From 729362d32daccd30b204c53d65a6e6ebaf1d5079 Mon Sep 17 00:00:00 2001 From: Saad Jbabdi <saad@fmrib.ox.ac.uk> Date: Mon, 30 Nov 2009 10:56:47 +0000 Subject: [PATCH] change default dof --- doc/fdt_reg.html | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/doc/fdt_reg.html b/doc/fdt_reg.html index 1adb00e..78ba5ce 100644 --- a/doc/fdt_reg.html +++ b/doc/fdt_reg.html @@ -10,17 +10,19 @@ href="../fsl.css"><TITLE>FSL</TITLE></HEAD> <p>If tractography results are to be stored in any space other than diffusion space then registration must be run. -<p>Registration within Fdt uses <a href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html" target="_top">flirt</a>. Registration can only be applied after <b>bedpostx</b> has been run. Typically, registration will be run between three spaces: -<ul><li>Diffusion space (using the nodif_brain image in the bedpostX directory)</li> +<p>Registration within FDT uses <a href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html" target="_top">FLIRT</a>. When using the GUI, registration can only be applied after <b>bedpostx</b> has been run. Typically, registration will be run between three spaces: +<ul><li>Diffusion space (using the <code>nodif_brain</code> image in the bedpostX directory.)</li> <li>Structural space (using the struct image in the bedpostX directory, e.g., the space of a high resolution T1-weighted image of the same subject)</li> -<li>Standard space (by default, the MNI152 brain stored within $FSLDIR/etc/standard)</li></ul> +<li>Standard space (by default, the MNI152 brain stored within $FSLDIR/data/standard)</li></ul> + +<p>Note that the structural (T1-weighted) image must have had <a href="http://www.fmrib.ox.ac.uk/fsl/bet/index.html" target="_top">BET</a> applied. The <code>nodif_brain</code> image should be the brain extracted version of the nodif image that is stored in the bedpostX directory. Create this image using <code>fslroi</code> then <code>bet</code> on the data if it does not already exist. (it is important that the user checks the quality of bet results on these images and adjust the settings in bet where appropriate). -<p>Note that struct must have had <a href="http://www.fmrib.ox.ac.uk/fsl/bet/index.html" target="_top">bet</a> applied. The nodif_brain image should be the brain extracted version of the nodif image that is automatically stored in the bedpostX directory. The user will have to manually apply bet to this image after running <b>bedpostx</b> and before running registration. (it is important that the user check the quality of bet results on these images and adjust the settings in bet where appropriate). <p>Transformation matrices, and their inverses, will be derived from diffusion to structural space and from structural to standard space. Relevant matrices will be concatenated to produce transformation matrices between diffusion and standard space. The resulting matrices are stored within -the 'xfms' subdirectory of the bedpost directory and named as follows: +the <code>xfms</code> subdirectory of the bedpostX directory and named as follows: + <ul><li>diff2str.mat - from diffusion to structural space</li> <li>str2diff.mat - from structural to diffusion space</li> @@ -30,8 +32,10 @@ the 'xfms' subdirectory of the bedpost directory and named as follows: <li>standard2str.mat - from standard to structural space</li></ul> <p>By default, transformation matrices between diffusion and structural space are -derived using 12 degrees of freedom, the mutual information cost -function and normal search; transformations matrices between structural and standard space +derived using 6 degrees of freedom, the correlation ratio cost +function and normal search; transformation matrices between structural and standard space are derived using 12 degrees of freedom, the correlation ratio cost function and normal search. These parameters may be adjusted if required using the drop down menus in the registration panel. + + -- GitLab