Description Usage Arguments Details Value See Also Examples
Compute the normalization values for each contrast parameter.
1 2 3 4 | ## S4 method for signature 'MRIaggr'
calcNormalization(object, param, mu_type = "mean", sigma_type = "sd",
rm.CSF = FALSE, rm.WM = FALSE, rm.GM = FALSE,
verbose = optionsMRIaggr("verbose"), update.object = FALSE, overwrite = FALSE)
|
object |
an object of class |
param |
the contrast parameters to normalize. character vector. REQUIRED. |
mu_type |
the type of centering. Can be |
sigma_type |
the type of scaling. Can be |
rm.CSF |
should the cerebral spinal fluid observations be excluded ? logical. |
rm.GM |
should the grey matter observations be excluded ? logical. |
rm.WM |
should the white matter observations be excluded ? logical. |
verbose |
should the execution of the function be traced ? logical. |
update.object |
should the resulting normalization values be stored in |
overwrite |
if normalization values are already stored in |
FUNCTION:
If any of the rm.CSF
, rm.WM
or rm.GM
is set to true, then the values of the parameters remaining to FALSE
(among CSF
, WM
and GM
) are summed. Voxels with value under 0.5 are discarded.
Note that rm.CSF
, rm.GM
and rm.WM
cannot be set simultaneously to TRUE
.
An list containing the normalization values, one element for each type of normalization.
selectNormalization
to select the normalization values.
calcTissueType
to compute a probabilistic classification of the brain observations in WM/GM/CSF.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## load a MRIaggr object
data("MRIaggr.Pat1_red", package = "MRIaggr")
## compute normalization values
res <- calcNormalization(MRIaggr.Pat1_red, param = c("DWI_t0","T2_FLAIR_t2"),
update.object = TRUE, overwrite = TRUE)
## display
par(mfrow = c(2,4), mar = rep(1.5,4), mgp = c(2,0.5,0))
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2", num = 1:3,
legend = TRUE, window = NULL, main = "raw - slice ")
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2", num = 1:3,
norm_mu="contralateral", norm_sigma="contralateral",
legend = TRUE, window = NULL, main = "normalized - slice ")
## extract normalization
selectNormalization(MRIaggr.Pat1_red, type = "global", mu = TRUE, sigma = FALSE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.