Dear Amandine,
I am by no means an FSL expert, yet I would suggest directly trying the following command:
fslstats FA.nii -k ROI.nii -R -M -l 0.2 -R -M
Since options are applied in order, this should:
- apply a mask ROI.nii,
- output <min intensity> <max intensity>,
- output mean (for nonzero voxels),
- apply a threshold of 0.2,
- output the new <min intensity> <max tyintensity>,
- output the new mean (for nonzero voxels).
You could try it first on one FA map and one ROI, assert the command works as intended, and then check the outputs of the same command with multiple ROIs, or multiple FA maps.
Best regards,
--
Nicolas CORDIER
----- Mail original -----
> De: "anonymous" <[log in to unmask]>
> À: [log in to unmask]
> Envoyé: Mercredi 22 Mai 2013 14:59:21
> Objet: [FSL] threshold FA map
>
> Dear FSL experts,
>
> I would like to extract mean FA values in multiple ROIs in diffusion
> native space,
>
> In order to prevent partial volume effects, I would like to use a
> threshold of 0.2 for each FA map,
>
> So, I used the following command line :
>
> fslmaths FA.nii -thr 0.2 FA_02.nii
>
> Then, to extract mean FA in different ROIs, I used the following
> command lines :
>
> fslmeants -i FA_02.nii -m ROI.nii -o FAvalues_ROI.txt
> OR
> fslstats FA_02.nii -k ROI.nii -M >> FAvalues_ROI.txt
>
> Finally, for some ROIs I obtained mean FA values below 0.2,
>
> How is it possible ?
>
> Thanks a lot,
>
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