Hi,
What values are contained in the tract.nii.gz image where you believe the tract exists?
They need to be above 0.5 for fslstats to accept them as part of a valid mask.
All the best,
Mark
On 27 Aug 2013, at 15:03, Mohamood Adhil <[log in to unmask]> wrote:
> Hi,
>
> I am working in DTI data, I have several seed mask and I computed the tract running through every pair of seed mask and calculated the mean FA for every pair of seed mask for individual subject by masking the tract into subject FA image. The command I used is,
>
> fslstats FA_image.nii.gz -k tract.nii.gz -M
>
> I got the mean FA value for most of the pair of seed mask and for few pairs its showing the message "mask image is empty" and returning the value zero. I checked those images which returns zero in FSLView, by masking those tract into subject FA image, the tract exist and it is running between the respective pair of seed mask and also subject FA image looks well.
>
> could any one tell me what would be the reason of returning value zero. Any suggestion would be appreciated.
>
> Thank you in advance.
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