Merge pull request #60 from mandymejia/15.0

15.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ciftiTools
 Type: Package
 Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
-Version: 0.14.0
+Version: 0.15.1
 Authors@R: c(
     person(given = "Amanda",
            family = "Mejia",
@@ -50,6 +50,7 @@ Suggests:
     gridExtra,
     htmlwidgets,
     manipulateWidget,
+    webshot2,
     knitr,
     rmarkdown,
     png,

R/as.xifti.R

@@ -54,7 +54,7 @@
 #'  \code{\link{substructure_table}}. It is either a 3D data array 
 #'  (\eqn{i \times j \times k}) of integer brainstructure indices, or a \eqn{V_S} length
 #'  vector in spatial order with brainstructure names as factors or integer
-#'  indices. The indices should be 3-21 (1 and 2 correspond to left and right
+#'  indices. The indices should be 3-22 (1 and 2 correspond to left and right
 #'  cortex, respectively) or 1-19 (cortex labels omitted), with 0 representing
 #'  out-of-mask voxels.
 #'  

R/impute_xifti.R

@@ -0,0 +1,7 @@
+#' Impute \code{"xifti"} data
+#' 
+#' Impute masked values using the values of adjacent, non-masked locations.
+#' 
+#' @inheritParams xifti_Param
+#' @param mask A logical vector whose length matches the number of rows in
+#'  \code{xifti} object.

R/info_cifti.R

@@ -23,7 +23,8 @@ supported_intents <- function(){
 #' Substructure table
 #'
 #' Table of labels for cortex hemispheres (left and right) and subcortical
-#'  substructures. The names used by the CIFTI format and the names used by
+#'  substructures. The same labels used by the HCP data are here, plus "Other".
+#'  Names from the CIFTI format ("CIFTI_STRUCTURE_*") and the names used by
 #'  \code{ciftiTools} are given.
 #'
 #' The names used by \code{ciftiTools} are based on those in
@@ -57,7 +58,8 @@ substructure_table <- function(){
     c("PUTAMEN_LEFT",               "Putamen-L"),
     c("PUTAMEN_RIGHT",              "Putamen-R"),
     c("THALAMUS_LEFT",              "Thalamus-L"),
-    c("THALAMUS_RIGHT",             "Thalamus-R")
+    c("THALAMUS_RIGHT",             "Thalamus-R"),
+    c("OTHER",                      "Other")
   ))
   colnames(table) <- c("Original_Name", "ciftiTools_Name")
   table$Index <- seq_len(nrow(table))

R/make_xifti.R

@@ -76,7 +76,7 @@
 #'  \code{\link{substructure_table}}. It is either a NIFTI file path, 3D data array
 #'  (\eqn{i \times j \times k}) of integer brainstructure indices, or a \eqn{V_S} length
 #'  vector in spatial order with brainstructure names as factors or integer
-#'  indices. The indices should be 3-21 (1 and 2 correspond to left and right
+#'  indices. The indices should be 3-22 (1 and 2 correspond to left and right
 #'  cortex, respectively) or 1-19 (cortex labels omitted), with 0 representing
 #'  out-of-mask voxels.
 #'
@@ -93,18 +93,17 @@
 #'  the medial wall from the data values. \code{NULL} should be used if \code{NA}
 #'  or \code{NaN} are legitimate values that non-medial wall vertices might
 #'  take on.
-#' @param cifti_info (Optional) The result of \code{\link{info_cifti}}. If
-#'  GIFTI and/or NIFTI components from a CIFTI are being provided,
-#'  providing \code{cifti_info} gives metadata information that would otherwise
-#'  have to be inferred: the NIFTI intent, brainstructures present in the
-#'  original file, and miscellaneous metadata.
+#' @param cifti_info (Optional) The result of \code{\link{info_cifti}}, i.e. 
+#'  the metadata to put in \code{$meta$cifti}: the NIFTI intent, and 
+#'  miscellaneous metadata. If GIFTI and/or NIFTI components from a CIFTI are 
+#'  being provided, providing \code{cifti_info} gives information that would 
+#'  otherwise have to be inferred.
 #'
-#'  This argument is probably not necessary for end users: reading a CIFTI
-#'  should be done by providing \code{cifti_fname}, and for reading separate
-#'  GIFTI/NIFTI components \code{cifti_info} is not applicable.
-#'
-#'  Column names from \code{cortexL} and \code{cortexR} take precedence over column
-#'  names from \code{cifti_info}.
+#'  Column names from \code{cortexL} and \code{cortexR} take precedence over 
+#'  column names from \code{cifti_info}.
+#' 
+#'  \code{$meta$cifti$brainstructures} will be based on what data is provided
+#'  to \code{make_xifti} rather than \code{cifti_info}.
 #' @param surfL,surfR (Optional) Surface geometries for the left or right cortex.
 #'  Can be a surface GIFTI file path or \code{"surf"} object; see
 #'  \code{\link{make_surf}} for a full description of valid inputs.