Hi,
fslmeants takes the average over *all* voxels in the mask. Assuming
you are using the inverted lesion mask without any additional
processing, you now have 1s *everywhere* in the image that's
non-lesion, not just in the WM. So you are including a lot of voxels
that you don't want.
I'm assuming that your FA image already corresponds to WM only (0
anywhere else).
You have a couple of different options:
1) use fslstats (e.g. fslstats FA -k mask_inverted -M) (This will give
you the mean of the non zero voxels in the FA image, after it has been
masked mask_inverted.)
2) Mask the FA image with the inverted lesion mask and then use that
result with the -m option to fslmeants
I would go with option 1 as it's more straightforward.
On Mon, Apr 29, 2013 at 4:44 PM, Amandine Pelletier
<[log in to unmask]> wrote:
> Thanks !
>
> With this command line (fslmaths mask -mul -1 add 1 mask_inverted) I
> obtained lesion masks with values of 0 inside and values of 1 outside,
>
> Secondly, in order to obtain FA values in normal appearing white matter, I
> used the following command line:
>
> fslmeants -i FA.nii -m mask_inverted -o FA_outside_lesions.txt
>
> However, I obtained very low FA values around 0.024 ! Does anyone have an
> idea why I obtain these values ?
>
> Thanks a lot,
>
> Amandine
>
>
>
>
>
>
>
> 2013/4/29 Niels Bergsland <[log in to unmask]>
>>
>> Hi,
>> Then it sounds like you are using an older version of FSL as this
>> option was introduced in the FSL 5 release (if I recall correctly!)
>>
>> You can do this with the standard fslmaths though with the following
>> command:
>>
>> fslmaths MASK -mul -1 add 1 MASK_inverted
>>
>>
>>
>> On Mon, Apr 29, 2013 at 3:45 PM, Amandine Pelletier
>> <[log in to unmask]> wrote:
>> > Hi,
>> >
>> > I'm sorry but it seems that this option is not available in fslmaths,
>> >
>> > There is the option -bin but not the option -binv,
>> >
>> > Thanks for your help,
>> >
>> >
>> >
>> >
>> > 2013/4/29 Niels Bergsland <[log in to unmask]>
>> >>
>> >> Hi, you can easily do this using the -binv option in fslmaths
>> >>
>> >> On Mon, Apr 29, 2013 at 3:33 PM, Amandine Pelletier
>> >> <[log in to unmask]> wrote:
>> >> > Dear FSL experts,
>> >> >
>> >> > Using LST toolbox, I have performed the assessment of white matter
>> >> > hyperintensities volumes,
>> >> >
>> >> > Finally, I obtained a mask of white matter hyperintensities for each
>> >> > subject in native space,
>> >> >
>> >> > Using the command line fslmeants, I have extracted the FA values in
>> >> > the
>> >> > lesion masks,
>> >> >
>> >> > Now, I would like to extract the FA values outside the lesions (in
>> >> > normal appearing white matter),
>> >> >
>> >> > I need to reverse my lesion masks > that is to say I would like to
>> >> > obtain a mask with a value of 1 outside the mask and with a value of
>> >> > 0
>> >> > inside the mask,
>> >> >
>> >> > Does anyone can help me ?
>> >> >
>> >> > Thanks for your time and your help,
>> >> >
>> >> > Amandine
>> >>
>> >>
>> >>
>> >> --
>> >> Niels Bergsland
>> >> Integration Director
>> >> Buffalo Neuroimaging Analysis Center
>> >> 100 High St. Buffalo NY 14203
>> >> [log in to unmask]
>> >> (716) 859-7677
>> >
>> >
>> >
>> >
>> > --
>> > Amandine PELLETIER
>> > Doctorante en Neurosciences
>> > INCIA, UMR 5287
>> > Equipe Neurosciences Cognitives Humaines et Neuroimagerie
>> > [log in to unmask]
>>
>>
>>
>> --
>> Niels Bergsland
>> Integration Director
>> Buffalo Neuroimaging Analysis Center
>> 100 High St. Buffalo NY 14203
>> [log in to unmask]
>> (716) 859-7677
>
>
>
>
> --
> Amandine PELLETIER
> Doctorante en Neurosciences
> INCIA, UMR 5287
> Equipe Neurosciences Cognitives Humaines et Neuroimagerie
> [log in to unmask]
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]
(716) 859-7677
|