the problem is that the average surface has less surface area than any
individual. We keep track of this in the surface file itself (try mris_info
on it), then correct for it when we need to.
cheers,
Bruce
On Tue, 9 Jun 2009, Alex Fornito wrote:
No, sorry. What is the error?
On 09/06/2009
No, sorry. What is the error?
On 09/06/2009 17:31, "Douglas N Greve" wrote:
> Does this workaround account for the error in the raw area unavoidable
> on an average surface? If not, are you aware of it and is it important
> for your analysis?
>
> doug
>
> Alex Fornito wrote:
>> Rudolph's work
Does this workaround account for the error in the raw area unavoidable
on an average surface? If not, are you aware of it and is it important
for your analysis?
doug
Alex Fornito wrote:
Rudolph's workaround seems to do the trick.
Thanks!
On 06/06/2009 18:16, "Bruce Fischl" wrote:
yeah,
Rudolph's workaround seems to do the trick.
Thanks!
On 06/06/2009 18:16, "Bruce Fischl" wrote:
> yeah, I guess we disabled it since the surface area isn't representative
> of individual subjects. We could either change it to a warning with a
> -force flag or something, or you could run mri_annot
yeah, I guess we disabled it since the surface area isn't representative
of individual subjects. We could either change it to a warning with a
-force flag or something, or you could run mri_annotation2label and run
label_area on the individual labels.
Do you really want the surface area on the
-Original Message-
From: Alex Fornito
Thanks,
I did as you suggested, but got a different error telling me that
mris_anatomical_stats cannot be used with fsaverage as it is an average
subject.
You can try the following "hack": convert the annotation to a series of
labels, and t
Thanks,
I did as you suggested, but got a different error telling me that
mris_anatomical_stats cannot be used with fsaverage as it is an average
subject.
I am running v 4.2.0. Would I be able to run stats on fsaverage using a new
freesurfer version, or is there some other way around this?
I am
Hi Alex,
if all you care about is surface area you can probably just copy the
wm.mgz from any subject into the fsaverage/mri dir. Other stats will of
course then be incorrect. You also have to be careful as the fsaverage
surfaces contain less surface area (due to averaging) than individual
su
Hi,
I'm playing around with different ways of generating custom annotation files
using the fsaverage surface, and would like to estimate the surface area of
each ROI. I tried running mris_anatomical stats, but it seems to required
wm.mgz, which is not contained in the fsaverage directories (please
Hi Paul,
the mris_volume method probably includes hippocampus and amygdala, which
mris_anatomical_stats should remove, although the difference you are seeing
goes in the other direction, which I don't understand.
Bruce
On Fri, 21 Dec 2007, Paul Greenberg wrote:
Hi All,
I've processed a se
Hi All,
I've processed a set of 40 subjects with
freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 and am now working on
a series of morphometric analyses. I am comparing gray matter volumes
found in:
1) aparc.stats from recon-all, (same as output of
"mris_anatomical_stats" run from the comm
Yes, that is definitely an option although only one of our machines currently runs Linux. I'm sure we can work around that. Thanks for all the help. I'm sure we'll have more questions for you..:)Anil.
On 6/29/06, Bruce Fischl <[EMAIL PROTECTED]> wrote:
you could skip the aseg but then you'll need t
you could skip the aseg but then you'll need to manually edit the
surfaces, which can be time consuming. Running on more than one computer
isn't an option for you?
On Wed, 28 Jun 2006, Anil Roy wrote:
Hi Everyone,
Is there a way to process the minc files I have and only obtain the
anatomical
Hi Everyone,
Is there a way to process the minc files I have and only obtain the
anatomical stats without the entire recon-all process. I have a large
number of brains and it would take a couple of weeks if I was to take
every minc file and run recon-all.
Thanks - Anil.
_
HI,
I'm finishing a study I completed using an older version of freesurfer
(20040218), and have noticed that I get different values for surface area and
grey matter volume when using mris_anatomical_stats for my labels depending on
whether I use the mris_anatomical_stats that it is part of this
Hi Alex,
we've fixed a couple of small discrepancies in mris_anatomical_stats. I
would use the new version - it should be fine on old surfaces.
Bruce
On Tue, 27
Sep 2005, Fornito, Alexander wrote:
HI,
I'm finishing a study I completed using an older version of freesurfer
(20040218), and
ject:Re: [Freesurfer] anatomical stats
what do you mean it does not work? Because things aren't aligned? I'm
afraid you're on your own if you want the columns to be lined up. I'd
suggest a perl script.
doug
Fornito, Alexander wrote:
>-b doesn't seem to work.
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] anatomical stats
try -b
On Sat, 17 Sep 2005, Fornito, Alexander wrote:
I can create a log file, but in the output, the numbers are out of alignment, so you can't easily figure out what each n
ginal Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Sat 9/17/2005 10:33 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject:RE: [Freesurfer] anatomical stats
try -b
On Sat, 17 Sep 2005, Fornito, Alexander wrote:
> I can create a log file
roi_table 101 lh white
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 9/16/2005 9:51 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] anatomical stats
p.s. the flags should always come before the mandato
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 9/16/2005 9:51 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] anatomical stats
p.s. the flags should always come before the mandatory command line args.
On
Fri, 16 Sep 2005, Fornito, Al
p.s. the flags should always come before the mandatory command line args.
On
Fri, 16 Sep 2005, Fornito, Alexander wrote:
Hi,
I'm using the 20050905 distribution and it seems like mris_anatomical_stats is
trying to look for cor files, when I've run my analyses using mgz. Is there a
way to ch
try mris_anatomical_stats -mgz
On Fri, 16 Sep 2005, Fornito, Alexander
wrote:
Hi,
I'm using the 20050905 distribution and it seems like mris_anatomical_stats is
trying to look for cor files, when I've run my analyses using mgz. Is there a
way to change this, or have I got it wrong?. Here is
Hi,
I'm using the 20050905 distribution and it seems like mris_anatomical_stats is
trying to look for cor files, when I've run my analyses using mgz. Is there a
way to change this, or have I got it wrong?. Here is the output
mris_anatomical_stats 101 lh white
reading volume /data/flanders/wo
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 7/14/2005 8:04 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Anatomical stats for labels
the label is identified by the vertex indices, which allow it to
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Anatomical stats for labels
the label is identified by the vertex indices, which allow it to be
projected onto any surface.
On Thu, 14 Jul 2005, Fornito, Alexander wrote:
-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 7/13/2005 9:32 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Anatomical stats for labels
yes, if you specify pial it will be the pial surface area
: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Anatomical stats for labels
yes, if you specify pial it will be the pial surface area.
On Wed, 13 Jul
2005, Fornito, Alexander wrote:
> Cool, thanks.
> O
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Anatomical stats for labels
Hi Alex,
that's a bug - the volume is the total of the surface area of each
triangle times the average thickness there, so the pial will be different
from the white (should just take the average of t
s
included.
Hope this makes sense!
Thanks,
Alex
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 7/12/2005 1:09 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Anatomical stats for labels
Hi Alex,
th
Hi Alex,
that's a bug - the volume is the total of the surface area of each
triangle times the average thickness there, so the pial will be different
from the white (should just take the average of the two)
Bruce
On Mon, 11 Jul 2005, Fornito, Alexander wrote:
Hi,
I've noticed that when I r
Hi,
I've noticed that when I run mris_anatomical stats on a label, I get a
different value for "total gray matter volume" if I run it on the pial surface,
compared to if I run it on the white surface. Just wondering why this is, how
the total gray matter volume is calculated, and which one rep
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