Hi,
I'm afraid you've misunderstood me.
The "tail" is a separate command.
Also, the "time series" for a 3D volume is simply
the intensities (voxel values). It is just treated
as a time series of length 1.
So the command you need is:
fslmeants -i original_image -m masked_cluster.nii.gz --showall -o
out.txt
Then you can do:
tail -1 out.txt
to just get the intensities (voxel values).
Note that tail -1 is good for using an output *file*, rather
than with a pipe (if you don't understand this difference
then don't worry - just do what I say above in this email).
All the best,
Mark
On 19 Aug 2010, at 12:46, Moran Artzi wrote:
> ie. using --showall (or other utility) on a given VOI,
> fslmeants -i masked_cluster.nii.gz --showall -o out.txt
>
> how can I get all voxel values instead of time series
>
> Thanks
> Moran
>
>
>
>
> On Thu, Aug 19, 2010 at 1:10 PM, Moran Artzi <[log in to unmask]>
> wrote:
> Hi,
> Thanks a lot for your replay but I still have some problems
> running:
> fslmeants -i masked_cluster.nii.gz --showall "tail -2" -o out.txt
> results with huge file (dose not seem like single coordinate)
> What did I do wrong
>
> Thanks
> Moran
>
>
>
> On Thu, Aug 19, 2010 at 11:28 AM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Hi,
>
> You can use fslmeants with the --showall command (and the
> -i and -m to specify your intensity image and the appropriate
> VOI mask). This will give you an output that contains three
> rows with values for the x, y and z coordinates respectively,
> and then the row containing your intensities. If you do not
> need the coordinates then you can simply use "tail -2"
> to give you the required values (as there is a blank line at
> the very end that needs to be ignored).
>
> All the best,
> Mark
>
>
>
> On 19 Aug 2010, at 10:18, Moran Artzi wrote:
>
> Hi,
> Flowing FAST segmentation I got 3 VOIs.
> I want to extract the value of the voxels in each cluster to a text
> file in order to scatter-plot them
>
> The fslmaths -M option gives the entire cluster mean value.
> How can I get it's voxels values?
>
> Thanks
> Moran
>
>
>
>
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