From f8e0799e183dda3fbdcf11fa23091bacb27cd481 Mon Sep 17 00:00:00 2001 From: Saad Jbabdi <saad@fmrib.ox.ac.uk> Date: Fri, 20 Jul 2007 17:07:08 +0000 Subject: [PATCH] doc for vecreg --- doc/fdt_vecreg.html | 48 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 doc/fdt_vecreg.html diff --git a/doc/fdt_vecreg.html b/doc/fdt_vecreg.html new file mode 100644 index 0000000..69b2e2d --- /dev/null +++ b/doc/fdt_vecreg.html @@ -0,0 +1,48 @@ +<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 <input4Dvector> -o <output4D> -t <transformation> + +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> + -- GitLab