Hi,
All you need to do is run fslmeants with the --transpose
option, the run this through
awk '{ print $1 " " $2 " " $3 }'
to extract the first three columns, and then run the
output through img2stdcoord (which takes a text
file with three columns as input).
This will give you the coordinates in mm, which you
could stick back together with the rest of the fslmeants
output with "paste" (or MATLAB) if you wish.
I hope this helps.
All the best,
Mark
On 31 Mar 2010, at 18:28, Markus Gschwind wrote:
> Dear Mark!
> Thanks for the answer.
> Meanwhile the list was pausing... I was forced to be creative.
>
> I found that as a solution (in MATLAB) (only for the MNI_1mm template)
>
> A=load('fslmeants_output.txt')
> MNImat=[
> -1 0 0 90
> 0 1 0 -126
> 0 0 1 -72
> 0 0 0 1
> ];
> Atemp=MNImat*[A(1:3,:) ;ones(1,size(A,2))];
> A(1:3,:)=Atemp(1:3,:);
>
> It seems to be correct...
>
> Just by curiosity, I think it even would have worked faster with
> img2stdcoord. But I am not completely sure how I would use
> img2stdcoord on a .txt file and only on its first 3 lines (as the
> fslmeants_ouput happens to need it) and not on a image file.
>
> Could you explain that please?
>
> Thanks for your help,
> Best,
> Markus
>
>
> 2010/3/31 Mark Jenkinson <[log in to unmask]>
> Hi,
>
> I'm afraid that the --usemm only affects the input for -c (which it
> sort of says in the help text). So it always outputs voxel
> coordinates.
> If you want them in mm coordinates you'll have to use img2stdcoord
> to convert them (as part of a script).
>
> All the best,
> Mark
>
>
>
> On 27 Mar 2010, at 09:52, Markus Gschwind wrote:
>
> Dear all,
>
> Could anybody tell me how I could get the coordinates in the output
> of fslmeants --showall in MNI mm coordinates?
> I am trying the following
>
> fslmeants -i all_FA_skeletonised -m mymask.nii.gz -o
> all_FA_skeletonised_voxels_in_mymask.txt --usemm --showall
>
> but it still shows voxel coordinates. Is it not possible to use --
> usemm and --showall together?
>
> Thanks for any hints!
> Best
> Markus
>
>
> --
>
>
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition - Dept of
> Neurosciences
> University Medical Center (CMU)
> 1, Michel-Servet
> CH-1211 GENEVA - Switzerland
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
>
>
> --
>
>
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition - Dept of
> Neurosciences
> University Medical Center (CMU)
> 1, Michel-Servet
> CH-1211 GENEVA - Switzerland
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
