[ismrmrd] 14/281: Changes to documentation
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Wed Jan 14 20:00:49 UTC 2015
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a commit to annotated tag ismrmrd0.5
in repository ismrmrd.
commit 8cc3642ed74be274a7578b820118164662eaedfe
Author: Michael S. Hansen <michael.hansen at nih.gov>
Date: Sun Aug 19 11:57:05 2012 -0400
Changes to documentation
---
README.html | 73 ++++++++++++++++++------------------------------
doc/README.rst | 63 +++++++++++++++++++----------------------
doc/TODO.rst | 19 +++++++++++++
examples/data/README.txt | 17 +++++++++++
4 files changed, 92 insertions(+), 80 deletions(-)
diff --git a/README.html b/README.html
index 01a602d..678f91d 100644
--- a/README.html
+++ b/README.html
@@ -4,7 +4,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Docutils 0.8.1: http://docutils.sourceforge.net/" />
-<title>Magnetic Resonance Raw Data Standard</title>
+<title>ISMRM Raw Data Format (ISMRMRD)</title>
<style type="text/css">
/*
@@ -314,57 +314,31 @@ ul.auto-toc {
</style>
</head>
<body>
-<div class="document" id="magnetic-resonance-raw-data-standard">
-<h1 class="title">Magnetic Resonance Raw Data Standard</h1>
-
-<p>DRAFT - Version 0.1 - July 2012</p>
-<div class="section" id="todo">
-<h1>TODO</h1>
-<ul>
-<li><p class="first">Make More Example Datasets</p>
-<blockquote>
-<ul class="simple">
-<li>Radial</li>
-<li>Diffusion</li>
-<li>Phase contrast flow</li>
-</ul>
-</blockquote>
-</li>
-<li><p class="first">Flag definitions.</p>
-<blockquote>
-<ul class="simple">
-<li>Do we need more flags?</li>
-</ul>
-</blockquote>
-</li>
-<li><p class="first">Converters for vendor raw data</p>
-<blockquote>
+<div class="document" id="ismrm-raw-data-format-ismrmrd">
+<h1 class="title">ISMRM Raw Data Format (ISMRMRD)</h1>
+
+<div class="section" id="preamble">
+<h1>Preamble</h1>
+<p>A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. This document describes such a common raw data format and attempts to capture the data fields that are require to describe enough details about the magnetic resonance experiment to reconstruct images from the data.</p>
+<p>This standard was developed by a subcommittee of the ISMRM Sedona 2013 workshop. Comments and requests for additions/modifications can be sent to:</p>
<ul class="simple">
-<li>Siemens (Hansen)</li>
-<li>Philips (Kozerke? Boernert?)</li>
-<li>GE (Hargreaves?)</li>
-<li>Bruker (Hansen?)</li>
-</ul>
-</blockquote>
-</li>
+<li>Michael S. Hansen (michael.hansen AT nih DOT gov)</li>
+<li>Wally Block (wblock AT cae DOT wisc DOT edu)</li>
+<li>Mark Griswold (mag46 AT case DOT edu)</li>
+<li>Brian Hargreaves (bah AT stanford DOT edu)</li>
+<li>Peter Boernert (peter.boernert AT philips DOT com)</li>
+<li>Jim Pipe (Jim.Pipe AT DignityHealth DOT org)</li>
</ul>
+<p>The source code, examples, and example datasets can be found on the ISMRM Raw Data Sourceforge <a class="reference external" href="http://sourceforge.net/projects/ismrmrd">website</a>.</p>
+<p>To download the source code, clone the git archive:</p>
+<pre class="literal-block">
+git clone git://git.code.sf.net/p/ismrmrd/code ismrmrd-code
+</pre>
</div>
<div class="section" id="change-log">
<h1>Change log</h1>
<p>August 2012 - First draft.</p>
</div>
-<div class="section" id="preamble">
-<h1>Preamble</h1>
-<p>A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. This document describes such a common raw data format and attempts to capture all the data fields that are require to describe enough details about the magnetic resonance experiment to reconstruct images from the data.</p>
-<p>This standard was developed by a subcommittee of the ISMRM Sedona 2013 workshop. Comments and requests for additions/modifications can be sent to:</p>
-<ul class="simple">
-<li>Michael S. Hansen (<a class="reference external" href="mailto:michael.hansen@nih.gov">michael.hansen@nih.gov</a>)</li>
-<li>Wally Block (<a class="reference external" href="mailto:wblock@cae.wisc.edu">wblock@cae.wisc.edu</a>)</li>
-<li>Mark Griswold (<a class="reference external" href="mailto:mag46@case.edu">mag46@case.edu</a>)</li>
-<li>Brian Hargreaves (<a class="reference external" href="mailto:bah@stanford.edu">bah@stanford.edu</a>)</li>
-<li>Peter Boernert (<a class="reference external" href="mailto:peter.boernert@philips.com">peter.boernert@philips.com</a>)</li>
-</ul>
-</div>
<div class="section" id="overview">
<h1>Overview</h1>
<p>The raw data format combines a mix of flexible data structures (XML header) and fixed structures (equivalent to C-structs). A raw data set consist of 2 sections:</p>
@@ -635,7 +609,13 @@ std::cout << "Number of encoding spaces: " << cfg->enco
</div>
<div class="section" id="matlab-example-code-and-datasets">
<h1>Matlab Example Code and Datasets</h1>
-<p>The <tt class="docutils literal">examples</tt> folder contains datasets and some matlab code to illustrate simple interaction with the ISMRMRD data format. For instance, to reconstruct a 2D Cartesian acquisition (10 image repetitions), type (from the <tt class="docutils literal">examples/matlab</tt> folder):</p>
+<p>The <tt class="docutils literal">examples</tt> folder contains some matlab code to illustrate simple interaction with the ISMRMRD data format. The examples use test data sets, wich can be downloaded from the Sourceforge <a class="reference external" href="http://sourceforge.net/projects/ismrmrd">website</a>. Go to the <tt class="docutils literal">examples/data</tt> folder and type the following to download the data:</p>
+<pre class="literal-block">
+wget https://sourceforge.net/projects/ismrmrd/files/data/3D_partial_fourier.h5
+wget https://sourceforge.net/projects/ismrmrd/files/data/simple_gre.h5
+wget https://sourceforge.net/projects/ismrmrd/files/data/simple_spiral.h5
+</pre>
+<p>For instance, to reconstruct a 2D Cartesian acquisition (10 image repetitions), type (from the <tt class="docutils literal">examples/matlab</tt> folder):</p>
<pre class="literal-block">
>> images = simple_cartesian_recon('../data/simple_gre.h5');
Reconstructing image 1....done
@@ -728,6 +708,7 @@ Reconstructing image 10....done
<xs:element minOccurs="0" name="systemVendor" type="xs:string"/>
<xs:element minOccurs="0" name="systemModel" type="xs:string"/>
<xs:element minOccurs="0" name="systemFieldStrength_T" type="xs:float"/>
+ <xs:element minOccurs="0" name="relativeReceiverNoiseBandwidth" type="xs:float"/>
<xs:element minOccurs="0" name="receiverChannels" type="xs:unsignedShort"/>
</xs:all>
</xs:complexType>
diff --git a/doc/README.rst b/doc/README.rst
index d80eca8..00105c9 100644
--- a/doc/README.rst
+++ b/doc/README.rst
@@ -1,46 +1,34 @@
-Magnetic Resonance Raw Data Standard
-*************************************
+ISMRM Raw Data Format (ISMRMRD)
+*******************************
-DRAFT - Version 0.1 - July 2012
+Preamble
+---------
-TODO
--------------------------
+A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. This document describes such a common raw data format and attempts to capture the data fields that are require to describe enough details about the magnetic resonance experiment to reconstruct images from the data.
+
+This standard was developed by a subcommittee of the ISMRM Sedona 2013 workshop. Comments and requests for additions/modifications can be sent to:
-* Make More Example Datasets
+* Michael S. Hansen (michael.hansen AT nih DOT gov)
+* Wally Block (wblock AT cae DOT wisc DOT edu)
+* Mark Griswold (mag46 AT case DOT edu)
+* Brian Hargreaves (bah AT stanford DOT edu)
+* Peter Boernert (peter.boernert AT philips DOT com)
+* Jim Pipe (Jim.Pipe AT DignityHealth DOT org)
- - Radial
- - Diffusion
- - Phase contrast flow
+The source code, examples, and example datasets can be found on the ISMRM Raw Data Sourceforge website_.
-* Flag definitions.
+.. _website: http://sourceforge.net/projects/ismrmrd
- - Do we need more flags?
+To download the source code, clone the git archive::
-* Converters for vendor raw data
+ git clone git://git.code.sf.net/p/ismrmrd/code ismrmrd-code
- - Siemens (Hansen)
- - Philips (Kozerke? Boernert?)
- - GE (Hargreaves?)
- - Bruker (Hansen?)
Change log
----------
August 2012 - First draft.
-Preamble
----------
-
-A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. This document describes such a common raw data format and attempts to capture all the data fields that are require to describe enough details about the magnetic resonance experiment to reconstruct images from the data.
-
-This standard was developed by a subcommittee of the ISMRM Sedona 2013 workshop. Comments and requests for additions/modifications can be sent to:
-
-* Michael S. Hansen (michael.hansen at nih.gov)
-* Wally Block (wblock at cae.wisc.edu)
-* Mark Griswold (mag46 at case.edu)
-* Brian Hargreaves (bah at stanford.edu)
-* Peter Boernert (peter.boernert at philips.com)
-
Overview
---------
@@ -98,15 +86,15 @@ Each acquisition is preceded by the following fixed layout structure:
.. include:: ../ismrmrd.h
:literal:
- :start-line: 116
- :end-line: 141
+ :start-line: 118
+ :end-line: 143
Where EncodingCounters are defined as:
.. include:: ../ismrmrd.h
:literal:
- :start-line: 100
- :end-line: 112
+ :start-line: 102
+ :end-line: 114
The interpretation of some of these fields may vary from sequence to sequence, i.e. for a Cartesian sequence, ``kspace_encode_step_1`` would be the phase encoding step, for a spiral sequence where phase encoding direction does not make sense, it would be the spiral interleave number. The ``encoding_space_ref`` enables the user to tie an acquisition to a specific encoding space (see above) in case there are multiple, e.g. in situations where a calibration scan may be integrated in the acq [...]
@@ -243,7 +231,14 @@ Again, this is not a requirement for using the ISMRMRD format, the XML can be pa
Matlab Example Code and Datasets
--------------------------------
-The ``examples`` folder contains datasets and some matlab code to illustrate simple interaction with the ISMRMRD data format. For instance, to reconstruct a 2D Cartesian acquisition (10 image repetitions), type (from the ``examples/matlab`` folder):
+The ``examples`` folder contains some matlab code to illustrate simple interaction with the ISMRMRD data format. The examples use test data sets, wich can be downloaded from the Sourceforge website_. Go to the ``examples/data`` folder and type the following to download the data::
+
+ wget https://sourceforge.net/projects/ismrmrd/files/data/3D_partial_fourier.h5
+ wget https://sourceforge.net/projects/ismrmrd/files/data/simple_gre.h5
+ wget https://sourceforge.net/projects/ismrmrd/files/data/simple_spiral.h5
+
+
+For instance, to reconstruct a 2D Cartesian acquisition (10 image repetitions), type (from the ``examples/matlab`` folder):
::
diff --git a/doc/TODO.rst b/doc/TODO.rst
new file mode 100644
index 0000000..7f68a55
--- /dev/null
+++ b/doc/TODO.rst
@@ -0,0 +1,19 @@
+TODO
+-------------------------
+
+* Make More Example Datasets
+
+ - Radial
+ - Diffusion
+ - Phase contrast flow
+
+* Flag definitions.
+
+ - Do we need more flags?
+
+* Converters for vendor raw data
+
+ - Siemens (Hansen)
+ - Philips (Kozerke? Boernert?)
+ - GE (Hargreaves?)
+ - Bruker (Hansen?)
diff --git a/examples/data/README.txt b/examples/data/README.txt
new file mode 100644
index 0000000..92962b7
--- /dev/null
+++ b/examples/data/README.txt
@@ -0,0 +1,17 @@
+ISMRM Raw Data Example files
+-----------------------------
+
+
+
+Please download the example data files from:
+
+https://sourceforge.net/projects/ismrmrd/files/data/
+
+On Linux command line, simply type:
+
+wget https://sourceforge.net/projects/ismrmrd/files/data/3D_partial_fourier.h5
+wget https://sourceforge.net/projects/ismrmrd/files/data/simple_gre.h5
+wget https://sourceforge.net/projects/ismrmrd/files/data/simple_spiral.h5
+
+
+
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