doc for vecreg

f8e0799e · Saad Jbabdi · d9b89f37 · f8e0799e
Commit f8e0799e authored 17 years ago by Saad Jbabdi
--- a/doc/fdt_vecreg.html
+++ b/doc/fdt_vecreg.html
+<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE>
+<BODY BACKGROUND="fdt_images/fsl-bg.jpg">
+<h3>Registration of vector images using vecreg</h3>
+<p>
+<IMG ALIGN=RIGHT height=200 SRC="fdt_images/fdt_vecreg.gif"
+ALT="vecreg applied to V1">  
+After running dtifit or bedpost, it is often useful to register vector data to another space. For example, one might want to represent V1 for different subjects in standard space. <b>vecreg</b> is a command line tool that allows to perform such registration.<br>
+Vector images cannot be registered by simply applying a transformation (as calculated by, say, flirt) to every voxel's coordinates. The corresponding vectors have to be reoriented accordingly (see D. Alexander 2001, IEEE-TMI 20:1131-1139). vecreg perform this operation for you.
+The image shows the effect of applying vecreg (right) to the V1 image on the left, compared to simply apply voxelwise transformation (e.g. using applyxfm4D) to the vectors (centre).
+<br><br>
+<b> Important: </b> vecreg does not calculate a transformation, but simply applies a given transformation to the input vector field. vecreg can apply a linear transformation calculated with FLIRT, or a non-linear transformation calculated using either IRTK or FNIRT, using a warpfield calculated by dof2warp.
+<p>
+types of vectors that may be used for vecreg<br>
+from dtifit: V1,V2,V3<br>
+from bedpost: dyads1, dyads2, etc. <br>
+<p>
+<h3>Command-line utility</h3>
+<b>using a flirt matrix</b><br>
+vecreg -i input_vector -o output_vector -r reference_image -t flirt_transform.mat<br>
+<b>using a warpfield</b><br>
+vecreg -i input_vector -o output_vector -r reference_image -w warp_field<br>
+<br>
+<b>more options</b><br>
+<pre>
+Usage: 
+vector_flirt -i &lt;input4Dvector&gt; -o &lt;output4D&gt; -t &lt;transformation&gt;
+Compulsory arguments (You MUST set one or more of):
+        -i,--input      filename of input vector
+        -o,--output     filename of output registered vector
+        -r,--ref        filename of reference (target) volume
+Optional arguments (You may optionally specify one or more of):
+        -v,--verbose    switch on diagnostic messages
+        -h,--help       display this message
+        -t,--affine     filename of affine transformation matrix
+        -w,--warpfield  filename of 4D warp field for nonlinear registration
+        --interp        interpolation method : nearestneighbour (default) or trilinear or sinc
+        -m,--mask       brain mask in input space
+</pre>