Hello again,
I'm sorry about all these questions.
My analysis is being based on Morey et al. and I would like to know why do
they not divide the study in left hippocampus and right hippocampus? Is it
related with the type of comparison, once they are only worried about the
comparison between meth
Can you please take a look to my previous posted hippocampi values? What do
you think about them?
Thank you for your prompt help.
Best regards,
Ana Arruda
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not that I know of. Our manual data have hippocampi that are pretty
symmetrical.The automatically generated segmentations are also very
symmetric.
doug
On 10/09/2012 01:28 PM, Ana Arruda wrote:
> Dear experts,
>
> About the previous subject I have one more question.
>
> Based on Morey, et al. a
Dear experts,
About the previous subject I have one more question.
Based on Morey, et al. article we can say that there is better results for
the right hippocampus. Generally, it is known that right hippocampus volume
is often bigger than left hippocampus.
So, is there any possible explanation fo
Yes, you're right. But in that case, these changes would be quite similar
for right-hippocampus too.
Based on my analysis and literature, Freesurfer has more accurate measures
than FSL. The doctors are quite conservative about boundaries so that
measures are the smallest between Freesurfer and FSL
Hi Ana
the point is that even if you aren't segmenting individual structures, if
some are not in your manual protocol but are in ours, then lateralization
in them will cause lateralization differences in the degree of overlap
between the two
cheers
Bruce
On Wed, 3
Oct 2012, Ana Arruda wrot
I haven't gone so far. I've just done the simplest way. I've search the
proper commands just to do the hippocampus segmentation, but not its
subfields. All my analysis was made with the left and right-hippocampus
volumes from the *aseg.stats *file.
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kind of. There are natural lateralizations in the brain that are taken into
account. Not sure what is known about lateralizations of hippocampal
subfield and white matter components though
Bruce
On Wed, 3 Oct 2012, Ana Arruda wrote:
> Thank you very much!
>
> About the previous question, do
Thank you very much!
About the previous question, do the softwares use the same criteria for
each hippocampus?
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The information in th
Hi Ana
yes, our Neuron (2002) and NeuroImage (2004) papers describe the
techniques.
cheers
Bruce
On Wed, 3 Oct 2012, Ana Arruda wrote:
I'm not sure about this, but probably the doctors use the same methods for
left-hippocampus and right-hippocampus. The softwares, FSL and Freesurfer,
don't
I'm not sure about this, but probably the doctors use the same methods for
left-hippocampus and right-hippocampus. The softwares, FSL and Freesurfer,
don't have a different away to operate in either hippocampus. Do you agree?
That way of operating confuses me on how to interpret the differences fo
maybe the fimbria/alveus is different on the left than the right? Not
sure, but if the protocols are different it's very difficult to make any
meaningful comparison
Bruce
On Tue, 2 Oct 2012, Ana Arruda wrote:
That fact can explain the differences between manual and automatic
segmentations. Bu
That fact can explain the differences between manual and automatic
segmentations.
But how can I explain the differences just for the left-hippocampus values
in Freesurfer? Comparing percent volume difference between
Freesurfer-Manual and FSL-Manual, the percent is bigger in left-hippocampus
for Fre
if their definition of what is and is not hippocampus differs from the
one we use then you will get different volumes. You need to find out what
they defined as part of it and see if it matches our protocol
cheers
Bruce
On Tue, 2 Oct 2012, Ana
Arruda wrote:
> The manual protocol was made by
The manual protocol was made by doctors.They traced the hippocampus
segmentation based on their knowledge of anatomical structures.
For automatic segmentation I've used the following command:
recon-all -i input_suject_name -autorecon1 -autorecon2 -s
output_subject_name
and after this simulation
Hi Ana
it can depend on your manual tracing protocol. For example: are
fimbria/alveus part of your definition of hippocampus? For us they are.
cheers
Bruce
On Tue, 2 Oct 2012, Ana Arruda wrote:
>
> Dear experts,
>
> About the differences between FSL and Freesurfer, I've noticed that the
> l
Dear experts,
About the differences between FSL and Freesurfer, I've noticed that the
left-hippocampus volumes measured by Freesurfer are always bigger than the
left-hippocampus volumes measured by FSL. Is there any reason that can
explain that?
According to the literature, the percent volume dif
Hi Ana
you can check out:
http://surfer.nmr.mgh.harvard.edu/fswiki#Articles.validation
there are a bunch of comparison studies there.
cheers
Bruce
On Mon, 28 May 2012, Ana Arruda wrote:
> I really appreciate your help. Thank you.
>
> Has anyone on the list ever compared FSL and Freesurfer?
>
I really appreciate your help. Thank you.
Has anyone on the list ever compared FSL and Freesurfer?
Thanks,
Ana
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The information in
Hi,
this is not a direct comparison but at least indicates similar volumes in
FSL-FIRST and Freesurfer.
br J Psychiatry. 2012 Jan;200(1):30-6.
hth,
-joost
On Sun, May 27, 2012 at 2:09 PM, Martin Reuter
wrote:
> Hi Ana,
>
> Sorry I can't help more. Have never compared fsl and FS directly. Kee
Hi Ana,
Sorry I can't help more. Have never compared fsl and FS directly. Keep in mind
that any consistent differences may also depend on the software version.
Maybe other people on the list have done some comparisons.
Best Martin
On May 26, 2012, at 13:59, Ana Arruda wrote:
> Thanks for your
Thanks for your help Martin.
However I don't have just a single subject with that discrepancy. My data
has 18 subjects and most of the results obtained with Freesurfer are bigger
than FSL.
Thank you again,
Ana
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Hi Ana,
if this is on a single subject, anything can happen.
Also you can run that in a single step:
recon-all -i ... -autorecon1 -autorecon2 -s output_name
Best, Martin
On Fri, 2012-05-25 at 18:48 +0100, Ana Arruda wrote:
> Dear experts,
>
> I'm an MSc student and part of my final project i
Frederick,
Freesurfer uses FSL's motion correction tool 'flirt'. FSL v3.2 is
distributed with Freesurfer, which is a bit out of date.
You can download and use the newest FSL if you like. Just set the
environment var FSL_DIR before calling Freesurfer setup, like this:
setenv FSL_DIR /whereeve
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