Hi Katie,
FreeSurfer operates mostly in "FreeSurfer Space", which is voxel resolution of
1mm^3 and sagittal orientation.
You can compare orig.mgz to the original input to see what the difference
between native space and FreeSurfer Space would be.
eTIV is computed using the transformation matri
External Email - Use Caution
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 Cauti
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 6
.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 Email -
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 Email - Use Caution
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 + Ce
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 com
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 avai
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
Bruc
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 images
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 :
> Dear Bruce,
>
> I think of a file which also shows the partial v
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 lo
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 :
> Dear Bruce,
>
> Is there a file generated by freesurfer which stores the subcortical
> segmentations together with the information
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 Bruce,
Is there a file generated by freesurfer which stores the subcortical
segmentations together with the information of partial volume
estimates?
Thanks,
Gabor
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harva
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 caudat
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
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 as
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 --subj
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 hippocamp
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
ide
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 ha
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
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?
They are in the header now (see below for example). Those values in the
old file should not be used (which is why we removed them for later
versions).
doug
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter
volume, 253760.315035, mm^3
# Measure rhCortex, rhCortexVol, Right h
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 d
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.harva
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 els
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 pa
Thanks. That seemed to work just fine.
Jared
Bruce Fischl wrote:
I think recon-all -subjid -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
Jared,
You can do recon-all -segstats 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
On We
I think recon-all -subjid -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 recreate this
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
Hi Joan,
The aseg.mgz file is the actual segmentation volume. FreeSurferColorLUT.txt
is simply a text look up table with label numbers, colors, and identifying
tags. In the most recent versions of Freesurfer you do not need to include
this in your command line, it will open with this automatical
EMAIL 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 Grev
available to
you so you can replace a binary and re-run recon-all -segstats -s subjid
Jenni
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL 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
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 f
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
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 d
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
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, Soft-Tissu
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
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