TYVM, Juan Eugenio and Bruce.
I am a neurologist and Professor in Federal University of Rio de Janeiro. I am confortable with Linux and scripts but, as a physician, eigenvectors  will be really hard. I will try to get some help inside University. But if I correctly understood, it seems an elegant way to make tool that will work with several hippocampi with greater consistency than manual approach. Your step by step directions worked great, Juan. But I had to make a Left and a Right file. When I tried to concat right and left subfields in teh same file I got an error saying that right and left Ca1 dimensions did not match. Thank you again.
Em Qui, 2013-04-18 às 11:29 -0400, Juan Eugenio Iglesias escreveu: 
I agree with Bruce. You can use MRIread.m to read in the data.

Regarding the other question: first you need to combine the posteriors
of all the subfields into a single posterior for the whole hippocampus.
You can do that like this:

mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o
posteriorWholeHippocampus.mgz

Then you can threshold the posterior at probability 0.5 to obtain a
binary hippocampal mask:

mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o
binaryHippocampalMask.mgz

Finally, you can generate a surface by tesselating the mask:

mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile

You can visualize the output with

freeview -v posteriorWholeHippocampus.mgz -f surfaceFile

Cheers,

/Eugenio







On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote:
> 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
> > >
> > >
> > 
> >