Ok, now I understand.

Thanks a lot Mark. Just one think, I feel more clear the 3D representation for the results. If I'm not wrong, that option is not available when using volumetric output (.nii) plus randomise, is not it?

In case I would rather prefer the 3D representation, then I should assume that results are FDR corrected as the most. Am I wrong?

thanks again,

Best
Daniel



El 09/06/2013 01:50, Mark Jenkinson escribió:

Hi,
The new version of FSL creates a nifti file as the output of vertex
analysis, rather than a vtk surface. If you want the vtk surface then
you need to add the --surfaceout option to the first_utils command,
although we recommend the newer way of doing it, using a volumetric
output and randomise.
All the best,
Mark
On 7 Jun 2013, at 09:31, Daniel Ferreira <[log in to unmask]> wrote:

Dear experts,
I am performing vertex analysis with FIRST as indicated in the userguide (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide#Surface-based_Vertex_Analysis [1]).
The problem is that after running first_utils I only get the .txt file but not the .vtk one.
This is my first_utils command and the .txt file is attached as well:
first_utils --vertexAnalysis --usebvars -i R_Thal_all.bvars -d /home/daniel/FIRST_documents/OCBneg_mayor_OCBpos.mat -o shape_analysis/OCBneg_mayor_OCBpos_R_Thal --useReconNative --useRigidAlign -v >& shape_analysis/OCBneg_mayor_OCBpos_R_Thal.txt
Any idea?
Thanks a lot in advance
Daniel <OCBneg_mayor_OCBpos_R_Thal.txt>

Links:
------
[1]
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide#Surface-based_Vertex_Analysis