Hi All,
Two questions:
1. I am interested in subcortical gray matter volumes such as hippocampus, amygdala, & basal ganglia. Can someone recommend some good references looking at the accuracy of Freesurfer relative to the "gold standard" approach of hand-tracing these structures?
2. Most of the problems that require quality checks for Freesurfer relate to defining the cortical surface and the grey-white boundary. As far as I can tell, there is rarely a need to edit Freesurfer's definitions of subcortical gray. Am I correct in this?
Thanks! Fred
Hi Fred
1. Yes, this has been done multiple times, including in our original 2002 paper: https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf
2. You can manually edit, but it's a lot more work. In the cortex minor interventions can lead to large improvements in accuracy. Unfortunately we have no such algorithm subcortically. That said, things are usually quite accurate except in a small percentage of cases.
cheers Bruce
On Wed, 1 Aug 2012, Fred Sanders wrote:
Hi All, Two questions:
- I am interested in subcortical gray matter volumes such as hippocampus,
amygdala, & basal ganglia. Can someone recommend some good references looking at the accuracy of Freesurfer relative to the "gold standard" approach of hand-tracing these structures?
- Most of the problems that require quality checks for Freesurfer relate to
defining the cortical surface and the grey-white boundary. As far as I can tell, there is rarely a need to edit Freesurfer's definitions of subcortical gray. Am I correct in this?
Thanks! Fred
In my data-set I have observed that Freesurfer has a tendency to include some amygdala into the hippocampal head, despite a visible strip of alveus white-matter segregating hippocampus from amygdala in my images. Has this tendency been noticed by others? If so, has anyone found a non-manual correction? Best, - Josh
On Thu, Aug 2, 2012 at 7:37 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Fred
- Yes, this has been done multiple times, including in our original 2002
paper: https://surfer.nmr.mgh.**harvard.edu/ftp/articles/**fischl02-labeling.pdfhttps://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf
- You can manually edit, but it's a lot more work. In the cortex minor
interventions can lead to large improvements in accuracy. Unfortunately we have no such algorithm subcortically. That said, things are usually quite accurate except in a small percentage of cases.
cheers Bruce
On Wed, 1 Aug 2012, Fred Sanders wrote:
Hi All,
Two questions:
- I am interested in subcortical gray matter volumes such as hippocampus,
amygdala, & basal ganglia. Can someone recommend some good references looking at the accuracy of Freesurfer relative to the "gold standard" approach of hand-tracing these structures?
- Most of the problems that require quality checks for Freesurfer relate
to defining the cortical surface and the grey-white boundary. As far as I can tell, there is rarely a need to edit Freesurfer's definitions of subcortical gray. Am I correct in this?
Thanks! Fred
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Joshua Lee