.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.2.
.TH DCMSTACK "1" "September 2015" "dcmstack 0.7.0dev" "User Commands"
.SH NAME
dcmstack \- DICOM to NIfTI converter
.SH DESCRIPTION
usage: dcmstack [\-h] [\-\-force\-read] [\-\-file\-ext FILE_EXT] [\-\-allow\-dummies]
.IP
[\-\-dest\-dir DEST_DIR] [\-o OUTPUT_NAME]
[\-\-output\-ext OUTPUT_EXT] [\-d] [\-\-embed\-meta] [\-g GROUP_BY]
[\-\-voxel\-order VOXEL_ORDER] [\-t TIME_VAR]
[\-\-vector\-var VECTOR_VAR] [\-\-time\-order TIME_ORDER]
[\-\-vector\-order VECTOR_ORDER] [\-l]
[\-\-disable\-translator DISABLE_TRANSLATOR] [\-\-extract\-private]
[\-i INCLUDE_REGEX] [\-e EXCLUDE_REGEX] [\-\-default\-regexes] [\-v]
[\-\-strict] [\-\-version]
[src_dirs [src_dirs ...]]
.PP
Stack DICOM files from each source directory into 2D to 5D volumes, optionally
extracting meta data.
.SS "positional arguments:"
.TP
src_dirs
The source directories containing DICOM files.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "Input options:"
.TP
\fB\-\-force\-read\fR
Try reading all files as DICOM, even if they are
missing the preamble.
.TP
\fB\-\-file\-ext\fR FILE_EXT
Only try reading files with the given extension.
Default: .dcm
.TP
\fB\-\-allow\-dummies\fR
Allow DICOM files that are missing pixel data, filling
that slice of the output nifti with the maximum
representable value.
.SS "Output options:"
.TP
\fB\-\-dest\-dir\fR DEST_DIR
Destination directory, defaults to the source
directory.
.TP
\fB\-o\fR OUTPUT_NAME, \fB\-\-output\-name\fR OUTPUT_NAME
Python format string determining the output filenames
based on DICOM tags.
.TP
\fB\-\-output\-ext\fR OUTPUT_EXT
The extension for the output file type. Default:
\&.nii.gz
.TP
\fB\-d\fR, \fB\-\-dump\-meta\fR
Dump the extracted meta data into a JSON file with the
same base name as the generated Nifti
.TP
\fB\-\-embed\-meta\fR
Embed the extracted meta data into a Nifti header
extension (in JSON format).
.SS "Stacking Options:"
.TP
\fB\-g\fR GROUP_BY, \fB\-\-group\-by\fR GROUP_BY
Comma seperated list of meta data keys to group input
files into stacks with.
.TP
\fB\-\-voxel\-order\fR VOXEL_ORDER
Order the voxels so the spatial indices start from
these directions in patient space. The directions in
patient space should be given as a three character
code: (l)eft, (r)ight, (a)nterior, (p)osterior,
(s)uperior, (i)nferior. Passing an empty string will
disable reorientation. Default: LAS
.TP
\fB\-t\fR TIME_VAR, \fB\-\-time\-var\fR TIME_VAR
The DICOM element keyword to use for ordering the
stack along the time dimension.
.TP
\fB\-\-vector\-var\fR VECTOR_VAR
The DICOM element keyword to use for ordering the
stack along the vector dimension.
.TP
\fB\-\-time\-order\fR TIME_ORDER
Provide a text file with the desired order for the
values (one per line) of the attribute used as the
time variable. This option is rarely needed.
.TP
\fB\-\-vector\-order\fR VECTOR_ORDER
Provide a text file with the desired order for the
values (one per line) of the attribute used as the
vector variable. This option is rarely needed.
.SS "Meta Extraction and Filtering Options:"
.TP
\fB\-l\fR, \fB\-\-list\-translators\fR
List enabled translators and exit
.TP
\fB\-\-disable\-translator\fR DISABLE_TRANSLATOR
Disable the translators for the provided tags. Tags
should be given in the format "0x0_0x0". More than one
can be given in a comma separated list. If the word
"all" is provided, all translators will be disabled.
.TP
\fB\-\-extract\-private\fR
Extract meta data from private elements, even if there
is no translator. If the value for the element
contains non\-ascii bytes it will still be ignored. The
extracted meta data may still be filtered out by the
regular expressions.
.TP
\fB\-i\fR INCLUDE_REGEX, \fB\-\-include\-regex\fR INCLUDE_REGEX
Include any meta data where the key matches the
provided regular expression. This will override any
exclude expressions. Applies to all meta data.
.TP
\fB\-e\fR EXCLUDE_REGEX, \fB\-\-exclude\-regex\fR EXCLUDE_REGEX
Exclude any meta data where the key matches the
provided regular expression. This will supplement the
default exclude expressions. Applies to all meta data.
.TP
\fB\-\-default\-regexes\fR
Print the list of default include and exclude regular
expressions and exit.
.SS "General Options:"
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Print additional information.
.TP
\fB\-\-strict\fR
Fail on the first exception instead of showing a
warning.
.TP
\fB\-\-version\fR
Show the version and exit.
.PP
IT IS YOUR RESPONSIBILITY TO KNOW IF THERE IS PRIVATE HEALTH INFORMATION IN
THE METADATA EXTRACTED BY THIS PROGRAM.