Hi,
Dear FSL experts,It is recommended to use Susan before tissue segmentation using FAST because it emphasizes the boundaries and improve the problem with pve.
No - that's incorrect. We do not recommend Susan in general, because it modifies the intensities at the boundary and hence can lead to less PV than was truly present. You should not think of partial volume (pve being the estimate of this) as a problem. It is the truth, as within a voxel near a tissue border there will be a mixture of tissues within that voxel and this is what the pve represents.
If you have very noisy images then we would generally recommend changing the parameters in FAST (especially -H and -R) to try and improve the results. However, it is normally not necessary to do too much, as summing the pve to get tissue volumes also suppresses noise, as does smoothing inside of VBM.
So I would recommend that you do not continue to use Susan in this context.
All the best,Mark
I can not attach the images because of the load limit for the mail.2. Is it better to apply it to the whole image (3D) or for every sclice of the image?1. The number that appears in red (the Brightness intensity....is it normal?) I found in the fsl mailing list forum that brightness intensity in FEAT is set to 0.75 * the constrasts between the median brain intensit and the background, so as not to blur the brain edge" (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1209&L=FSL&P=R48933&1=FSL&9=A&J=on&K=3&d=No+Match%3BMatch%3BMatches&z=4).Now I have two questions I would be more than grateulf if any of you could answer:Well, I have tried it and I have seen that once I enter the image the brightness intensity is automatically calculated....and, using the default settings I get the following:
cd /home/rosalia/Desktop/PRUEBA_SUSAN
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PRUEBA_SUSAN$ fsl
/usr/share/fsl/5.0/bin/susan /home/rosalia/Desktop/PRUEBA_SUSAN/C1_160_crop 50.1963013 3 3 1 0 /home/rosalia/Desktop/PRUEBA_SUSAN/C1_160_crop_susan
Finished
Best regards,
Rosalia.