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