Hello,
I'm working on hippocampus segmentations obtained by Freesurfer to compare with manual and FSL segmentations. Do I have to normalize to make these comparisons more accurate? If so, what volume do I have to use? I've read about eTIV but I would like to confirm if there is any value for normalization purpose in the aseg.stats file.
What does ICV include? Does it include the CSF between the brain and the skull?
Best regards,
Ana Arruda
Hi Ana,
when comparing to manual labels or other segmentation methods you do not need to normalize. But other methods and even manual segmentations may follow a different protocol, so it can be expected that some method gives consistently different (e.g. smaller) values.
ICV in FreeSurfer is computed via the scaling needed to map a scan into Talairach space, where ICV values are known. The Talairach ICV values were established using a protocol that included CSF. Take a look at the Buckner paper (should be on the wiki, there is also a page about eTIV (estimated total intacranial volume).
Best, Martin
On Oct 6, 2012, at 12:35 PM, Ana Arruda wrote:
Hello,
I'm working on hippocampus segmentations obtained by Freesurfer to compare with manual and FSL segmentations. Do I have to normalize to make these comparisons more accurate? If so, what volume do I have to use? I've read about eTIV but I would like to confirm if there is any value for normalization purpose in the aseg.stats file.
What does ICV include? Does it include the CSF between the brain and the skull?
Best regards,
Ana Arruda _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
Thanks a lot Martin.
I really get confused about normalization. I've already done the comparisons and the values between methods, as you said, are different. Although I haven't understood why, in this case, I don't have to normalize. My advisor told me to normalize all the brain values from the patients. Do you have any idea what did he mean with that? I thought that this suggestion would be related to hippocampus volume.
Ana Arruda
Hi Ana,
if you work on a study comparing groups or age effects, that analyzes hippocampal volume, then you would usually normalize that volume. People have different head sizes and therefore differently sized hippocampi. To remove headsize differences researchers often normalize voumes by ICV.
If you are interested in comparing the hippocampal volume between methods (manual and different automatic methods) and not between subjects, you do not need to normalize. ICV will be computed differently by different packages so you would just add more noise. Furthermore for your manual hippocampus labels you probably won't have manual ICV.
Best, Martin
On Oct 6, 2012, at 1:25 PM, Ana Arruda wrote:
Thanks a lot Martin.
I really get confused about normalization. I've already done the comparisons and the values between methods, as you said, are different. Although I haven't understood why, in this case, I don't have to normalize. My advisor told me to normalize all the brain values from the patients. Do you have any idea what did he mean with that? I thought that this suggestion would be related to hippocampus volume.
Ana Arruda
--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
It's clear now. Thank you very much.
And you're right about manual ICV, I have only two images for each patient with the area of the biggest plan in the brain, commissural area.
Best regards,
Ana Arruda
freesurfer@nmr.mgh.harvard.edu
-
Ana Arruda -
Martin Reuter