flexconn_predict: Predict from FLEXCONN model

In neuroconductor/flexconn: FLEXCONN Model

Description

Predict from FLEXCONN model

Usage

flexconn_predict_patch(
  model,
  t1,
  flair,
  t2 = NULL,
  mask = NULL,
  patchsize,
  verbose = TRUE,
  ...,
  batch_size = 1
)

flexconn_predict(
  model,
  t1,
  flair,
  t2 = NULL,
  mask = NULL,
  type = c("volume", "patch"),
  patchsize,
  verbose = TRUE,
  normalize = TRUE,
  ...,
  batch_size = 1
)

flexconn_predict_with_patches(
  model,
  t1,
  flair,
  t2 = NULL,
  mask = NULL,
  patchsize,
  verbose = TRUE,
  ...,
  batch_size = 1
)

flexconn_predict_with_volume(
  model,
  t1,
  flair,
  t2 = NULL,
  verbose = TRUE,
  normalize = TRUE,
  ...,
  batch_size = 1
)

Arguments

model	A keras model object trained
t1	3D array or nifti image
flair	3D array or nifti image
t2	3D array or nifti image, optional if model has this
mask	binary 3D array or nifti image, but of the whole area of prediction, not the ground truth
patchsize	Vector of length 2 (or more)
verbose	print diagnostic messages
...	additional arguments to get_patches
batch_size	Size of batches for prediction. Integer. Passed to predict.keras.engine.training.Model.
type	type of prediction to use, patch-based or slice/volume based
normalize	Run normalize_image on the image before prediction

Value

A vector of predictions, based on the indices of the mask

Note

If mask = NULL, a mask will be generated for t1 > 0.

Examples

## Not run: 
model_file = tempfile(fileext = ".h5")
base_url = paste0("https://github.com/muschellij2/flexconnr",
"/raw/master/inst/extdata/")
model_url = paste0(base_url, "21atlases/",
"atlas_with_mask1/FLEXCONNmodel2D_35x35_17-10-2017_21-53-35.h5")
download.file(model_url, destfile = model_file)

t1_file = tempfile(fileext = ".nii.gz")
download.file(paste0(base_url, "T1.nii.gz"), destfile = t1_file)

flair_file = tempfile(fileext = ".nii.gz")
download.file(paste0(base_url, "FLAIR.nii.gz"), destfile = flair_file)

model = keras::load_model_hdf5(model_file)
res = flexconn_predict(model,
t1 = t1_file,
flair = flair_file)

## End(Not run)

neuroconductor/flexconn documentation built on Sept. 25, 2020, 10:51 a.m.