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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