Hi Bruce and Josh,
the sum of all the hippo-subfields included all (the fimbria as well)
except the fissure. We don't have hippo-subfields values related to the
alveus (we run the standard command -hippo-subfields -all).
As suggested by Eugenio and Koen, we are going to use the -hippo-subfields
sure. Good luck
Bruce
On Sun, 3 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce and Josh, the sum of all the hippo-subfields included
all (the fimbria as well) except the fissure. We don't have
hippo-subfields values related to the alveus (we run the standard command
-hippo-subfields -all).
I have noticed that Freesurfer tends to include white matter in superior
hippocampus (e.g. alveus), perhaps this is not included in the
hipposubfields volumes?
Wondering, if I were to take a hand traced hippocampus rename it to
aseg.mgz, and made sure that the label matched what Freesurfer
alveus (and fimbria) are defined to be part of the hippocampus in the
aseg. Did you include them in your calculation of subfield hippocampal
volume?
On Tue, 26 Feb 2013, Joshua Lee wrote:
I have noticed that Freesurfer tends to include white matter in superior
hippocampus (e.g. alveus),
Dear Gari,
The subfield module uses a different, independent method to segment the
hippocampus, and consistency with ASEG results is not explicitly
enforced. That said, the subfield module is inialialized with the ASEG,
and the results should be pretty close to each other, for the most part.
Have
Hi again,
like I said in my previous emails, the measurements from the subfield
tools are based on .5x.5x.5 voxels, so you have to divide them by 8 to
convert them to cubic milliliters. Then, if you add up the volumes from
the subfields (without including the hippocampal fissure), you should get
It is whole-brain minus cerebellum and brain stem. But the current
release has a bug and should not be trusted. See the email I sent out
last week or look at the Release Notes page on our wiki for how to
download a patch and regenerate the results.
doug
Rashmi Singh wrote:
Thanks so much
oh, sorry, I do remember now that we took that out (I think we put it
back in for the next release). The work-around is to run
mri_binarize --i brain.mgz --min 0.1 --count count.dat --o junk.mgh
You can delete junk.mgh. The file count.dat will have info about the
number of voxels in the
You'll have to run it on each subject. Easy to do with a script. You can
then cat the data into one fine (they are just text files).
doug
Rashmi Singh wrote:
Thanks Doug,
Do I need to run the following for each subject or can is there a way to
run it with input for all my subjects in one go
No, it does not. All volumes are volumes in native anatomical space.
doug
Rashmi Singh wrote:
Hello.
I am using FreeSurfer to generate subcortical volumes and cortical
thickness for my subjects.
Does FreeSurfer normalizes the subcortical volumes to the whole brain
volume for each
In the aseg.stats file there is a value for the whole brain volume.
doug
Rashmi Singh wrote:
I would like know how can I get the sub-cortical volumes normalized it to
the whole brain.
Thanks,
Rashmi.
On 2/28/12 3:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
No, it does
In the aging process there's overall cortical atrophy.
Other papers like ours shows that too:
https://surfer.nmr.mgh.harvard.edu/pub/articles/Oliveira_JAD2010.pdf
Cheers
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de
the Volume_mm3 entry is the raw volume in native space.
cheers
Bruce
On Fri, 6 Aug 2010, Zhangyuanchao wrote:
Hi, expert,
I would like to measure the volume of hippocampus, is there any way i can
obtain the raw volume of hippocampus for each subject? How can I obtain it?
In fact, in the
p...@netfilter.com.br 写道：
发件人: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
主题: Re: [Freesurfer] hippocampus volume
收件人: Zhangyuanchao woshizhan...@yahoo.cn
抄送: freesurfer@nmr.mgh.harvard.edu
日期: 2010年8月6日,周五,下午10:22
look at the aseg.stats
sum left with right
structures have the same
problem as the hippocampus?
Is there any detailed description on aseg.stats?
Thanks!
--- 10ÿÿ8ÿÿ6, Pedro Paulo de Magalhães Oliveira Junior
p...@netfilter.com.br ÿÿ
ÿÿ: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
: Re: [Freesurfer
The most correlative brain structure with hippocampus (or amygdala) in the
normal population
is the best normalization referenece. I believe the intracrainal volume is the
best reference volume for the volume normalization.
Best regards!
Woo-Suk, Tae
Chucheon, Korea
--- Original
When we compute the aseg.stats, we include partial volume correction, we
don't just count up the voxels in hippo.
doug
Guang Zeng wrote:
Hi, there,
I use the following matlab code to find right and left hippocampus in
aseg.mgz
%%
filename =
This is due to partial volume correction. Use the hippo volumes from
aseg.stats.
doug
Guang Zeng wrote:
Hi, there,
I ran a subject through FreeSurfer pipeline. I found that the size of
left and right hippocampus in aseg.stats are
larger than that of left and right hippocampus in
Hi Guang,
it's because the partial-volume correction will be a bit different. Use the
one from the aseg.stats, as there's no reason to use the different wm
labels as different partial volume classes.
cheers
Bruce
On Thu, 17 Sep 2009, Guang Zeng wrote:
Hi, there,
I ran a subject through
Hi Guang,
the volumes should be comparable to the unconformed ones.
cheers,
Bruce
On
Tue, 8 Sep 2009, Guang Zeng wrote:
Hi, there,
I converted a subject from nii (160x256x256) to mgz (256 x 256 x 256 ), and
then sent it to
the FreeSurfer pipeline.
Now, I'd like to compare the resulted
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