22 6:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aseg.stats - eTIV volume space
External Email - Use Caution
Hi FreeSurfer experts,
I apologize if this question has been addressed, but I was unable to find a
definitive answer elsewhere.
I am using the aseg.stats file
External Email - Use Caution
Hi FreeSurfer experts,
I apologize if this question has been addressed, but I was unable to find a
definitive answer elsewhere.
I am using the aseg.stats file to extract the estimated Total Intracranial
Volume (eTIV) value to be used as a
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Hi Doug,
thanks for the confirmation!
All the best,
Tim
> On October 18, 2019 at 4:01 PM "Greve, Douglas N.,Ph.D."
> wrote:
>
>
> They are just different names
>
> On 10/17/19 11:52 AM, Tim Schäfer wrote:
> > External Email - Use
They are just different names
On 10/17/19 11:52 AM, Tim Schäfer wrote:
> External Email - Use Caution
>
> Dear fs experts,
>
> I'm parsing aseg.stats files for subjects to extract global brain measures
> and noticed that at least 2 names changed from FreeSurfer 5.1 versus
> FreeSurfer
External Email - Use Caution
Dear fs experts,
I'm parsing aseg.stats files for subjects to extract global brain measures and
noticed that at least 2 names changed from FreeSurfer 5.1 versus FreeSurfer 6.
It seems that:
* "EstimatedTotalIntraCranialVol" is in v6, but
.harvard.edu] *On Behalf Of *Greve,
> Douglas N.,Ph.D.
> *Sent:* Tuesday, November 20, 2018 1:50 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] aseg.stats calculations
>
> On 11/20/18 1:37 PM, Song, Da-Yea wrote:
>
> *External
20, 2018 1:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aseg.stats calculations
On 11/20/18 1:37 PM, Song, Da-Yea wrote:
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Hello,
I had a question regarding the aseg.stats and was hoping to get some help.
1. How is the TotalGray
On 11/20/18 1:37 PM, Song, Da-Yea wrote:
External Email - Use Caution
Hello,
I had a question regarding the aseg.stats and was hoping to get some help.
1. How is the TotalGray calculated? On the wiki page it mentioned that it
is the sum of lhCortex + rhCortex + SubCortGray +
External Email - Use Caution
Hello,
I had a question regarding the aseg.stats and was hoping to get some help.
1. How is the TotalGray calculated? On the wiki page it mentioned that it
is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried
calculating
Dear FS team,
I would like to obtain Total Brain Volume using metrics provided in
aseg.stats. I have the idea of obtaining it as a
result of white matter + grey matter.
WM is provided in CorticalWhiteMatter and GM could be obtained with:
TotalGreyMatter -
With the version 5.3 asegstats2table, you will always get these. In
version 6, you'll have the opportunity to get only the segs you specify.
On 08/10/2016 12:38 PM, shi yao wang wrote:
> Dear FS experts:
> How can I only out put the volume value in the aseg.stats file?
>
> I applied following
Dear FS experts:
How can I only out put the volume value in the aseg.stats file?
I applied following command: but it will produce a table with lots of
values such as brainsegvol, brainsegvolnotvent, which I donot want to use.
thanks
asegstats2table --subjects 004 021 040 067 080 092 \
Johnathan, can you point us to source of the issues you are concerned
about? Is there a paper or website?
thanks
doug
On 6/8/16 9:46 AM, Bruce Fischl wrote:
> Hi Jonathan
>
> as far as we know, FreeSurfer is the most reliable and robust
> longitudinal brain morphometry tool that is publicly
Hi Jonathan
as far as we know, FreeSurfer is the most reliable and robust
longitudinal brain morphometry tool that is publicly available. We are
working to improve it (always!), but the answer to your question is yes,
certainly 5.3 and the upcoming 6.0 are both excellent longitudinal tools
Hello
Are the volume and thickness measures in FreeSurfer's aseg.stats and
aparc.stats accurate and reliable enough to assess changes in volume and
thickness longitudinally? I have heard there have been some
accuracy/reliability issues in these files in older versions of FreeSurfer. Is
the
Dear Bruce,
I think of a probability map for each segmented structure, like the
partial volume images for WM, GM and CSF in FSL. Is there anything
like that in Freesurfer?
Thanks,
Gabor
2014-05-09 22:48 GMT+02:00 Gabor Perlaki petzinger.ga...@gmail.com:
Dear Bruce,
I think of a file which
Hi Gabor
the partial volume estimates are not the probabilities. We could output
p-values, but that won't give you partial volume estimates.
Bruce
On Thu, 15 May
2014, Gabor Perlaki wrote:
Dear Bruce,
I think of a probability map for each segmented structure, like the
partial volume
Dear Bruce,
I think of a file which also shows the partial volume estimates for
the segmented structures.
Thanks,
Gabor
2014-05-07 22:31 GMT+02:00 Gabor Perlaki petzinger.ga...@gmail.com:
Dear Bruce,
Is there a file generated by freesurfer which stores the subcortical
segmentations together
Hi Gabor,
sorry, I still don't know what you mean. The volume estimates in aseg.stats
do include partial volume estimates. Do you mean to include only the volume
of a structure that comes from partial volume voxels? Would that really be
useful? For something like the hippocampus it will be a
Dear Bruce,
Is there a file generated by freesurfer which stores the subcortical
segmentations together with the information of partial volume
estimates?
Thanks,
Gabor
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what information would you want?
Bruce
On Wed, 7 May 2014, Gabor Perlaki wrote:
Dear Bruce,
Is there a file generated by freesurfer which stores the subcortical
segmentations together with the information of partial volume
estimates?
Thanks,
Gabor
Dear all,
I've loaded the mri/aseg.mgz in slicer3D and done a label statistics
on the image. The left caudate was reported to be 4005 mm^3 and the
right caudate to be 4011 mm^3 by Slicer3D. However, these numbers are
somewhat different from the values reported in aseg.stats: 3757 mm^3
and 3901
Hi Gabor
we do partial volume correction when we compute the aseg.stats
cheers
Bruce
On Tue, 6 May
2014, Gabor Perlaki wrote:
Dear all,
I've loaded the mri/aseg.mgz in slicer3D and done a label statistics
on the image. The left caudate was reported to be 4005 mm^3 and the
right caudate to
Dear all,
I've run the freesurfer on 3 subjects and converted the aseg.mgz into
*.nii.gz in the native space:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii.gz
I've did a stats on left and right hippocampal volumes in the native space
using fslstats:
fslstats aseg2raw.nii.gz -l
Hi Gabor
the volumes must change with reslicing. As to why they get consistently
bigger in the hippocampus I'm not sure, probably something to do with
its geometry
cheers
Bruce
On Fri, 17 Jan 2014, Gabor Perlaki wrote:
Dear all,
I've run the freesurfer on 3 subjects and converted the
Try using mri_label2vol instead of mri_convert. mri_convert just does a
mapping whereas mri_label2vol knows that this is a segmentation
doug
On 1/17/14 8:23 AM, Bruce Fischl wrote:
Hi Gabor
the volumes must change with reslicing. As to why they get consistently
bigger in the hippocampus
Dear freesurfers.
I'm using freesurfer for two weeks. I'm currently trying to make a script
to get asegstats resultats for 100 patients.
I did this script in tcsh :
foreach filename (t1_)
asegstats2table --subjects ${filename} \
--segno 12 18 14\
--tablefile asegstats.txt
end
The
On Monday, December 03, 2012 13:46:11 charles laidi wrote:
Dear freesurfers.
I'm using freesurfer for two weeks. I'm currently trying to make a script
to get asegstats resultats for 100 patients.
I did this script in tcsh :
foreach filename (t1_)
asegstats2table --subjects
Hi, all, anyone knows that if the ICV in the aseg.stats means the whole volumes
inside the skull or the total volumes of GM and WM? Does it include the CSF
between the skull and the cortex? Thanks.
Natalie
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yes, that is a consequence of partial volume correction. If you have a 3
class boundary (two of which are hippocampal subdivisions), we will compute
different partial volume fractions than if you have a 2 class boundary. I
wouldn't expect it to be a huge effect, but they definitely won't be
Yes, I'm glad that Bruce confirmed this. Good. The majority had
deviations that were in the range of 20-40 voxels which seems
intuitively in the right range. The ones that concerned me were those
that inexplicably deviated in the range of 600 to 1000 voxels out of
4000 or so voxels in the
Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill
tool to relabel the *entire* left hippocampus segmentation to
'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left
hippocampus volume from the original aseg.stats be identical to the volume
of
Hi Joshua
probabilities are computed internally, but not stored nor used in volume
calcualtions. Are you actually doing a 3D fill? I don't think the
hippocampus label is guaranteed to be connected. Can you try instead
replacing every voxel in matlab with the hippocampus index to your new one?
Hi Bruce,
First, let me add that if I run the mri_segstats without the --pv flag, the
two will have identical volumes. This indicates to me that we captured all
the voxels into the new label.
Joshua
-
Joshua Lee
Graduate Student
Center for Mind and Brain
Department of Psychology
University of
hmmm, that is convincing. I don't think there's anything in mri_segstats
that knows about the meaning of any of the indices, but maybe Doug can
correct me?
On Wed, 16 May 2012, Joshua Lee wrote:
Hi Bruce,
First, let me add that if I run the mri_segstats without the --pv flag, the
two will
Hi all,
In the aseg.stats and wmparc.stats output files in *version 4.2.0*, there
were four volumes named:
Left-Cerebral-White-Matter
Left-Cerebral-Cortex
Right-Cerebral-White-Matter
Right-Cerebral-Cortex
Does anyone happen to know what the corresponding volumes are in *version
5.1*? They don't
Dear Freesurfer Experts,
I have ran recon-all on a T1 SPGR image of a control subject without error.
The outputs look reasonable (visually). However, the numbers I got from
aseg.stats do not make sense (they are way off). Any thoughts?
# Title Segmentation Statistics
#
#
Does the aseg look correct? If so, how about the aparc+aseg?
On Wed, 30 Dec
2009, Hui J Yu wrote:
Dear Freesurfer Experts,
I have ran recon-all on a T1 SPGR image of a control subject without error.
The outputs look reasonable (visually). However, the numbers I got from
aseg.stats do
Hi:
In the aseg.stats file, some columns has the title: normMean,
normRange, etc... What is the meaning of the word norm ?...
Sincerely,
--
Gonzalo Rojas Costa
Department of Radiology
Clínica Las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel:
that means it's from the norm.mgz volume
Gonzalo Rojas wrote:
Hi:
In the aseg.stats file, some columns has the title: normMean,
normRange, etc... What is the meaning of the word norm ?...
Sincerely,
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone
Just run recon-all with the -segstats option, should take about 5 min or so
Kellen Mobilia wrote:
I would like to pose a brief question.
Somehow in the process running brains through autorecon one of my
subjects aseg.stats files became messed up and as far as I am able to
tell everything
Irene,
Have you checked if these patients who don`t have aseg.stats in their stats
directory have the recon-all finished correctly.
Best Regards
Pedro Paulo Jr
2008/8/14 irene [EMAIL PROTECTED]
Hi all,
I need data which are in the aseg.stats file (which is in the stats file).
Some
Jared,
You can do recon-all -segstats subjid for each subject. This uses the
aseg.mgz to create the aseg.stats, however, if the new aseg.mgz you
generated with the script I sent you is named something other than
aseg.mgz, then you will want to change it to aseg.mgz for this to
work.
Allison
I think recon-all -subjid subject -segstats
should do itOn Wed, 30 Jan 2008, Jared
Conley wrote:
FreeSurfer Community,
Is there an easy, quick way to regenerate the aseg.stats file? This
particular file was deleted accidentally for a few subjects and we wondered
if we could quickly
FreeSurfer Community,
Is there an easy, quick way to regenerate the aseg.stats file? This
particular file was deleted accidentally for a few subjects and we
wondered if we could quickly recreate this file without having to run
recon-all again. All the other files in the subject directory
You should get that from ?h.aparc.stats. These will be more accurate as
they are derived directly from the surface whereas aseg.stats goes
through the volume.
doug
Joan Fisher wrote:
Hello --
The aseg.stats output that I have itemizes the size of the structures
up to line 86, but there are
Hello --
The aseg.stats output that I have itemizes the size of the structures up
to line 86, but there are only zeros after that.
For example, if I wanted to know the wm or ctx for the rh middle
temporal gyrus, there's a line devoted to that, but no values.
Is there an option that I should be
It turns out that the segmentation is fine in aseg.mgz (although for
some reason I am unable to view the segmentation with
FreeSurferColorLUT.txt as it says it wasn't valid or wasn't found even
though it is in my directory) and yet the aseg.stats table was not
generated.
(Doug?) How does one
:
recon-all -segstats -s subjid
Jenni
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Joan Fisher
Sent: Sunday, March 25, 2007 10:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] aseg.stats
It turns out that the segmentation is fine in aseg.mgz
I have just changed the way that DEV version recon-all creates the
aseg.stats file. Previously, it would report everything that it found
in FreeSurferColorLUT.txt. This included a lot of stuff that would
never be in the subcortical segmentation, and this made the aseg.stats
file very messy.
The
Hi,
So where can I download this update?
Would I have to download the whole version of freesurfer?
Thanks,
HweeLing
On 8/1/06 10:09 AM, Doug Greve [EMAIL PROTECTED] wrote:
I have just changed the way that DEV version recon-all creates the
aseg.stats file. Previously, it would report
I should have mentioned one more thing. If you want to re-run
recon-all so that it only re-creates the stats/aseg.stats table, then run
recon-all -s subject -segstats
doug
On Mon, 31 Jul 2006, Doug Greve wrote:
I have just changed the way that DEV version recon-all creates the
aseg.stats
PROTECTED] On Behalf Of Lee HL
Sent: Monday, July 31, 2006 10:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aseg.stats
Hi,
So where can I download this update?
Would I have to download the whole version of freesurfer?
Thanks,
HweeLing
On 8/1/06 10:09 AM, Doug Greve [EMAIL
Hi all,
Can anyone tell me how freesurfer defines Intracranial
volume, Brain segmentation volume and Brain mask volume? What is the difference
between the 3 measures?
-Dhruman
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Freesurfer@nmr.mgh.harvard.edu
the Intracranial volume we estimate using the method proposed by Denise
Head and Randy Buckner - look at the det of the talairach xform and use
it to infer ICV (what they call eTIV).
Brain segmentation volume: volume of all brain voxels in the aseg
Brain mask volume: volume of all voxels after
Dhruman,
At the top of this page is a link to the ICV estimation paper:
http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
Nick
On Fri, 2006-06-30 at 12:45 -0400, Bruce Fischl wrote:
the Intracranial volume we estimate using the method proposed by Denise
Head and Randy Buckner - look at the
Dear all,
I would like to know what some of the abbreviations of areas in the
aseg.stats file stand for, in particular:
Left-F3orb
Left-lOg
Left-aOg
Left-mOg
Left-pOg
Left-Stellate
Left-Porg
Left-Aorg
and Right-Thalamus vs Right-Thalamus-Proper
Where may I find documentation on these names?
Hi Sasha,
the Right-Thalamus-Proper is what's used, not Right-Thalamus. The rest are
CMA labels, and hopefully Dave Kennedy will respond (or you could look in
his or Nikos Makris' papers).
cheers,
Bruce
On Mon, 15
May 2006, Sasha Wolosin wrote:
Dear all,
I would like to know what some
Hi Sasha,
Besides the Right-Thalamus-Proper, as Bruce pointed out, none of those
are typically labeled during the normal aseg run by recon-all. In the
aseg.stats file you will likely find a bunch of zeros listed for these,
and other things that are not labeled (i.e., Spinal-Cord,
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