Hi All,
There is a large variability between labs. An extensive effort has begun
for produce a "Harmonized Protocol for Hippocampal Volumetry", see:
http://www.hippocampal-protocol.net/SOPs/index.html
This group has been working on this goal for a few years. Good resources
at their site, par
Hi Joshua
I'll cc Jean Augustinack and Stephan Heckers, who I know have opinions on
this issue :)
cheers
Bruce
On Thu, 17 Nov 2011, Joshua Lee wrote:
There is great variability between the different segmentation protocols used
by different research groups, and I think people are eager for
There is great variability between the different segmentation protocols
used by different research groups, and I think people are eager for a
standard to facilitate comparison and replication. By becoming part of
Freesurfer, I suspect that your segmentation algorithm will become that
standard.
Luc
Hi Joshua,
I'm not a neuroanatomist so I can't really answer that question. My
aim has just been to replicate what a human expert has given us as
segmentation examples on a number of different subjects.
I know that different labs follow very different conventions for
labeling the subfields manual
At least by my reading of the Duvernoy Human Hippocampus atlas, the most
anterior and posterior extents of the hippocmapus (perhaps just a slice at
the tips in most scans) are almost entirely composed of the CA1 subfield.
Thoughts?
Joshua
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
D
Thanks Koen.
On Thu, Nov 17, 2011 at 6:14 AM, Koen Van Leemput
wrote:
> The answer is close to what Shashwath suggested, except that the
> "Hippocampus" segmentation is really computed at the same time as all
> the other subfields. For unfortunate reasons, the tail of the
> hippocampus that is no
The answer is close to what Shashwath suggested, except that the
"Hippocampus" segmentation is really computed at the same time as all
the other subfields. For unfortunate reasons, the tail of the
hippocampus that is not further subdivided in our manual training
segmentations was called "Hippocampu
Hi Allan and Joshua,
The hippocampal subfield segmentation really just uses a few output
files generated by the usual FreeSurfer volumetric stream, so the
short answer is that it should be perfectly possible to use 5.1 to do
hippocampal subfield segmentation on FreeSurfer results processed with
5.
Thanks Shashwath.
On Wed, Nov 16, 2011 at 2:04 PM, Shashwath wrote:
> Alan- I believe the label "hippocampus" here refers to the remaining hippo
> segment after the algorithm has completed labelling of all subfields. In
> essence this would not be a measure that conveys very meaningful info.
>
Alan- I believe the label "hippocampus" here refers to the remaining hippo
segment after the algorithm has completed labelling of all subfields. In
essence this would not be a measure that conveys very meaningful info.
Sent from my iPhone
On Nov 16, 2011, at 1:01 PM, Alan Francis wrote:
> H
Hi Koen and FreeSurfers:
I have a 3T dataset that has undergone processing using 5.1. I have also
run the Hippo sub fields command. Here are my results:
[root@NeuroImage-Gamma mri]# kvlQuantifyPosteriorProbabilityImages
$FREESURFER_HOME/data/GEMS/compressionLookupTable.txt posterior_right_*
poste
Thats an interesting suggestion, givien my recently reported issues with
the talairach in FreeSurfer 5.1.
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Wed, Nov 2, 2011 at 11:41 AM, Bruce Fischl wrote:
> I belie
I believe so, but Koen is the one who would know for sure
Bruce
On Wed, 2 Nov
2011, Alan Francis wrote:
Hello Bruce et al,
I have a dataset processed in 5.0. Can I use the Hippocampal Sub-Field
Segmentation tools of 5.1 to process these?
thanks so much,
Alan
BIDMC/ Psychiatry
__
Hello Bruce et al,
I have a dataset processed in 5.0. Can I use the Hippocampal Sub-Field
Segmentation tools of 5.1 to process these?
thanks so much,
Alan
BIDMC/ Psychiatry
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mg
Hi Joshua,
The version of the hippocampal subfield segmentation routines
currently in FreeSurfer will only work out of the box on the usual
FreeSurfer-resampled 1mm isotropic data. If you are technically
skilled, it should be possible to tweak things to make it work on
other data (we don't assume
Dear Experts,
I've been collecting hi-res hippocampal scans with a 32 ch coil on a 3T
Siemens Trio to manually segment hippocampal subfields. However, I wonder
whether the protocol is appropriate for use with the new Freesurfer subfield
segmentation tool.
Specifically, our hi-res scan does not ca
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