Hi,
If I understand things correctly you want a set of 2983 individual values, corresponding to the voxel intensities. If that is the case then the following command should do it:
fslmeants -i T2flair -m lesionROI --showall > values.txt
And in the values.txt file the first three lines contain the x, y and z voxel coordinates and the fourth line will contain the intensity values. You can extract this fourth line on its own by:
sed -n 4p values.txt > vals.txt
All the best,
Mark
> On 1 Mar 2017, at 18:21, Sourajit Mitra Mustafi <[log in to unmask]> wrote:
>
> Hi all,
> I have a lesion ROI in T2-Flair map.
>
> Normally using fslstats, I get the mean, median and standard deviation of the value of the T2-Flair inside the said ROI, fslstats -M, -S, -P 50 etc.
>
> However now I want to get values of T2-FLair from each non-zero voxel in that ROI.
>
> Suppose the said lesion ROI has 2983 non zero-voxels, I want 2983 values of T2-Flair, one belonging to one voxel of the corresponding ROI.
>
> If there is a simple fsl command to get that it will be great. I can try to do in MATLAB , change the image matrix to single column one... but if a
>
> FSL command can get me this ... my data analysis Pipeline will be more streamlined.
>
>
> Please help me out in this
>
> kind regards
> sourajit
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