Hello person,
The command you include here looks perfectly good to me and works on data that I have here.
You are correct that both input and output coordinates need to be in mm (the second column of the FSLView coordinates).
Are you sure that your matrix is the correct matrix that registers the anatomy.nii.gz image to the standard image?
If you still cannot get things to work then feel free to send us the data (the anatomy image and the matrix) to our upload site (see the Support page of the FSL website).
All the best,
Mark
On 15 Jan 2013, at 13:52, Thien Bao <[log in to unmask]> wrote:
> Dear people,
>
> Suppose that I have a point in native space (162,106,140) (in mm not in voxel). I want to convert it to MNI space (in mm). I use the command:
>
> echo "162 106 140" | img2stdcoord -img anatomy.nii.gz -std $FSLDIR/data/standard/MNI152_T1_1mm -xfm flirt_T1.mat -mm
>
> where flirt_T1.mat is the result of flirt.
>
> And I get the result: 159.763 99.4584 158.416 - it is in MNI space (in mm not in voxel - am I right, here?)
>
> After that, I recheck by using fslview, but this position (159.763 99.4584 158.416) is totally faraway from the position (162 106 140) in native space. (both of them are in mm not voxel).
>
> Could you please point me out something wrong here?
>
> It is very urgent for me. So, if someone know what is wrong here, please let me know.
>
> Thank you very much for your help.
>
> Regards,
>
> T.Bao
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