Hi Cheol,
I am a bit confused by your question. The atlases that we use help with
the segmentation on the surface reconstruction steps when we process a new
volume. If the outcomes look resonable to you, then all is good. Did I
answer your question?
Lilla
On Fri, 30 Mar 2012, Cheol Han wrote:
Dear Lilla
I appreciate your answers. It was very helpful. Just another follow-up question. I think
freesurfer itself ended without errors and the skull-stripped and surfaces look okay. I
think in the recommended reconstruction Pipeline, "check segmentation" is
related to
checking atlas worked. Still, I wonder there is a gold standard to check the
atlas (Deksian atlas) works okay. .
Thanks again!
Best
Cheol
Cheol Han, Ph.D
Computational Neuroscience and Neuroinformatics
Department of Brain and Cognitive Sciences
Seoul National University
Korea
On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei <lzol...@nmr.mgh.harvard.edu>
wrote:
Hi Cheol,
I am using freesurfer for patients with various neural disease. I
wonder the the
freesurfer atlas is applicable to them: dementia (with Lewy bodies,
DLB),
epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some
studies already
used freesurfer for some of the diseases in the list,) I believe
epilepsy
patients with lobectomy cannot be applicable.
If the malformation or the difference between normal control acquisitions and
your scans is significant the FS pipeline, using the FS atlas is not going to
be successful. Withuot seeing your data I cannot tell which population from the
above is going to be
affected, but if in doubt just try processing one or two representative samples
from the different populations and assess how successful the processing is.
Also is there age limit for the freesurfer atlas? How young can the atlas
work
for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper
bound? 80 year-old?
The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data
quality but we had success all the way down to that age. I am not aware of any upper
limits. Again, if you are processing these kind of "extreme" populations, make
sure
that you inspect the outcome of the FS recon pipeline carefully before
proceeding with any type of analysis.
Lilla
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