[med-svn] r5621 - trunk/packages/elastix/trunk/debian

Fri Dec 24 23:42:08 UTC 2010

Author: smr
Date: 2010-12-24 23:42:08 +0000 (Fri, 24 Dec 2010)
New Revision: 5621

Added:
   trunk/packages/elastix/trunk/debian/copyright
   trunk/packages/elastix/trunk/debian/elastix.1
   trunk/packages/elastix/trunk/debian/transformix.1
Log:
Add copyright, manpages.

Added: trunk/packages/elastix/trunk/debian/copyright
===================================================================

--- trunk/packages/elastix/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/elastix/trunk/debian/copyright	2010-12-24 23:42:08 UTC (rev 5621)
@@ -0,0 +1,35 @@
+Name: elastix
+Maintainer: Stefan Klein and Marius Staring
+Source: http://elastix.isi.uu.nl/
+
+
+Elastix Copyright Notice:
+
+      Copyright (c) 2004-2010 University Medical Center Utrecht
+      All rights reserved.
+
+
+Elastix was initially developed by Stefan Klein and Marius Staring
+under contract to the Image Sciences Institute, University Medical
+Center Utrecht, The Netherlands.
+
+Elastix is distributed under the new and simplified BSD license
+approved by the Open Source Initiative (OSI)
+[http://www.opensource.org/licenses/bsd-license.php].  This license
+may be found in file /usr/share/common-licenses/BSD.
+
+The software is partially derived from the Insight Segmentation and
+Registration Toolkit (ITK), which is also distributed under the new
+and simplified BSD licence.  The ITK is required by Elastix for
+compilation of the source code.
+
+The copyright of the files in the Common/KNN/ann_1.1 subdirectory is
+held by a third party, the University of Maryland. The ANN package is
+distributed under the GNU Lesser Public Licence v2.1.  This license
+may be found in file /usr/share/common-licenses/LGPL-2.1.  
+
+In the Debian package of elastix, ANN is statically linked.  Clause 3
+of the LGPL is hereby invoked to re-license ANN under the GNU Public
+License, v2 (see /usr/share/common-licenses/GPL-2).  The elastix
+package as a whole is therefore under the GPL v2 license.
+

Added: trunk/packages/elastix/trunk/debian/elastix.1
===================================================================
--- trunk/packages/elastix/trunk/debian/elastix.1	                        (rev 0)
+++ trunk/packages/elastix/trunk/debian/elastix.1	2010-12-24 23:42:08 UTC (rev 5621)
@@ -0,0 +1,39 @@
+.TH ELASTIX "1" "December 2010" "elastix version: 4.400" "User Commands"
+.SH NAME
+elastix \- manual page for elastix version: 4.400
+.SH SYNOPSIS
+\fBelastix\fP \fImandatory-args\fR [\fIoptional-args\fR]
+.SH DESCRIPTION
+elastix registers a moving image to a fixed image.
+The registration\-process is specified in the parameter file.
+.PP
+.SH OPTIONS
+Call elastix from the command line with mandatory arguments:
+.TP
+\fB\-f\fR        fixed image
+.TP
+\fB\-m\fR        moving image
+.TP
+\fB\-out\fR      output directory
+.TP
+\fB\-p\fR        parameter file, elastix handles 1 or more "\-p"
+.PP
+Optional extra commands:
+.TP
+\fB\-fMask\fR    mask for fixed image
+.TP
+\fB\-mMask\fR    mask for moving image
+.TP
+\fB\-t0\fR       parameter file for initial transform
+.TP
+\fB\-priority\fR set the process priority to high or belownormal (Windows only)
+.TP
+\fB\-threads\fR  set the maximum number of threads of elastix
+.PP
+The parameter\-file must contain all the information necessary for elastix to run properly. That includes which metric to use, which optimizer, which transform, etc.
+It must also contain information specific for the metric, optimizer, transform, ...
+For a usable parameter\-file, see the website.
+.SH "SEE ALSO"
+.BR transformix (1)
+.PP
+Check the website http://elastix.isi.uu.nl, or mail elastix.support at gmail.com.

Added: trunk/packages/elastix/trunk/debian/transformix.1
===================================================================
--- trunk/packages/elastix/trunk/debian/transformix.1	                        (rev 0)
+++ trunk/packages/elastix/trunk/debian/transformix.1	2010-12-24 23:42:08 UTC (rev 5621)
@@ -0,0 +1,41 @@
+.TH TRANSFORMIX "1" "December 2010" "transformix version: 4.400" "User Commands"
+.SH NAME
+transformix \- manual page for transformix version: 4.400
+.SH SYNOPSIS
+\fBtransformix\fP \fImandatory-args\fR [\fIoptional-args\fR]
+.SH DESCRIPTION
+transformix applies a transform on an input image and/or generates a deformation field.
+The transform is specified in the transform\-parameter file.
+.PP
+.SH OPTIONS
+Call transformix from the command line with mandatory arguments:
+.TP
+\fB\-out\fR      output directory
+.TP
+\fB\-tp\fR       transform\-parameter file, only 1
+.PP
+Optional extra commands:
+.TP
+\fB\-in\fR       input image to deform
+.TP
+\fB\-def\fR      file containing input\-image points
+.IP
+the point are transformed according to the specified transform\-parameter file
+use "\-def all" to transform all points from the input\-image, which effectively generates a deformation field.
+.PP
+.TP
+\fB\-jac\fR      use "\-jac all" to generate an image with the determinant of the spatial Jacobian
+.TP
+\fB\-jacmat\fR   use "\-jacmat all" to generate an image with the spatial Jacobian matrix at each voxel
+.TP
+\fB\-priority\fR set the process priority to high or belownormal (Windows only)
+.TP
+\fB\-threads\fR  set the maximum number of threads of transformix
+At least one of the options "\-in", "\-def", "\-jac", or "\-jacmat" should be given.
+.PP
+The transform\-parameter file must contain all the information necessary for transformix to run properly. That includes which transform to use, with which parameters, etc.
+For a usable transform\-parameter file, see the output of elastix.
+.SH "SEE ALSO"
+.BR elastix (1)
+.PP
+Check the website http://elastix.isi.uu.nl, or mail elastix.support at gmail.com.


