Dear Jeong,
Vertex analysis results are about where there are geometric changes in
the shapes that are segmented. There is no equivalent to the TBSS
all_FA_skeletonised image.
The script you have been running, to convert vtk outputs to MNI volumes
will allow you to take the thresholded vertex analysis outputs and create
a mask in MNI space if you want this. However, there is no other output
from FIRST that you would use this mask with. If you had another type
of quantity that you wanted to examine in the region where there is a
shape difference, then you could use this mask for this. It all depends on
what you want to do.
I hope this helps.
All the best,
Mark
On 14 Nov 2011, at 14:44, SUBSCRIBE FSL B. Jeong wrote:
> Dear Mark,
>
> Please let me explain what I want to say.
> In TBSS, if I want to get each subject's FA value in a certain area (e.g., the area showing group differences), I would make ROI mask from statistical map and extract FA values from 4D volume such as 'all_FA_skeletonised.nii.gz' using fslmaths command.
>
> In FIRST, I thought that something like the 4D volume may be the concatenated '*_{region}_all.bvars' file. But I can not see what would be in the bvars file with texteditor or matlab.
> If I only want to work on the statistically significant vertices, I have to get each subject's values in the vertices area (e.g., the vertices which shows significant differences between two groups) from the all.bvars or other relevant file.
> Could you explain what I should do or what I have to type in command line?
>
> I wonder whether I ask correctly or not.
> Please let me know what I missed in terms of the basic concept in vertex analysis.
>
> Thank you,
>
> Jeong
>
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