Hi Gabriel,
1. Using pre-processed data obtained with an older version of FreeSurfer should be OK, as long as you remember that the obtained results might/will be different from the ones you'd get if you had run the whole analysis from scratch.
2. The generic label "hippocampus" is used to denote the tail of the hippocampus, where no attempt is made to further subdivide between the different subfields. This is admittedly not a great naming convention - sorry for the confusion.
3. You should not do any correction on the obtained volumes: "partial volume" here merely means the effect of voxels containing a mix of different subfields simultaneously. The "non-partial volume" results here only indicate that this effect is not explicitly modeled when you call the hippocampal subfield segmentation routine with its default settings.
Hope this helps,
Koen
On Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamilla ggonesc@upo.es wrote:
Dear Freesurfer experts
I'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...
If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields? I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?
second, when I apply the "kvlQuantifyHippocampalSubfieldSegmentations.sh" I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e. volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissure c_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626
and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is "0.5*0.5*0.5mm^3".
Many thanks in advanced, Gabriel
--
PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville
- Spain -
Email: ggonesc@upo.es http://www.upo.es/neuroaging/es/
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