From 05e3b786c42a28fa7b92c9c7117fa48471a094a5 Mon Sep 17 00:00:00 2001
From: Stephen Smith <steve@fmrib.ox.ac.uk>
Date: Sun, 12 Sep 2004 08:01:12 +0000
Subject: [PATCH] CVS:
----------------------------------------------------------------------
---
doc/fdt_biggest.html | 9 +++++----
doc/fdt_display.html | 4 +++-
doc/fdt_thresh.html | 12 ++++++------
3 files changed, 14 insertions(+), 11 deletions(-)
diff --git a/doc/fdt_biggest.html b/doc/fdt_biggest.html
index a8a8ada..9c81b56 100644
--- a/doc/fdt_biggest.html
+++ b/doc/fdt_biggest.html
@@ -12,10 +12,11 @@ from that voxel reaching the target mask. <b>find_the_biggest</b> classifies
seed voxels according to the target mask with which they show the highest
probability of connection. It is run as follows:
<p><b>find_the_biggest list_of_volumes outputname</b>
-Where the list of volumes is the outputs of <b>Connectivity based seed
-classification</b> (i.e., files named seeds_to_target1 etc etc) and threshold
-is experessed as a number of samples
+Where the list of volumes is the outputs of <b>Connectivity-based seed
+classification</b> (i.e., files named seeds_to_target1 etc etc).
+
<p><IMG ALIGN=RIGHT height=300 SRC="fdt_images/fdt_seeds2targets_thal.gif"
ALT="connectivity-based classification of thalamus">
<p>The example on the right uses ProbTrack and find_the_biggest to perform hard segmentation
-of the thalamus on the basis of its connections to cortex
\ No newline at end of file
+of the thalamus on the basis of its connections to cortex.
+
diff --git a/doc/fdt_display.html b/doc/fdt_display.html
index 7376abc..cf50281 100644
--- a/doc/fdt_display.html
+++ b/doc/fdt_display.html
@@ -9,4 +9,6 @@ possible to display these vectors using <b>RGB</b> coding (where the colours
red,green and blue represent diffusion in the x,y,z axes respectively) or
using <b>lines</b> where a line at each voxel represent the principle
diffusion direction at that voxel. For more details see the relevant fslview
-<a href="http://www.fmrib.ox.ac.uk/fsl/fslview/dti_tutorial.html">tutorial</a>
\ No newline at end of file
+<a href="http://www.fmrib.ox.ac.uk/fsl/fslview/dti_tutorial.html"
+target="_top">tutorial</a>.
+
diff --git a/doc/fdt_thresh.html b/doc/fdt_thresh.html
index 95d83f7..5a791f5 100644
--- a/doc/fdt_thresh.html
+++ b/doc/fdt_thresh.html
@@ -3,7 +3,7 @@ BACKGROUND="fdt_images/fsl-bg.jpg">
<h3>proj_thresh</h3>
<b>proj_thresh</b> is a command line utility that provides an alternative way of
expressing connection probability in connectivity-based segmentation. It is
-run on the output of <b>connectivity-based seed
+run on the output of the <b>connectivity-based seed
classification</b> mode within <a href="fdt_probtrack.html"> <b>ProbTrack</b></a>.
<p>The output of <b>Connectivity-based seed classification</b> is a single volume for
each target mask, named <b>seeds_to_{target}</b> where {target} is replaced
@@ -12,10 +12,10 @@ value of each voxel within the seed mask is the number of samples seeded
from that voxel reaching the target mask.
<br><b>proj_thresh</b> is run as follows:
<p><b>proj_thresh list_of_volumes threshold</b></p>
-Where the list of volumes is the outputs of <b>Connectivity based seed
-classification</b> (i.e., files named seeds_to_target1 etc etc) and threshold is experessed as a number of samples
+Where the list of volumes is the outputs of <b>Connectivity-based seed
+classification</b> (i.e., files named seeds_to_target1 etc etc) and threshold is expressed as a number of samples
<br>For each voxel in the seeds mask that has a value above threshold for at
-least target mask, <b>proj_thresh</b> calculates the number of samples reaching each target mask
+least one target mask, <b>proj_thresh</b> calculates the number of samples reaching each target mask
as a proportion of the total number of samples reaching any target mask. The
-output of <b>proj_thresh</b> is a single volume for each target mask, names
-<b>???</b> where seed voxels will have values between zero and one.
\ No newline at end of file
+output of <b>proj_thresh</b> is a single volume for each target mask.
+
--
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