.TH dcm2image "1" "Jul 20 2012" "CMTK 2.2.2" "The Computational Morphometry Toolkit"
.SH NAME
dcm2image \- DICOM to Image
.SH SYNOPSIS
\fBdcm2image\fR SearchDirList 
.SH DESCRIPTION
Combine sets of DICOM slices to 3D image stacks
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Input Options
.TP 5
\fB\-\-recurse\fR, \fB\-r\fR
Recurse into directories
.SS Output Options
.TP 5
\fB\-\-out-pattern\fR \fI<string>\fR, \fB\-O\fR \fI<string>\fR
Output image path pattern. Use the following substitutions: printf-style %d variante (image number); %n (image number with automatic number of digits); %N (like %n, but with a hyphen '-' before number if there is more than one image); %D (DICOM SeriesDescription); %R (DICOM RepetitionTime - MRI only); %E (DICOM EchoTime - MRI only); %T (RawDataType - vendor-specific, currently GE MRI only)
.B [Default: "image%n.nii"]
.TP 5
\fB\-\-xml\fR, \fB\-x\fR
Write XML sidecar file for each created image.
.TP 5
\fB\-\-embed\fR
Embed DICOM information into output images as 'description' (if supported by output file format).
Supported values: "StudyID_StudyDate", "PatientName", "SeriesDescription", "None", where the default is "StudyID_StudyDate", or use one of the following:
.RS 5
.TP 5
\fB\-\-StudyID_StudyDate\fR
StudyID, tag (0020,0010), then underscore, followed by StudyDate, tag (0008,0020). Date is appended because StudyID is four digits only and will repeat sooner or later.
\fB[This is the default]\fR
.TP 5
\fB\-\-PatientName\fR
Patient name, tag (0010,0010)
.TP 5
\fB\-\-SeriesDescription\fR
Series description, tag (0008,103e)
.TP 5
\fB\-\-None\fR
Embed no information - leave 'description' field empty.
.RE
.SS Filtering Options
.TP 5
\fB\-\-filter\fR \fI<string>\fR
Filter DICOM files and include only those matching the given pattern of the form 'TagName=text', such that the value of the DICOM tag with the given name contains the given text. If multiple filter patterns are provided via repeated use of this option, only files that match ALL patterns are included.
.TP 5
\fB\-\-exclude\fR \fI<string>\fR
Exclude all DICOM files matching the given pattern of the form 'TagName=text', such that the value of the DICOM tag with the given name contains the given text. If multiple exclusion patterns are provided, all files are excluded that match ANY of the patterns.
.SS Sorting Options
.TP 5
\fB\-\-no-sort\fR
Do NOT sort files by file name (sorting determines image stack order when resolving spatial collisions)
.TP 5
\fB\-\-sort-by-name\fR
Sort files lexicographically by file name. Use this when instance numbers are non-unique.
.TP 5
\fB\-\-sort-by-instance\fR
Sort files by image instance number. Use this when file names are different lengths, etc.
\fB[This is the default]\fR
.SS Stacking Options
.TP 5
\fB\-\-ignore-acq-number\fR
Ignore 'AcquisitionNumber' tag for image grouping, i.e., do not separate stacks based on this tag.
.TP 5
\fB\-\-no-orientation-check\fR
Disable checking of image orientations (to avoid rounding issues)
.TP 5
\fB\-\-tolerance\fR \fI<double>\fR
Tolerance for floating-point comparisons (must be >= 0; 0 = exact matches only; default: 1e-5)
.B [Default: 1e-05]
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, and Daniel B. Russakoff
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH ACKNOWLEDGMENTS
From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging and Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).