Thank you very much Anderson, just started FSLVBM_3_proc with sigma 5, hopefully it'll work.
Well, in our study we compared 3 groups and we couldnt find difference between two. The reviewer suggests that the small Kernels are better for subcortical structures and larger kernels for cortex (which is actually in contrast to what I had read in a recent review paper). So he recommends using a larger Kernel to reveal the possible cortical GM differences between those 2 groups, which we couldnt find with 7 mm.
Best regards
Cagri
On Sat, 7 Jan 2012 21:18:03 +0000, Anderson Winkler <[log in to unmask]> wrote:
>Hi Cagri,
>
>This can be changed. Perhaps the easiest is if you open the file
>${FSLDIR}/bin/fslvbm_3_proc and change the line 103 (for FSL 4.1.9),
>adding or removing sigmas you want:
>
>* for j in 2 3 4 ; do*
>
>If you want, for instance, sigmas = 5 and 8 mm, just add:
>
>* for j in 2 3 4 5 8 ; do*
>
>Then run again the pipeline from this script onwards.
>
>I wonder, though, what would be the rationale for the reviewer's
>request, as we often wish to have less smoothing...
>
>Hope it helps!
>
>All the best,
>
>Anderson
>
>
>
>On 07/01/12 16:01, Cagri Yuksel wrote:
>> Dear FSLers,
>>
>> We were asked by a reviewer to repeat our VBM study with a FWHM kernel size of 12 mm (we reported results in sigma 3mmx2.3=7 mm). However as far as I know from the FSL-VBM website the highest kernel size FSL allows for VBM analysis is 9 mm (sigma 4x2.3).
>> Is there a way of doing the VBM analysis with FWHM 12 mm kernel ?
>>
>> Thank you,
>>
>> Cagri Yuksel
>>
>>
>
>
