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Manpage of datastats
datastats
Section: User Commands (1)
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NAME
datastats - Computes simple statistics of each diffusion weighted measurement within a region of interest.
Useful for estimating the noise level.
SYNOPSIS
datastats
[-schemefile <filename> -bgmask <filename>]
DESCRIPTION
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.
EXAMPLES
Create a mask for data file SubjectA.Bfloat:
mask -inputfile SubjectA.Bfloat -schemefile A.scheme -bgthresh 200 -outputdatatype short > SubjectA_M200.Bshort
Compute the statistics:
datastats -inputfile SubjectA.Bfloat -schemefile A.scheme -bgmask SubjectA_M200.Bshort
Foreground voxel count: 3248
Component E(S) E(S^2) Var(S) Std(S)
1 1.388036E02 2.061075E04 1.344318E03 3.666494E01
2 1.376616E02 2.016732E04 1.216598E03 3.487977E01
3 1.378830E02 2.030152E04 1.289794E03 3.591370E01
4 1.391675E02 2.067510E04 1.307506E03 3.615945E01
5 1.381736E02 2.036596E04 1.274002E03 3.569317E01
:
:
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:
datastats -inputfile SubjectA.Bfloat -schemefile A.scheme -bgmask A_BG.img -maskdatatype char
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.
AUTHORS
Daniel Alexander <camino@cs.ucl.ac.uk>
SEE ALSO
mask(1), restore(1), mbalign(1), modelfit(1).
BUGS
No known bugs.
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- EXAMPLES
-
- OPTIONS
-
- AUTHORS
-
- SEE ALSO
-
- BUGS
-
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