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image2voxel

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NAME

image2voxel - Converts scanner-order data in a supported image format to voxel-order data.

SYNOPSIS

image2voxel -inputfile <image> | -imagelist <file> [options]

DESCRIPTION

Converts image files into the voxel ordering required by the Camino toolkit. By default, the output data type is float.

Two data formats are supported. The input may be a single file containing all components or a list of files containing each component separately, in order.

The 3D format is a series of files, each containing a single volume for one diffusion-weighted measurement. The order of the volumes must match the order of the corresponding measurements in the scheme file.

To convert 3D files to voxel order, pass a text file containing a list of images. For separate header / image pairs, list the headers:

dwi1.hdr
dwi2.hdr
...
dwiN.hdr

for files that contain a single image, list the images

dwi1.nii
dwi2.nii
...
dwiN.nii

for each of the N measurements. The order of the names in the file must match the order of the scheme file (see camino(1)). The program assumes that the images are in the same directory as the image list file, unless told otherwise with the -imageprefix option.

Scalar images (a single component per voxel) can usually be read directly into Camino, however they may be converted to raw format using this program.

EXAMPLES

Convert a 4D scanner order data file ScannerOrder.img, for which the measurement volume has size 128x128x60 and the acquisition scheme acquires 6 measurements with b=0 and 54 diffusion-weighted measurements, to voxel order. The header ScannerOrder.hdr has height=128, width=128, depth=60, nImages=60.

image2voxel -inputfile ScannerOrder.hdr > VoxelOrder.Bfloat

This is equivalent to the command:

scanner2voxel -voxels 983040 -components 60 < ScannerOrder.img > VoxelOrder.Bfloat

Convert NIfTI images stored as 3D volumes, listed in the file volumes.txt, to voxel order, and output the results as double

image2voxel -imagelist volumes.txt -outputdatatype double > VoxelOrder.Bdouble

Do the same thing, but this time the 3D volumes are in the directory ./data

image2voxel -imagelist volumes.txt -imageprefix ./data/ -outputdatatype double > VoxelOrder.Bdouble

Set the prefix to root when the image list contains absolute paths

image2voxel -imagelist volumes.txt -imageprefix / -outputdatatype double > VoxelOrder.Bdouble

OPTIONS

-inputfile <image> | -4dimage <file>: Path to the input image file or header to be converted.
-imagelist <filename>: Name of a file containing a list of 3D images, each containing a single diffusion-weighted measurement. The order of the headers in the list must match the order of the corresponding measurements in the scheme file.
-imageprefix <prefix>: Path to prepend onto filenames in the imagelist. Has no effect on paths specified on the command line with -4dimage. The default prefix is the directory containing the image list. This option is used when the imagelist is not in the same directory as the images it describes.
-outputdatatype <data type of output>: Specifies the data type of the output data. The data type can be any of the following strings: "char", "short", "int", "long", "float" or "double". The default output data type is float.

AUTHORS

Philip Cook <camino@cs.ucl.ac.uk>

BUGS

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Time: 02:07:11 GMT, December 04, 2017

Image2voxel