Hi,
1 - You can use fslmaths to create large masks. For instance:
fslmaths inputimage -mul 0 -add 1 -roi 20 100 34 100 12 100 0 1
outputimage
would create a 100x100x100 mask, starting at 20,34,12 in voxel
coords.
You can also create spherical ones by using the -roi to create a
centre voxel
and then apply a spatial filter with a spherical kernel.
2 - There isn't a command line way to do this, but you could do
something
with matlab by loading in the text file and then using the save_avw
command that you can find in $FSLDIR/etc/matlab (you need to use
the addpath function in matlab to make sure it can also see the
supporting
functions)
3 - You can print out any flirt cost function value as described in:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=FSL&P=R14314&X=728B053B67CD2C87E9&Y=mark%40fmrib.ox.ac.uk
All the best,
Mark
On 4 Nov 2008, at 17:59, Siamak Yousefi wrote:
> Dear Mark,
>
> Thank you very much for your nice comment. I exactly meant
> registering by
> applying mask on cost function.
>
> I have some other problems in this regard. i'd be grateful if
> someone can help
> me:
>
> 1. I started to create a mask. I opened my original image using FSL
> view, I
> used the create mask option. However, creating by pen is very
> difficult. I
> mean I want to have a cube in the center of my volume (3-D image) as a
> mask, for example, 100*100*100. I couldn't create it by pen. Is
> there any
> other method to create it.
>
> 2. Is it possible for me to create an artifitial Nifti image or
> another format that
> is readable by fsl using a text file editor?
>
> 3. Is there any command in FSL for comparing the result of two
> registration
> methods from the similarity point of view (e.g. information based
> similarity
> metric)?
>
> thanks in advanve
>
