Dear Mark,
Thanks for replying and I have a couple quick follow up question to verify I understand the process correctly.
I need to create a study specific average by putting all the hippo masks into common space and averaging them with fslmaths.
I can then use distancemap to create the signed distance maps
distancemap -i (subject_hippo) -m (average shape) -o output
I am guessing I should only perform this on the boundary voxels.
After a couple iterations of this it will allow me to create a 4d file I can use as my input for randomise correct?
Also, as purely an aesthetic thought this will give me data that I can use to perform statistics on but the .vtk files are generated in the original pipeline and not with this method. Is there another command that can generate the vectors or is that wishful thinking.
Thanks,
Jeremy
>Hi,
>The current version of FIRST uses signed distances to the average shape as the inputs to randomise in its vertex analysis. So >you would need to create the equivalent input for your images in order to do the same analysis. This would be possible with >masks and the tool "distancemap" although it is not provided as a simple option just yet.
>All the best,
> Mark
>>On 16 Dec 2013, at 20:05, Jeremy Strain <[log in to unmask]> wrote:
>> Dear FSL List,
>> I was wanting to run the vertex analysis on hippocampus volumes that I manually edited after running first. My population is predominantly patients and the fully automatic model seemed to not identify the hippocampus correctly. Searching through the forums it seems that it is not possible to use first on manually segmented masks to generate new bvars. However, the most recent post about this topic was in 2012 I believe so is this still the case or is a new option is available.
>>
>> Thanks,
>> Jeremy
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