Hi Derek,
We do not use the standard FS pipeline for the analysis of the age group
of your interest. In general, we have seen it being successfully used
on subjects down to 4.5yrs of age, but 25 mo is quite young to be analyzed
by the adult template. I assume, without seeing your data, that yo
is.edu <mailto:dandr...@ucdavis.edu>
*From: * on behalf of Douglas
Greve
*Reply-To: *Freesurfer support list
*Date: *Friday, August 10, 2018 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children
It should be preserving total
fornia Davis
Telephone: +1 916 703 0360
Email: dandr...@ucdavis.edu<mailto:dandr...@ucdavis.edu>
From: on behalf of Douglas Greve
Reply-To: Freesurfer support list
Date: Friday, August 10, 2018 at 10:25 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Su
It should be preserving total surface area. Can you send your
mris_preproc command line and the terminal output? It might be something
with 5.1 as well.
On 8/9/18 3:49 PM, Derek Sayre Andrews wrote:
External Email - Use Caution
Dear Freesurfer Developers and Experts,
I have been ex
External Email - Use Caution
Hi Derek,
you could try creating a study-specific template to replace fsaverage with
make_average_subject and then re-run your reconall.
Best,
Laurel
Laurel Raffington
Postdoctoral Researcher
Center for Lifespan Psychology
Max Planck Institu
It will not be one surface area for all voxels, each voxel will have
it's own surface area. If you have a particular voxel in mind, then you
can create a volume where that voxel is 1.0 and the rest 0, then map it
to the surface and to fsaverage and see how big it gets.
On 6/13/17 9:26 PM, Mat
rom: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, May 8, 2017 5:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface area
Yes, I would recommend making some kind of adjustment. As with all su
...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, May 8, 2017 5:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface area
Yes, I would recommend making some kind of adjustment. As with all such
adjustments, the adjustment you choose will dictate how you interpret the
Yes, I would recommend making some kind of adjustment. As with all such
adjustments, the adjustment you choose will dictate how you interpret
the results (eg, a eTIV adjustment means something different that an
adjustment for whole brain volume). For surface area, I usually adjust
the eTIV. It
yes, it looks like it is correcting then.
Bruce
On Tue, 29 Mar 2016, Jaiashre
Sridhar wrote:
Douglas,
This is my command line:
label_area lh fsaverage lh.temporalpole
Output:
bash-3.2$ label_area lh fsaverage lh.temporalpole
reading /Volumes/project/fsaverage/surf/lh.smoothwm...
adjusti
,
Jaiashre.
Re: [Freesurfer] Surface area of an fsaverage
label<https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg46383.html>
2016-03-29<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=date:20160329&o=newest&f=1>
Thread<https://
Hi Jaiashre, please include previous correspondences so I know the context
thanks
doug
On 03/29/2016 02:37 PM, Jaiashre Sridhar wrote:
> Douglas,
>
> This is my command line:
> label_area lh fsaverage lh.temporalpole
>
> Output:
> bash-3.2$ label_area lh fsaverage lh.temporalpole
> reading /Volume
Douglas,
This is my command line:
label_area lh fsaverage lh.temporalpole
Output:
bash-3.2$ label_area lh fsaverage lh.temporalpole
reading /Volumes/project/fsaverage/surf/lh.smoothwm...
adjusting for group surface area 1.31 (82220 / 62822)
fsaverage: lh.temporalpole - 512.352 square mm
Thanks,
what is your command line?
On 03/28/2016 05:50 PM, Jaiashre Sridhar wrote:
> Hello,
>
> I have used label_area to compute the surface area of a desikan label
> on fsaverage. Is the correction factor taken into account during
> computation with this function?
>
> Thanks,
> Jaiashre.
>
>
> ___
Hi Jaiashre,
yes, it should do the correction for average surface area, and should
print out a message indicating it is doing so. Something like:
adjusting for group surface area ...
cheers
Bruce
On Mon, 28
Mar 2016, Jaiashre Sridhar wrote:
Hello,
I have used label_area to compute the
if it's saved as a surface you can get it from mris_anatomical_stats. If
you want only a region within the surface, create a label and use the -l
option
cheers
Bruce
On Tue, 8 Sep 2015, Jockwitz, Christiane wrote:
Dear all,
I would like to extract the surface area from the outer smoothed
Hi Christiane,
You can use mris_info lh.pial-outer-smoothed
Best,
Marie
On Sep 7, 2015, at 10:57 PM, "Jockwitz, Christiane"
mailto:c.jockw...@fz-juelich.de>>
wrote:
Dear all,
I would like to extract the surface area from the outer smoothed hull of a
particular region of interest that is
There is not such a script. You can do a different check though by
computing the mean area on the crown and in the fundus in the native
subject space, then comparing these numbers across subjects to see if
the effect holds. This test gets around the problems of sampling areal
measures into a s
Greve"
发送时间: 2014年3月6日 星期四
收件人: "沈庄明" , "free surfer"
抄送:
主题: Re: [Freesurfer] Surface area in aparc stats
Hi Zhuangming, please remember to post to the list. Thanks! I
don't underst
or surface are computed when FreeSurfer calculates the surface area.
Thanks!
Zhuangming Shen
[IMAGE]
-原始邮件-
发件人: "Douglas Greve"
发送时间: 2014年3月6日 星期四
收件人: "沈庄明" , "free surfer"
抄送:
主题: Re: [Freesurfer] Surface a
收件人:freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Surface area in aparc stats
By default, the surface area is computed from the white surface (ie, boundary
between WM and GM). It is possible to compute it from the pial surface (ie,
boundary between GM and background)
doug
On 3/5/14 9:14 PM,
r@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*抄送:*
*主题:* Re: [Freesurfer] Surface area in aparc stats
By default, the surface area is computed from the white surface
(ie, boundary between WM and GM). It is possible to compute it
from the pial surfa
By default, the surface area is computed from the white surface (ie,
boundary between WM and GM). It is possible to compute it from the pial
surface (ie, boundary between GM and background)
doug
On 3/5/14 9:14 PM, ??? wrote:
Hi all,
I need to know how is the SurfArea in ?h.aparc.stats ca
On 06/10/2013 02:18 AM, Andreas Berger wrote:
> Hi,
>
> basically, i would like to use the area measure for group analysis, but i'm
> not sure whether that's ok to do. my questions would be:
>
> is it suitable for group analysis?
yes
>
> what should i cite if i do?
We don't have a citation specifi
Hi,
basically, i would like to use the area measure for group analysis, but i'm
not sure whether that's ok to do. my questions would be:
is it suitable for group analysis?
what should i cite if i do?
is surface area represented vertex-wise, with a vertex' adjacent face's area
added and divide
Hi Andreas, it is not the same method but somewhat related. The method
assures that total area (or volume) is preserved when mapping between
subjects. How much detail do you need?
doug
On 06/04/2013 05:21 AM, Andreas Berger wrote:
> Hello FreeSurfers,
>
> after reading this [1] paper about me
Dear Anderson,
Thanks for the suggestions. I will give it a go.
All the best,
Shantanu
On Sat, February 16, 2013 10:14 am, Anderson M. Winkler wrote:
> Dear Shantanu,
>
> An implementation that runs in Matlab or Octave is available here:
> http://brainder.org/download/areal
>
> I was planning t
Dear Shantanu,
An implementation that runs in Matlab or Octave is available here:
http://brainder.org/download/areal
I was planning to write a compiled version that could be integrated more
easily in FS. However, just by the time as the paper was published, I moved
to another country and started
Yes, it is probably best to do it with those as those have the averages
across the subjects used to create the atlas. If you just use the area
of the cluster on the pial, it will be somewhat smaller.
doug
On 09/06/2012 01:53 PM, Ritobrato Datta wrote:
> Hi Doug,
>
> I need to dump the surfa
hmmm, something seems badly wrong here. You shouldn't have any vertex
indices over 150K or so. If you load that annot file onto the surface in
tksurfer does it look right? Does tksurfer complain when you try to load
it?
On Fri, 18 May 2012, Inês Violante wrote:
Hi,
It repeats this several t
Hi,
It repeats this several times and
MRISreadAnnotationIntoArray: vertex index out of range: 775162420
i=2E340A34, in_array_size=157940
annot file: CS/label/lh.aparc.annot
MRISreadAnnotationIntoArray: vertex index out of range: 775162420
i=2E340A34, in_array_size=157940
annot file: CS/la
Hi Ines, this is a good thing to post to the list since there are others
that might know better than me. Also, please include the full terminal
output.
thanks
doug
On 05/18/2012 11:51 AM, Inês Violante wrote:
> Thanks a lot!
>
> Just another question:
> I get this message for one of my subjec
yes, but you might want to change the name of the stats file so that you
don't overwrite the one that is there
doug
On 05/18/2012 11:39 AM, Inês Violante wrote:
> Thank you.
>
> I've tried this command:
>
> mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
> AC/label/lh.aparc.annot -c ./apar
Thank you.
I've tried this command:
mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a
AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial
Would this be appropriate?
ines
On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve
wrote:
> And you can get the full command line from the
> $subj
And you can get the full command line from the
$subject/scripts/recon-all.log file
doug
On 05/18/2012 10:41 AM, Michael Harms wrote:
> The last argument of mris_anatomical_stats allows you to specify the
> surface to use (pial in your case)
>
> cheers,
> -MH
>
>
> NAME
> mris_anatomical_
You should be able to get the correct syntax by checking the recon-
all.log file for an example.
cheers,
-MH
On Fri, 2012-05-18 at 15:48 +0100, Inês Violante wrote:
> Hi,
>
> Thanks Michael.
> However, when I try to do this using the aparc.annot file:
>
> mris_anatomical_stats -l CS/label/lh.a
Hi,
Thanks Michael.
However, when I try to do this using the aparc.annot file:
mris_anatomical_stats -l CS/label/lh.aparc.annot -b CS lh pial
I receive this error:
mris_anatomical_stats: could not scan # of lines from CS/label/lh.aparc.annot
I imagine this happens because the mris_anatomical_s
The last argument of mris_anatomical_stats allows you to specify the
surface to use (pial in your case)
cheers,
-MH
NAME
mris_anatomical_stats
SYNOPSIS
mris_anatomical_stats [options]
[]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
> Hi,
>
> I need to know the s
What is your mri_segstats and mri_surfcluster cmds? The area computed
from the triangles of the fsaverage subject are not representative of
the average of the individual subjects that go into fsaverage. For this
reason, we usually use the lh.area file inside of fsaverage to compute
the area (th
I don't know if that has ever been explored.
doug
krista kelly wrote:
> Great! Do you know if it is better to use one surface area (i.e. WM or
> pial) over the other when investigating differences between groups?
>
> On Tue, Oct 18, 2011 at 2:24 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard
The white surface.
doug
krista kelly wrote:
> When I extract surface area data using the following commands, which
> measure of surface area am I getting, the pial surface, the WM
> surface, or the total of both combined?
>
> aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh
> -
Hi Jürgen,
that can happen if the different parts of it are differentially scaled in
the spherical warp. For example if an individual has a secondary fold that
is uncommon in the atlas population.
cheers
Bruce
On Thu, 3 Feb 2011, Jürgen Hänggi wrote:
Dear FS experts
Sorry, for reposting t
Jeff,
Posting this back to the list so that others can see your reply.
cheers,
-MH
Forwarded Message
From: Jeff Sadino
To: Michael Harms
Subject: Re: [Freesurfer] Surface Area and Cortical Volume
Date: Wed, 29 Sep 2010 17:29:45 -1000
Hi Michael,
After reading your answer
perhaps an alternative is to use the surface area measure of an ROI,
namely the aparc regions, to conduct a group analysis, as the vertex
distribution problem is averaged-out over the region.
n.
On Wed, 2010-09-29 at 21:02 -0700, Don Hagler wrote:
> The area maps do contain the actual surface are
The surface area is the actual area of the surface. I think you may be
thinking of the jacobian, which measures the amount of stretching needed
to register with the surface atlas. Total cortical volume is available
from the "header" of the aseg.stats file, and that is a surface-based
measure.
The area maps do contain the actual surface area of each vertex with units of
mm^2. The problem is that the area at a given vertex depends on how many
vertices a given patch of
cortex was divided into, which is initially uniform but then varies
arbitrarily due
to topology correction, rend
ne 29, 2010 5:26 PM
To: Liang, Kelvin
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Surface-Area Weighted Average of Cortical Thickness
I doubt it's going to make that much difference, but if I had to choose,
I'd choose the formula that you have below (note the the areas
I doubt it's going to make that much difference, but if I had to choose,
I'd choose the formula that you have below (note the the areas should be
added together in the denominator).
doug
Liang, Kelvin wrote:
> Dear FreeSurfer Experts,
>
> I'd like to merge my cortical thickness measures across
, 2009 3:16 PM
To: Douglas N Greve
Cc: Elizabeth Selgrade; 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] Surface area of subcortical structures
or use mri_extract_label instead of mri_binarize, like this, to get the left
hippocampus:
mri_extract_label aseg.mgz 17 lh
sure, you could use mri_tessellate to cover it with triangles, then
mris_info to get the surface area. You'll need to get the structure
index from the FreeSurferColorLUT.txt file to pass to mri_tessellate
cheers,
Bruce
On Wed, 16 Sep 2009, Elizabeth
Selgrade wrote:
> Hello,
>
> Is there a wa
or use mri_extract_label instead of mri_binarize, like this, to get the
left hippocampus:
mri_extract_label aseg.mgz 17 lh.hippo.mgz
mri_tessellate lh.hippo.mgz 128 lh.hippo.unsmoothed
mris_smooth lh.hippo.unsmoothed lh.hippo
mris_info lh.hippo |& grep total_area
this seems to work.
'17' is the
There's not an easy way. You could binarize the structure
(mri_binarize), then build a surface around it (mri_tessellate), maybe
smooth it (mris_smooth), then compute the surface area (mris_info). This
would be a completely untested method though:).
Elizabeth Selgrade wrote:
> Hello,
>
> Is the
If you pass 'mris_curvature_stats' a '-l ' it will output,
amongst other, the surface area of the ROI, e.g.:
$>mris_curvature_stats -l rh curv
(will calculate a bunch of stats on the rh.curv file of -- just
ignore and look for:)
...
...
ROI Surface Area:
...
...
-=R
Barnali Basu wrote
this reference may be relevant:
Discrete Differential-Geometry Operators for Triangulated 2-Manifolds
(Mark Meyer, Mathieu Desbrun, Peter Schröder and Alan H. Barr),
VisMath 2002
the pdf is available at:
www.multires.caltech.edu/pubs
cheers,
roberto
On Wed, Apr 29, 2009 at 9:17 PM, Richard Frye
not that I know of.
Bruce
On Wed, 29 Apr 2009, Richard Frye wrote:
What is the best reference regarding the calculation of surface area and
surface curvature and are there any studies looking at the reliability of
these measures?
Thanks
Best Wishes,
Richard E. Frye, M.D., Ph.D., F.A.A.P.
Assi
You'll find surface area measurements for each cortical parcellation area
in your ?h.aparc.stats file within the stats directory for each subject.
Allison
On Wed, 3 Sep 2008, Barkay, Gavriel wrote:
Can I do surface area measurement using freesurfer?
--
Gavriel Barkay M.D. M.Sc.
Psychopharmaco
I agree. You could look at the jacobians across subjects, which will sort
of get at what you want, or surface area by parcellation unit is a good
idea.
On Fri, 23 Feb 2007, Don Hagler wrote:
Just a comment: Surface area on a vertex-wise basis doesn't seem very
informative. Before topology fi
Just a comment: Surface area on a vertex-wise basis doesn't seem very
informative. Before topology fixing, the surface area should be about the
same for all vertices (differences should be more or less random). Topology
fixing will add or remove vertices, so the surface area in a "fixed" regi
Hi Aaron,
they are generated from the ?h.white and the ?h.pial surfaces, and should
be what you want.
cheers,
Bruce
On Thu, 22 Feb 2007, Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I was interested in comparing surface area between two groups on a
node-by-node basis (something like average are
Yes, that is exactly what this is. You can run mris_preproc with --meas
area and then continue with mri_glmfit just as if you were doing a
thickness analysis.
doug
Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I was interested in comparing surface area between two groups on a
node-by-node ba
Hi Sasha,
it uses the ?h.white by default, but you can change that by giving
mris_anatomical_stats an additional argument (e.g. ?h.pial) at the end of
the cmd line
Bruce
On Thu, 29 Jun 2006, Sasha Wolosin wrote:
Dear all,
Are the regional surface areas computed by mris_anatomical_stats
usin
Thanks. Can I make mris_anatomical_stats use the pial surface instead?
>>> Doug Greve <[EMAIL PROTECTED]> 6/29/2006 1:29 pm >>>
White.
doug
Sasha Wolosin wrote:
>Dear all,
> Are the regional surface areas computed by mris_anatomical_stats
>using the ?h.white surface or the ?h.pial surface?
>T
White.
doug
Sasha Wolosin wrote:
Dear all,
Are the regional surface areas computed by mris_anatomical_stats
using the ?h.white surface or the ?h.pial surface?
Thanks,
Sasha
Disclaimer:
The materials in this e-mail are private and may contain Protected Health
Information. Please note that
63 matches
Mail list logo
