Reads a data file from the acquisition scheme specified in the schemefile. The ROI can be
specified in a mask file or by thresholding the b=0 image using -bgthresh. The program
computes the mean, mean squared, variance and standard deviation of each image in the
foreground region specified by the mask file.
Useful for estimating the noise level (as required for restore or mbalign) or signal to
noise. An estimate of the noise level sigma (standard deviation of each component of the
complex noise on the signal) is sqrt(E(S^2)/2) from an ROI entirely in background. Eg,
draw an ROI in background on the FA image from the data set using MRIcro. (The mask
volume should be the same size as one component of the full DWI data set.) Save the mask
as an analyze image ROI->Export ROI as Analyze Image; Save [Sun]. MRIcro saves the mask
as type char, so to measure the statistics in the region run:
If the ROI is truly in background, you should see little variation among the different
diffusion weighted images, so can choose any to compute sigma.
OPTIONS
-inputfile <file>
Diffusion-weighted MRI data file in voxel order.
-schemefile <file>
Schemefile.
-bgthresh <integer>
The threshold on the average b=0 measurement.
-inputdatatype <data type of input>
Specifies the data type of the input file. The data type can be any of the following
strings: "char", "short", "int", "long", "float" or "double". See camino(1).
-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". See camino(1).
-bgmask <Mask file>
Mask file name. The mask file contains zero in background voxels and non-zero in
foreground. The mask must be big endian; the default data type is 16-bit shorts, but can
be changed using the -maskdatatype option.
-maskdatatype <char|short|int|long|float|double>
Specifies the type of the mask file; must be big-endian byte ordering.