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build
View file @ 7787c2da
......@@ -221,13 +221,13 @@ except:
def SVN_last_changed (filename):
def git_last_changed (filename):
try:
process = subprocess.Popen ([ 'svn', 'info', filename ], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
process = subprocess.Popen ([ 'git', 'log', '--pretty=format:%ad', '--date=short',
'-n', '1', 'master', '--',filename ], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
if process.wait() != 0: raise 0
for line in process.stdout:
if line.startswith ('Text Last Updated:'):
return line.split(':')[1].split()[0].strip()
return as_str(line)
except:
return None
......@@ -711,15 +711,16 @@ MRtrix version #VERSION#<br>
def gen_doc ():
shutil.rmtree (doc_dir, True)
shutil.copytree (os.path.join (misc_dir, doc_dir), doc_dir)
os.makedirs (os.path.join (doc_dir, 'commands'));
gen_command_html_help()
for root, dirs, files in os.walk (doc_dir):
for entry in files:
if entry[0] == '.': continue
if not entry.endswith ('.html'): continue
fname = os.path.join (root, entry)
timestamp = SVN_last_changed (os.path.join (misc_dir, fname))
timestamp = git_last_changed (os.path.join (misc_dir, fname))
if not timestamp:
timestamp = SVN_last_changed (os.path.join (cmd_dir, entry.replace (".html", cpp_suffix)))
timestamp = git_last_changed (os.path.join (cmd_dir, entry.replace (".html", cpp_suffix)))
if not timestamp:
timestamp = '-'
with fopen(fname, 'r') as fd:
......
cmd/tracks2prob.cpp
View file @ 7787c2da
......@@ -127,9 +127,9 @@ class Voxel
z (_z_) { }
Voxel (const Point& p) :
x (round (p[0])),
y (round (p[1])),
z (round (p[2]))
x (std::round (p[0])),
y (std::round (p[1])),
z (std::round (p[2]))
{
assert (gsl_finite (p[0]) && gsl_finite (p[1]) && gsl_finite (p[2]));
}
......
debian/changelog
View file @ 7787c2da
mrtrix (0.2.13-1) unstable; urgency=medium
* Fresh upstream release
* debian/rules
+ export CPP_MARCH= to avoid addition of --march=native by upstream.
(patch debian_build_cfg was adjusted since now we can avoid patching)
* debian/patches
- glib-single-include.patch and size_t-ftbfs -- fully upstreamed
- fix-build-error-round -- upstream provided an alternative resolution
* debian/mrtrix-doc.install
* docs now are under src/doc
* debian/rules
* remove autogenerated lib/svn_revision.h upon clean
-- Yaroslav Halchenko <debian@onerussian.com> Fri, 24 Aug 2018 17:32:48 -0400
mrtrix (0.2.12-2.1) unstable; urgency=medium
* Non-maintainer upload.
* Fix build error with ambigous call to round (closes: #816570)
-- Willi Mann <willi@debian.org> Sat, 21 Oct 2017 16:22:07 +0200
mrtrix (0.2.12-2) unstable; urgency=medium
* Add patch to include <cstddef> to fix FTBFS due to missing size_t.
......
debian/mrtrix-doc.install
View file @ 7787c2da
doc/* usr/share/doc/mrtrix-doc/html
src/doc/* usr/share/doc/mrtrix-doc/html
debian/patches/debian_build_cfg
View file @ 7787c2da
Description: Change buildsystem setup for Debian
We cannot use --march, because we need to support many of them -- not even
'native', as it will over-optimize for the build machine.
Forwarded: not-needed
Author: Michael Hanke <michael.hanke@gmail.com>
--- a/sysconf/linux.py
+++ b/sysconf/linux.py
@@ -6,7 +6,7 @@
lib_suffix = '.so'
cpp = [ 'g++', '-c', '$flags$', '$gtk$', '$path$', '$src$', '-o', '$obj$' ]
-cpp_flags = [ '-Wall', '-pedantic', '-march=native', '-fPIC', '-fno-strict-aliasing', '-DGL_GLEXT_PROTOTYPES', '-DUSE_TR1' ]
+cpp_flags = [ '-Wall', '-pedantic', '-fPIC', '-fno-strict-aliasing', '-DGL_GLEXT_PROTOTYPES', '-DUSE_TR1' ]
ld = [ 'g++', '$flags$', '$path$', '$obj$', '$mrtrix$', '$gsl$', '$gtk$', '$lz$', '-o', '$bin$' ]
ld_flags = [ '-Wl,-rpath,$ORIGIN/../lib' ]
--- a/build
+++ b/build
@@ -180,6 +180,15 @@
@@ -180,6 +180,15 @@ if profile:
ld_flags = ld_flags_profile
ld_lib_flags = ld_lib_flags_profile
......
debian/patches/glib-single-include.patch deleted 100644 → 0
View file @ 6d30428e
--- a/lib/file/dicom/select_cmdline.cpp
+++ b/lib/file/dicom/select_cmdline.cpp
@@ -24,6 +24,7 @@
*/
+#include <glib.h>
#include "file/dicom/image.h"
#include "file/dicom/series.h"
#include "file/dicom/study.h"
debian/patches/series
View file @ 7787c2da
debian_build_cfg
glib-single-include.patch
size_t-ftbfs
debian/patches/size_t-ftbfs deleted 100644 → 0
View file @ 6d30428e
--- mrtrix-0.2.12.orig/src/dwi/SH.cpp
+++ mrtrix-0.2.12/src/dwi/SH.cpp
@@ -34,6 +34,7 @@
*/
+#include <cstddef>
#include <gsl/gsl_sf_legendre.h>
#include "image/position.h"
#include "image/interp.h"
debian/rules
View file @ 7787c2da
......@@ -6,6 +6,9 @@ include /usr/share/octave/debian/defs.make
# same for Matlab
include /usr/share/matlab/debian/defs.make
# To avoid --match=native since wouldn't be supported on some platforms
export CPP_MARCH=
# one ring to rule them all ...
%:
dh $@
......@@ -30,6 +33,7 @@ override_dh_clean:
./build -system=linux clean
find . -name '*.pyc' -delete
-rm mrtrix.xpm
-rm lib/svn_revision.h
dh_clean
@rm -f debian/mrtrix.links
......
doc/commands/average.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="index.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>average</th>
<td><a href="cat_tracks.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
average an image along a specific axis.
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; average [ options ] image1 output </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>image1</b></td>
<td>the first input image.</td></tr>
<tr><td><b>output</b></td>
<td>the output image.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-axis</b>&nbsp;<i>axis</i></td>
<td>specify axis along which averaging should be performed. By default, the program will use the last non-singleton axis of the input image.
<table class=opts>
<tr><td><i>axis</i></td>
<td>the concatenation axis</td></tr>
</table></td></tr>
<tr><td nowrap><b>-geometric</b></td>
<td>produce geometric mean. By default, the program will produce the arithmetic mean.</td></tr>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/cat_tracks.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="average.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>cat_tracks</th>
<td><a href="cleanup_ANTS_warp.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
Concatenate two track files
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; cat_tracks [ options ] output track1 track2 [ track2 ... ] </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>output</b></td>
<td>the output file containing the tracks.</td></tr>
<tr><td><b>track1</b></td>
<td>the first input tracks file.</td></tr>
<tr><td><b>track2</b> [ multiples allowed ]</td>
<td>the second input tracks file.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/cleanup_ANTS_warp.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="cat_tracks.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>cleanup_ANTS_warp</th>
<td><a href="csdeconv.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
clean up warp field generated by ANTS (or more specifically, WarpMultiImageTransform, replacing background voxels with NaN when they map to regions outside the original image.
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; cleanup_ANTS_warp [ options ] unit_warp ants_warp clean_warp </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>unit_warp</b></td>
<td>the original unit warp image</td></tr>
<tr><td><b>ants_warp</b></td>
<td>the warp image as produced by WarpMultiImageTransform.</td></tr>
<tr><td><b>clean_warp</b></td>
<td>the output cleaned-up warp image.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/csdeconv.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="cleanup_ANTS_warp.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>csdeconv</th>
<td><a href="dicom_filename.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
perform non-negativity constrained spherical deconvolution.
</p>
<p>
Note that this program makes use of implied symmetries in the diffusion profile. First, the fact the signal attenuation profile is real implies that it has conjugate symmetry, i.e. Y(l,-m) = Y(l,m)* (where * denotes the complex conjugate). Second, the diffusion profile should be antipodally symmetric (i.e. S(x) = S(-x)), implying that all odd l components should be zero. Therefore, this program only computes the even elements.
</p>
<p>
Note that the spherical harmonics equations used here differ slightly from those conventionally used, in that the (-1)^m factor has been omitted. This should be taken into account in all subsequent calculations.
</p>
<p>
Each volume in the output image corresponds to a different spherical harmonic component, according to the following convention:
</p>
<p>
[0] Y(0,0)
</p>
<p>
</p>
<p>
[1] Im {Y(2,2)}
</p>
<p>
[2] Im {Y(2,1)}
</p>
<p>
[3] Y(2,0)
</p>
<p>
[4] Re {Y(2,1)}
</p>
<p>
[5] Re {Y(2,2)}
</p>
<p>
</p>
<p>
[6] Im {Y(4,4)}
</p>
<p>
[7] Im {Y(4,3)}
</p>
<p>
etc...
</p>
<p>
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; csdeconv [ options ] dwi response SH </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>dwi</b></td>
<td>the input diffusion-weighted image.</td></tr>
<tr><td><b>response</b></td>
<td>the diffusion-weighted signal response function for a single fibre population.</td></tr>
<tr><td><b>SH</b></td>
<td>the output spherical harmonics coefficients image.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-grad</b>&nbsp;<i>encoding</i></td>
<td>specify the diffusion-weighted gradient scheme used in the acquisition. The program will normally attempt to use the encoding stored in image header.
<table class=opts>
<tr><td><i>encoding</i></td>
<td>the gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2).</td></tr>
</table></td></tr>
<tr><td nowrap><b>-lmax</b>&nbsp;<i>order</i></td>
<td>set the maximum harmonic order for the output series. By default, the program will use the highest possible lmax given the number of diffusion-weighted images.
<table class=opts>
<tr><td><i>order</i></td>
<td>the maximum harmonic order to use.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-mask</b>&nbsp;<i>image</i></td>
<td>only perform computation within the specified binary brain mask image.
<table class=opts>
<tr><td><i>image</i></td>
<td>the mask image to use.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-directions</b>&nbsp;<i>file</i></td>
<td>specify the directions over which to apply the non-negativity constraint (by default, the built-in 300 direction set is used
<table class=opts>
<tr><td><i>file</i></td>
<td>a text file containing the [ el az ] pairs for the directions.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-filter</b>&nbsp;<i>spec</i></td>
<td>the linear frequency filtering parameters used for the initial linear spherical deconvolution step (default = [ 1 1 1 0 0 ]).
<table class=opts>
<tr><td><i>spec</i></td>
<td>a text file containing the filtering coefficients for each even harmonic order.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-normalise</b></td>
<td>normalise the DW signal to the b=0 image</td></tr>
<tr><td nowrap><b>-lambda</b>&nbsp;<i>value</i></td>
<td>the regularisation parameter lambda that controls the strength of the constraint (default = 1.0).
<table class=opts>
<tr><td><i>value</i></td>
<td>the value of lambda to use.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-threshold</b>&nbsp;<i>value</i></td>
<td>the threshold below which the amplitude of the FOD is assumed to be zero, expressed as a fraction of the mean value of the initial FOD (default = 0.1).
<table class=opts>
<tr><td><i>value</i></td>
<td>the value of lambda to use.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-niter</b>&nbsp;<i>number</i></td>
<td>the maximum number of iterations to perform for each voxel (default = 50).
<table class=opts>
<tr><td><i>number</i></td>
<td>the maximum number of iterations to use.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/dicom_filename.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="csdeconv.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>dicom_filename</th>
<td><a href="dir2amp.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
read a DICOM file and output a suitable filename for its storage.
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; dicom_filename [ options ] file </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>file</b></td>
<td>the DICOM file to be scanned.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/dir2amp.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="dicom_filename.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>dir2amp</th>
<td><a href="disp_profile.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
convert directions image to amplitudes.
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; dir2amp [ options ] directions amplitudes </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>directions</b></td>
<td>the input directions image. Each volume corresponds to the x, y & z component of each direction vector in turn.</td></tr>
<tr><td><b>amplitudes</b></td>
<td>the output amplitudes image.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/disp_profile.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="dir2amp.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>disp_profile</th>
<td><a href="dwi2SH.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
view spherical harmonics surface plots.
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; disp_profile [ options ] coefs </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>coefs</b></td>
<td>a text file containing the even spherical harmonics coefficients to display.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-response</b></td>
<td>assume SH coefficients file only contains even, m=0 terms. Used to display the response function as produced by estimate_response</td></tr>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
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doc/commands/dwi2SH.html deleted 100644 → 0
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="disp_profile.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>dwi2SH</th>
<td><a href="dwi2tensor.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
convert base diffusion-weighted images to their spherical harmonic representation.
</p>
<p>
This program outputs the spherical harmonic decomposition for the set measured signal attenuations. The signal attenuations are calculated by identifying the b-zero images from the diffusion encoding supplied (i.e. those with zero as the b-value), and dividing the remaining signals by the mean b-zero signal intensity. The spherical harmonic decomposition is then calculated by least-squares linear fitting.
</p>
<p>
Note that this program makes use of implied symmetries in the diffusion profile. First, the fact the signal attenuation profile is real implies that it has conjugate symmetry, i.e. Y(l,-m) = Y(l,m)* (where * denotes the complex conjugate). Second, the diffusion profile should be antipodally symmetric (i.e. S(x) = S(-x)), implying that all odd l components should be zero. Therefore, this program only computes the even elements.
</p>
<p>
Note that the spherical harmonics equations used here differ slightly from those conventionally used, in that the (-1)^m factor has been omitted. This should be taken into account in all subsequent calculations.
</p>
<p>
Each volume in the output image corresponds to a different spherical harmonic component, according to the following convention:
</p>
<p>
[0] Y(0,0)
</p>
<p>
</p>
<p>
[1] Im {Y(2,2)}
</p>
<p>
[2] Im {Y(2,1)}
</p>
<p>
[3] Y(2,0)
</p>
<p>
[4] Re {Y(2,1)}
</p>
<p>
[5] Re {Y(2,2)}
</p>
<p>
</p>
<p>
[6] Im {Y(4,4)}
</p>
<p>
[7] Im {Y(4,3)}
</p>
<p>
etc...
</p>
<p>
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; dwi2SH [ options ] dwi SH </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>dwi</b></td>
<td>the input diffusion-weighted image.</td></tr>
<tr><td><b>SH</b></td>
<td>the output spherical harmonics coefficients image.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-grad</b>&nbsp;<i>encoding</i></td>
<td>specify the diffusion-weighted gradient scheme used in the acquisition. The program will normally attempt to use the encoding stored in image header.
<table class=opts>
<tr><td><i>encoding</i></td>
<td>the gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2).</td></tr>
</table></td></tr>
<tr><td nowrap><b>-lmax</b>&nbsp;<i>order</i></td>
<td>set the maximum harmonic order for the output series. By default, the program will use the highest possible lmax given the number of diffusion-weighted images.
<table class=opts>
<tr><td><i>order</i></td>
<td>the maximum harmonic order to use.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-normalise</b></td>
<td>normalise the DW signal to the b=0 image</td></tr>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/dwi2tensor.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="dwi2SH.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>dwi2tensor</th>
<td><a href="erode.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
convert diffusion-weighted images to tensor images.
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; dwi2tensor [ options ] dwi tensor </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>dwi</b></td>
<td>the input diffusion-weighted image.</td></tr>
<tr><td><b>tensor</b></td>
<td>the output diffusion tensor image.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-grad</b>&nbsp;<i>encoding</i></td>
<td>specify the diffusion-weighted gradient scheme used in the acquisition. The program will normally attempt to use the encoding stored in image header.
<table class=opts>
<tr><td><i>encoding</i></td>
<td>the gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2).</td></tr>
</table></td></tr>
<tr><td nowrap><b>-ignoreslices</b>&nbsp;<i>slice</i>&nbsp;<i>volumes</i></td>
<td>ignore the image slices specified when computing the tensor.
<table class=opts>
<tr><td><i>slice</i></td>
<td>the z coordinate of the slice to be ignored</td></tr>
<tr><td><i>volumes</i></td>
<td>the volume numbers of the slice to be ignored</td></tr>
</table></td></tr>
<tr><td nowrap><b>-ignorevolumes</b>&nbsp;<i>volumes</i></td>
<td>ignore the image volumes specified when computing the tensor.
<table class=opts>
<tr><td><i>volumes</i></td>
<td>the volumes to be ignored</td></tr>
</table></td></tr>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>
doc/commands/erode.html deleted 100644 → 0
View file @ 6d30428e
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix 0.2.12 documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>
<table class=nav>
<tr>
<td><a href="dwi2tensor.html"><img src="../left.png"></a></td>
<td><a href="index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>erode</th>
<td><a href="estimate_response.html"><img src="../right.png"></a></td>
</tr>
</table>
<h2>Description</h2>
<p>
erode (or dilate) mask (i.e. binary) image
</p>
<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; erode [ options ] input output </p>
<h2>Arguments</h2>
<table class=args>
<tr><td><b>input</b></td>
<td>input mask image to be eroded.</td></tr>
<tr><td><b>output</b></td>
<td>the output image.</td></tr>
</table>
<h2>Options</h2>
<table class=args>
<tr><td nowrap><b>-dilate</b></td>
<td>perform dilation rather than erosion.</td></tr>
<tr><td nowrap><b>-npass</b>&nbsp;<i>numebr</i></td>
<td>the number of passes (default: 1).
<table class=opts>
<tr><td><i>numebr</i></td>
<td>the number of passes.</td></tr>
</table></td></tr>
<tr><td nowrap><b>-info</b></td>
<td>display information messages.</td></tr>
<tr><td nowrap><b>-quiet</b></td>
<td>do not display information messages or progress status.</td></tr>
<tr><td nowrap><b>-debug</b></td>
<td>display debugging messages.</td></tr>
<tr><td nowrap><b>-help</b></td>
<td>display this information page and exit.</td></tr>
<tr><td nowrap><b>-version</b></td>
<td>display version information and exit.</td></tr>
</table>
<p class=footer>
Donald Tournier<br>
MRtrix version 0.2.12<br>
Last updated 2014-02-25
</p>
</body>
</html>