Hi, Joshua Just answered this to Mohammad Zia in a previous message and I guess it is useful to you.
1- The name "Right-Hippocampus" is misleading you. The hippocampal subfields segmentation is atlas based. And the atlas was generated from expert manual segmentation. The problem is that the most posterior part of hippocampal tail is too small to allow a precise segmentation. So they know it was part of hippocampus but not being able to discriminate the subfields in this portion they named as hippocampus. This name in manual segmentation was preserved in FreeSurfer's automated process. So in this list, Rigth-Hippocapus does not mean the whole right hippocampus. It is just the portion of the right hippocampus not segmented in subfields. You can see more details at https://surfer.nmr.mgh.harvard.edu/pub/articles/VanLeemputHippocampus2009.pd... . There you can read:
Towards the tail of the hippocampus, the manual delineations no longer discern between the different subfields, but rather lump everything together as simply ‘‘hippocampus,’’
In my own data I renamed this to "right hippocampal tail complement" just to avoid this confusion.
2- Yes, just divide the "volumeInVoxels" value by eight (or multiply by 0.125, like Eugenio said) to get the volume in cubic milimeters.
Marcos. Em Sex, 2014-07-11 às 11:46 -0400, Joshua S escreveu:
Hi, I was doing a hippocampal subsectioning on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files
Thank you for any replies, From Joshua Segaran
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