NAME¶
dwi_mask_bad_slices - Find bad slices in set of diffusion-weighted images.
SYNOPSIS¶
dwi_mask_bad_slices DiffusionImagePaths
DESCRIPTION¶
This tool reads a set of 3D diffusion-weighted MR images and finds bad slices. A
bad slice in a diffusion image is detected as one whose mean intensity is
outside a specified interval around the mean of the means of all corresponding
slices from the remaining diffusion images.
OPTIONS¶
- --help
- Write list of basic command line options to standard output.
- --help-all
- Write complete list of basic and advanced command line options to standard
output.
- --wiki
- Write list of command line options to standard output in MediaWiki
markup.
- --man
- Write man page source in 'nroff' markup to standard output.
- --version
- Write toolkit version to standard output.
- --echo
- Write the current command line to standard output.
- --verbose-level <integer>
- Set verbosity level.
- --verbose, -v
- Increment verbosity level by 1 (deprecated; supported for backward
compatibility).
- --threads <integer>
- Set maximum number of parallel threads (for POSIX threads and
OpenMP).
- --b0count <integer>
- Number of b=0 images at the beginning of the image list. These are not
included in the bad slice detection or masking, but are also written to
the output directory for convenience. It is assumed that all b=0 images
are at the beginning of the list of input images, but not at the end or in
the middle. [Default: 0]
- --slice-orientation
- Define slice orientation of the diffusion images. Supported values:
"axial", "sagittal", "coronal",
"slice-x", "slice-y", "slice-z", where the
default is "axial", or use one of the following:
- --axial
- Axial slices [This is the default]
- --sagittal
- Sagittal slices
- --coronal
- Coronal slices
- --slice-x
- X coordinate axis is slice direction
- --slice-y
- Y coordinate axis is slice direction
- --slice-z
- Z coordinate axis is slice direction [This is the default]
Bad Slice Detection¶
- --stdev <double>
- Threshold for bad slice identification in units of intensity standard
deviations over all corresponding slices from the remaining diffusion
images. [Default: 3]
Output Options¶
- --convert-to
- Scalar data type for the output images. If your padding value is negative
but your input data unsigned, for example, make sure to select a signed
data type for the output. By default, the output data type is the same as
the input type. Supported values: "char", "byte",
"short", "ushort", "int", "uint",
"float", "double", or use one of the following:
- --char
- 8 bits, signed
- --byte
- 8 bits, unsigned
- --short
- 16 bits, signed
- --ushort
- 16 bits, unsigned
- --int
- 32 bits signed
- --uint
- 32 bits unsigned
- --float
- 32 bits floating point
- --double
- 64 bits floating point
- --padding-value <double>, -p
<double>
- Padding value to replace data of detected bad slices in output images.
[Default: -1]
- --output-directory <string>, -o
<string>
- File system path for writing images with bad slices masked out (i.e.,
filled with a padding value). [Default: NONE]
AUTHORS¶
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis,
Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
LICENSE¶
http://www.fsf.org/licensing/licenses/gpl.html
BUGS¶
Report bugs at
http://nitrc.org/projects/cmtk/
ACKNOWLEDGMENTS¶
CMTK is developed with support from the NIAAA under Grant AA021697, National
Consortium on Alcohol and Neurodevelopment in Adolescence (N-CANDA): Data
Integration Component. From April 2009 through September 2011, CMTK
development and maintenance was supported by the NIBIB under Grant
EB008381.