allenVectorTOmincVector: Rotates Allen data to MINC space

In DJFernandes/ABIgeneRMINC: Read, Write, and Analyzing Allen Gene Expression Raw Data

Rotates Allen data to MINC space

Description

Allen Gene Expression is stored as a 1-D array going from X=Anterior-to-Posterior, Y=Superior-to-Inferior, and Z=Left-to-Right (dimensions written from fastest changing index to slowest) MINC Data is stored as a 1-D array going from X=Left-to-Right, Y=Posterior-to-Anterior, Z=Inferior-to-Superior (dimensions written from fastest changing index to slowest) To compare Allen Gene expression data and MINC data, you have to rotate the Allen Gene Expression by 90 degrees about Z-axis and then 90 degrees about Y-axis This function rotates a 1-D allen vector to 1-D MINC space oriendation

Usage

allenVectorTOmincVector(allen.data, xyzDimSize = NULL, orientation.check = T)

Arguments

allen.data	data (either as array or 1D vector) in Allen Space Orientation
xyzDimSize	dimensions of Allen Space (in x,y,z). Default is c(67,41,58), the dimensions of Allen Gene Expression data
orientation.check	check orientation attribute.

Value

1-D vector in MINC space orientation

Examples

# Download gene expression files from the Allen Brain Institute
# In this example, I downloaded Pdyn expression energy (http://api.brain-map.org/grid_data/download/71717084)
# I included it in this library as an example

# Read Gene expression file
filename=system.file('extdata/Pdyn_P56_coronal_71717084_200um.zip',package="ABIgeneRMINC")
gene.expression.allen=read.raw.gene(filename)

# Rotate it to MINC Orientation
gene.expression.minc=allenVectorTOmincVector(gene.expression.allen)

# Rotate it back to Allen Orientation
gene.expression=mincVectorTOallenVector(gene.expression.minc)

# Going to minc orientation and back should NOT change any voxel values. Check that...
all(gene.expression == gene.expression.allen)

DJFernandes/ABIgeneRMINC documentation built on March 21, 2022, 12:05 p.m.