Hi Marcos
I would do it in matlab. Compute the spatial eigenvectors then divide the
hippocampus up along the primary eigenvector
cheers
Bruce
On Thu, 18 Apr 2013, Marcos
Martins da Silva wrote:
Thank you for your answer, Juan.
Yes, I want a surface of the whole hippocampus and I thought I had just
obtained that using
freeview and adding all hippo-subfield files. That resulted in the screenshot I
previously
attached. I just do not know how I can save the resultant surface.
After I checked "show as isosurface in 3D view" the low and high threshold
controls appeared.
The default threshold values on Freeview for low was 127.5 and high was 255.
When I played
with these controls, the size of the surfaces changed on 3D view. That is why I
made the
second question. I was trying to select the correct values for low and high
threshoulds so I
get an image consistent with the volume values we get after running
kvlQuantifyPosteriorProbabilityImages. After setting the correct values I would
like to save
the work as a surface so I could load the whole surface instead of loading each
individual
subfield file. But I did not find a "save as surface" option. So I used the
screenshot tool to
"save" the work. This way I could at least show you what I got but I thought it
was not the
best way to do it.
Relating to the last question about generating a new segmentation (anterior,
body and
posterior), you said I could use simple geometric rules to get it. Could you
tell me where I
can find instructions about how to do it?
Sorry, I am afraid I am a novice here and my questions are the best proof of
this, so I would
like to thank you for all your patience.
Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu:
Dear Marcos,
>
> > 1- How do I save the combined 3D view I got as a surface?
>
> Do you want a surface of the whole hippocampus? In that case I would
> suggest adding up the probability volumes from all the subfields and
> thresholding the resulting volume.
>
>
> > 2-I know the hippo-subifields .mgz files are probability maps and if I
> > guess right kvlQuantifyPosteriorProbabilityImages read these files to
> > count how many voxels you have in each subfield. I also guess it count
> > only the voxels with reasonable high probability to be part of each
> > subfield. If so, what is the minimum value between 1 and 255 the
> > program use to decide if a particular voxel is valid?
>
> The estimates of the volumes are based on soft probabilities, so all
> voxels with non-zero probability contribute towards the estimate. For
> instance, a voxel with value 255 contributes to the volume 255 times as
> much as a voxel with a value of 1.
>
>
> > 3- Is it possible to merge hippo-subfield .mgz files data and to
> > generate a different segmentation like anterior (anterior quarter),
> > body (the2 intermediate quarters) and posterior (posterior quarter).
>
> There are currently no scripts in FreeSurfer to generate such a
> partition. But you could always take a mask of the whole hippocampus
> (either from aseg.mgz of from the combination of all the subfields, like
> I mentioned in 1) and define some simple geometric rules to create it.
>
> Kind regards,
>
> Eugenio
>
>
>
>
> >
> > TY in advance
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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