Merge branch 'release-1.2.4.8'

Mouse-Imaging-Centre · Apr 8, 2015 · 29970d0 · 29970d0
2 parents dfe6cc4 + 24fd03b
commit 29970d0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: RMINC
-Version: 1.2.4.7
+Version: 1.2.4.8
 Date: 2014-07-29
 Title: Package for reading and analyzing MINC2 files
 Author: Jason Lerch <jason@mouseimaging.ca>, Jim Nikelski

diff --git a/NAMESPACE b/NAMESPACE
@@ -10,7 +10,7 @@ export( mincIO.getSliceX )
 export( mincIO.getSliceY )
 export( mincIO.getSliceZ )
 export( mincIO.makeNewSliceZ )
-export( mincIO.makeNewVolume )
+#export( mincIO.makeNewVolume )
 export( mincIO.putSlice )
 export( mincIO.readBySlice )
 export( mincIO.readByVoxel )
@@ -48,6 +48,7 @@ export( civet.organizeCivetDatFilesMidWhiteGrey )
 export( civet.readCivetDatFiles )
 export( civet.readAllCivetFiles )
 export( civet.CreateBrainViewFile )
+export( civet.CreateBrainViewROI )
 export( civetFilenames )
 
 #############################
@@ -117,6 +118,7 @@ export( verboseRun )
 export( vertexFDR )
 export( vertexLm )
 export( vertexAnova )
+export( vertexApply )
 export( vertexMean )
 export( vertexSum )
 export( vertexSd )
@@ -150,17 +152,17 @@ export( mincIO.readMincInfo )
 
 #############################
 # mincSlice_class.R
-export( mincIO.plotSlicePretty )
+#export( mincIO.plotSlicePretty )
 
 #############################
 # mincVolumeIO_class.R
-export( mincIO.makeNewVolumeX )
-export( mincIO.readVolumeX )
-export( mincIO.writeVolumeX )
+#export( mincIO.makeNewVolumeX )
+#export( mincIO.readVolumeX )
+#export( mincIO.writeVolumeX )
 
 #############################
 # mincVoxelIO_class.R
-export( mincIO.readByVoxelX )
+#export( mincIO.readByVoxelX )
 
 #############################
 # rmincLmeLoop.R

diff --git a/NEWS b/NEWS
@@ -1,3 +1,13 @@
+New in Version 1.2.4.8
+======================
+* error checking in mincLm with respect to the mask size and input volume sizes
+* minc volumes are properly closed, so there is no limit in the numeber of 
+  minc files that can be opened in a session anymore
+* added civet.CreateBrainViewROI, a function that generates ROI files that can
+  be read by brain-view2
+* added anatApply analogous to mincApply/vertexApply
+* updated default paths to reflect changes at MICe
+
 New in Version 1.2.4.7
 ======================
 * fixed 2 bugs in anatGetFile: 1) calls the correct program in the "labels" method, and 

diff --git a/R/civet.R b/R/civet.R
@@ -1109,6 +1109,48 @@ else
 write.table(roiObj,outputFileName,FALSE,TRUE," ","\n","NA",".",FALSE,FALSE)
 }
 
+###########################################################################################
+#' @description Create a brainview file of a specific ROI
+#' @name civet.CreateBrainViewROI
+#' @title civet.CreateBrainViewROI
+#' @param atlasFile File with Atlas label (string-label(int)) mappings
+#' @param atlasVertices File with vertex label(int) mappings
+#' @param region Region to plot -> Must match name in atlas file exactly
+#' @param civetVersion Version of CIVET 
+#' @details Create a .txt file that can be overlaid unto the model template (usually in the CIVET models directory)
+#' Currently only CIVET version 1.1.12 is supported.
+#' @seealso civet.CreateBrainViewFile
+#' @examples
+#' getRMINCTestData() 
+#' civet.CreateBrainViewROI("/tmp/rminctestdata/AAL.csv","/tmp/rminctestdata/AAL_atlas_left.txt","Left Insula")
+#' q()
+#' (The .txt file is written in the working directory and can be viewed via the command)
+#' brain-view2 $CIVET_DIR/models/surf_reg_model_left.obj ./LeftInsula.txt
+###########################################################################################
+civet.CreateBrainViewROI <- function(atlasFile,atlasVertices,region,civetVersion="1.1.12") {
+
+	if ( civetVersion != "1.1.12" ) {
+		warning(sprintf("This function has not been tested with Civet version %s. Use at your own risk.", civetVersion), immediate.=TRUE)
+	}
+
+	vertices = read.csv(atlasVertices,header=FALSE)
+	AALAtlas = read.csv(atlasFile)
+	reducedVertices = vertices[1:40962,1]
+	roiObj =  rep(0,length(reducedVertices))
+
+	# Find index of ROI
+	roiIndex <- which(AALAtlas[,3] == region)
+
+	# Match against label
+	roiLabel <- which(reducedVertices == AALAtlas[roiIndex,1],arr.ind=FALSE)
+
+	# Fill in label
+	roiObj[roiLabel] = 1
+
+	# Write out (remove spaces)
+	write.table(roiObj,gsub(" ","",paste(region,".txt",sep="")),FALSE,TRUE,"","\n","NA",".",FALSE,FALSE)
+}
+
 # =============================================================================
 #
 # Deprecated .. Deprecated .. Deprecated .. Deprecated .. Deprecated ..