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efb7fe84 · Stephen Smith · 189f769d · efb7fe84 · 189f769d · efb7fe84
Commit efb7fe84 authored 20 years ago by Stephen Smith
--- a/doc/fdt_eddy.html
+++ b/doc/fdt_eddy.html
 <HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
 <p><h3>Eddy Current Correction</h3>
-Eddy current in the gradient coils induce (approximate) stretches and shears
+Eddy currents in the gradient coils induce (approximate) stretches and shears
 in the diffusion weighted images. These distortions are different for
-different gradient directions. Eddy Current Correciton corrects for these
+different gradient directions. Eddy Current Correction corrects for these
 distortions, and for simple head motion, using affine registration to a
 reference volume.
 <p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the
-<b>FDT</b> button.  Use the top left drop down menu to select Eddy Current Correction.  
+<b>FDT</b> button.  Use the top left drop down menu to select <b>Eddy current correction</b>.  

-<p><b>Diffusion Weighted data:</b> Use the browse button to select your 4D
-analyze format series of diffusion weighted data.
+<p><b>Diffusion weighted data:</b> Use the browse button to select
+your diffusion weighted dataset (a 4D image).
 <br><b>Corrected output data:</b> Use the browse button to specify a filename for
 the corrected 4D dataset.
-<br><b>Reference Volume:</b> (default 0). Set the volume number for the reference volume
+<br><b>Reference volume:</b> (default 0). Set the volume number for the reference volume
 that will be used as a target to register all other volumes to. <br><br>
 <b>command line utility</b><br>
 eddy_correct &#60;4dinput&#62; &#60;4doutput&#62; &#60;reference_no&#62;

--- a/doc/fdt_images/gui_intro.gif
+++ b/doc/fdt_images/gui_intro.gif
--- a/doc/fdt_intro.html
+++ b/doc/fdt_intro.html
@@ -17,28 +17,29 @@ separately.
 The main FDT programmes, which are accesible from the GUI are:

 <ul><li><a href="fdt_eddy.html">eddycorrect</a> - for correction of eddy current distortion</li>
-<li><a href="fdt_bedpost.html">Bedpost</a> - for local modelling of diffusion parameters.</li>
-<li><a href="fdt_probtrack.html">ProbTrack</a> - for tractography and connectivity-based segmentation</li> 
-<li><a href="fdt_dtifit.html">DtiFit</a> - for local of fitting of diffusion tensors</li></ul>
+<li><a href="fdt_bedpost.html">bedpost</a> - for local modelling of diffusion parameters.</li>
+<li><a href="fdt_probtrack.html">probtrack</a> - for tractography and connectivity-based segmentation</li> 
+<li><a href="fdt_dtifit.html">dtifit</a> - for local of fitting of diffusion tensors</li></ul>

-<br>The FDT GUI also includes a <a href="fdt_reg.html">registration</a> option that registers images using <a
-href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html" target="_top"> FLIRT </a>
+<br>The FDT GUI also includes a <a
+href="fdt_reg.html">registration</a> option that registers images
+using <a href="../flirt/index.html" target="_top">FLIRT</a>.

 <p>Additional FDT programmes, that can be run only from the command line, are:
 <ul><li><a href="fdt_thresh.html">proj_thresh</a> - for thresholding some outputs
-of ProbTrack</li>
+of probtrack</li>
 <li><A href="fdt_biggest.html">find_the_biggest</a> - for performing hard
-segmentation on the outputs of connectivity-based thersholding in ProbTrack</li></ul>
+segmentation on the outputs of connectivity-based thresholding in probtrack</li></ul>

 <p>The probabilistic tractography tools within FDT are very flexible and allow
 the user to generate connectivity distributions from single or multiple
-voxels; to limit these distribution based on anatomical criteria and to
+voxels; to limit these distributions based on anatomical criteria and to
 perform segmentation based on the probability of connection to user-defined
 target regions.

-<p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the <b>FDT</b> button.
+<p>To call the FDT GUI, either run <b>Fdt</b> (<b>Fdt_gui</b> on Mac
+or Windows), or run <b>fsl</b> and press the <b>FDT</b> button.

 <p>For an overview of the local diffusion modelling and tractography used
-within FDT see the <a href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">appendix</a>
-
+within FDT see the <a href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">appendix</a>.

--- a/doc/fdt_pipeline.html
+++ b/doc/fdt_pipeline.html
@@ -4,8 +4,8 @@
 <p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the <b>FDT</b> button.

 <p>A typical processing pipeline (and approximate time required for each
-stage, based on an Intel 2.4GHz processor, and a 60 direction whole brain
-dataset of dimensions, at 2.5 mm isotropic resolution )
+stage, based on an Intel 2.4GHz processor, and a 60-direction whole brain
+dataset of dimensions 128x128x64, at 2.5 mm isotropic resolution)
 would consist of:
 <ol>
 <li>Any study or scanner-specific pre-processing (e.g., averaging of multiple

--- a/fdt.tcl
+++ b/fdt.tcl
@@ -356,7 +356,7 @@ proc fdt:dialog { w tclstartupfile } {
    $w.tool.menu add command eddy_current -label "Eddy current correction"
    $w.tool.menu add command bedpost      -label "BEDPOST Estimation of diffusion parameters"
    $w.tool.menu add command registration -label "Registration"
-    $w.tool.menu add command probtrack    -label "ProbTrack Probabalistic tracking"
+    $w.tool.menu add command probtrack    -label "ProbTrack Probabilistic tracking"
    $w.tool.menu add separator xutilsx
    $w.tool.menu add command dtifit       -label "DTIFit Reconstruct diffusion tensors"