be returned. This is used in |
thresholdPercent |
(default=0.1) voxels with lesions in less than this proportion of subjects will not be considered. I.e., 0.1 = 10%. |
binaryCheck |
(default=FALSE) set this to TRUE to verify that maps are binary. |
showInfo |
(default=TRUE) logical indicating whether to display information. |
List of objects named as follows:
patchimg
- antsImage with every voxel assigned a patch number
patchimg.samples
- antsImage mask of one representative voxel
for each patch. Can be used to extract the patchmatrix.
patchimg.size
- antsImage with the patch size at every voxel
patchimg.mask
- antsImage of the mask used to extract patches. Can
be used to put back results when combined with patchindx
.
patchindx
- vector of patch membership for each voxel. Can
be used to put back results in an image.
npatches
- number of unique patches in the image
nvoxels
- total number of lesioned voxels in patchimg.mask
patchvoxels
- vector of voxel count for each patch
patchvolumes
- vector of volume size for each patch
patchmatrix
- matrix of patches. This is used in lesymap to
save time when running repetitive analyses.
Dorian Pustina
1 2 3 4 5 6 7 | lesydata = file.path(find.package('LESYMAP'),'extdata')
filenames = Sys.glob(file.path(lesydata, 'lesions', '*.nii.gz'))
patchinfo = getUniqueLesionPatches(filenames[1:10]) # slower
lesions = imageFileNames2ImageList(filenames[1:10])
patchinfo = getUniqueLesionPatches(lesions) # faster
|
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