Are you talking about outliers across subject? Or across region? I would just
take the FS-supplied value instead of averaging the regions.
On 11/19/2020 2:14 AM, Stephanie K wrote:
External Email - Use Caution
Hi Bruce,
Thanks for the prompt reply. It is my understanding that
with nmovie_qt)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Stephanie K
Sent: Friday, November 20, 2020 6:25 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}
External Email - Use Caution
Hi Bruce,
No, I don’t think
t; Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K
> *Sent:* Thursday, November 19, 2020 4:19 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Mean thicknes
, 2020 4:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}
External Email - Use Caution
Hi Bruce,
Is it also necessary to remove outliers (eg. 3 SD from the mean) for
Freesurfer structural measures of MRI images that have been visually
mr.mgh.harvard.edu> *On Behalf Of *Stephanie K
> *Sent:* Thursday, November 19, 2020 2:14 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Mean thickness estimation
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
&g
Hi Stephanie
I think that is always a good idea, unless for some reason it isn’t possible
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mean thickness
External Email - Use Caution
Hi Bruce,
Thanks for the prompt reply. It is my understanding that l_thickness,
r_thickness and estimated intracranial volume are accurately measured.
Would I still need to identify and remove outliers if visual inspection of
the images has not been
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mean thickness estimation
External Email - Use Caution
Hi,
I want to estimate the mean cortical thickness. For this I have summed the
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However,
I also have
External Email - Use Caution
Hi,
I want to estimate the mean cortical thickness. For this I have summed the
thickness across all 34 regions mapped to the Desikan-Killiany atlas.
However, I also have the average mean thickness of left and right
hemispheres (direct output variables
you will have to create a binary mask from the sig map by thresholding at a
given level, eg,
mri_binarize --i sig.mgh --min 2 --o sig.bin2.mgh
Then run
mri_segstats --i y.mgh --seg sig.bin2.mgh --id 1 --avgwf y.bin2.dat
where y.mgh is the --y input to mri_glmfit
--id 1 means to take the
External Email - Use Caution
Hello Freesurfer developers,
I wanted to extract mean thickness values of all participants from the
uncorrected significance maps obtained from mri glmfit for structural data
instead of extracting it from the corrected maps from glmfit sim. Is there
a
arvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
> Verzonden: zondag 6 maart 2016 16:14
> Aan: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Onderwerp: Re: [Freesurfer] mean thickness
>
> Hi Caroline
>
> how did you generate
Hi Caroline
how did you generate the Gnumeric file? And what operating
system/hardware are you using? Also, please send us the recon-all.log for
one of the subjects that you see this happening
cheers
Bruce
On Fri, 4 Mar 2016,
Caroline Beelen wrote:
Dear Freesurfer team,
Forgive me
Dear Freesurfer team,
Forgive me if this is a foolish question...
I wanted to overlook cortical thickness, area and volume measures in Gnumeric
file after recon-all (checking edits made). However, for several subjects I
noticed that the values of mean thickness (final column) were calculated
Thanks Doug,
I used the first link and works perfectly now!
Best regards,
Amirhossein Manzouri
On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
I just ran it, and it works fine. It may be that I need to give you more
libraries.
Start with this one
Dear Doug,
Kindly find attached a sample of my lh.aparc.stats file!
Best regards,
Amirhossein Manzouri
On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Can you send me your lh.aparc.stats file?
doug
On 05/14/2014 01:41 PM, amirhossein manzouri wrote:
Can you send me your lh.aparc.stats file?
doug
On 05/14/2014 01:41 PM, amirhossein manzouri wrote:
Yes!
On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
Is the mean thickness in the ?h.aparc.stats file? Something like
#
Is the mean thickness in the ?h.aparc.stats file? Something like
# Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm
On 05/13/2014 05:18 PM, amirhossein manzouri wrote:
Hi,
The same result! the last is insula !
Best regards,
Amirhossein Manzouri
On Mon, May 12, 2014 at 5:05
Yes!
On May 14, 2014 7:16 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Is the mean thickness in the ?h.aparc.stats file? Something like
# Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm
On 05/13/2014 05:18 PM, amirhossein manzouri wrote:
Hi,
The same result! the last
Hi,
The same result! the last is insula !
Best regards,
Amirhossein Manzouri
On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
greve/aparcstats2table
On 05/12/2014 03:41 AM,
Hi again,
I think I missed my question, How can I get the Mean Thickness of each
hemisphere for several subjects using the aparcstats2table command?
On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri a.h.manzo...@gmail.com
wrote:
Dear Doug,
I have read this post(
Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table
On 05/12/2014 03:41 AM, amirhossein manzouri wrote:
Hi again,
I think I missed my question, How can I get the Mean Thickness of each
hemisphere for several subjects using the aparcstats2table
Dear Doug,
I have read this post(
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html)
regarding
extracting Mean Cth of each hemisphere and I just get insula as the last
and totally 34 numbers, I use
aparcstats2table --hemi lh --subjects bert -m thickness --tablefile
: [Freesurfer] mean thickness over hemisphere in stats file
Hi Ines
I think mris_anatomical_thickness is your best bet. You probably want to
specify the ?h.cortex.label file with the -l flag so that it ignores
non-cortical regions
cheers
Bruce
On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote:
Dear
Dear experts,
please excuse my question, I'm a beginner. I really searched for an answer in
the archive, but I couldn't find out what I was doing wrong.
I would like to write the mean cortical thickness of a hemisphere in the stats
file. I read one can do that by using -m thickness.
Where in
Hi Ines
I think mris_anatomical_thickness is your best bet. You probably want to
specify the ?h.cortex.label file with the -l flag so that it ignores
non-cortical regions
cheers
Bruce
On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote:
Dear experts,
please excuse my question, I'm a
you can also use mri_segstats with the --slabel option (spec
?h.cortex.label) and the thickness as the input
On 08/09/2013 09:36 AM, Bruce Fischl wrote:
Hi Ines
I think mris_anatomical_thickness is your best bet. You probably want
to specify the ?h.cortex.label file with the -l flag so
. Tully tully.la...@googlemail.com
Date: Saturday, March 9, 2013 5:58 PM
To: Anderson M. Winkler wink...@fmrib.ox.ac.uk
Cc: free freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mean thickness covariate, mean area covariate,
mri_anatomical_stats for multiple subjects
Hi Anderson
...@fmrib.ox.ac.uk
Cc: free freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mean thickness covariate, mean area covariate,
mri_anatomical_stats for multiple subjects
Hi Anderson,
Thanks, that reference is particularly helpful.
Re: the usage of the white versus pial area question - I believe
Hello freesurfers,
It appears that prior discussions on the listserv have recommended using
mean cortical thickness (rather than ICV) as a covariate for thickness
analyses (predominantly recommended by Michael Harms). I have three
questions about this:
1. Is there a paper that I could cite
Hi Laura,
1. Is there a paper that I could cite that recommends using mean
cortical thickness rather than ICV?
If it helps, we used cortical thickness and area as covariate for the
respective analysis of regional thickness and area. Brain volume, which is
more closely related to ICV,
Hi Anderson,
Thanks, that reference is particularly helpful.
Re: the usage of the white versus pial area question - I believe that the
default area calculation in freesurfer is the white surface area, so unless
one specifies the pial in calculations, the standard surface area output
for surface
Hi Laura,
I think yes, sounds right. Maybe run both ways and see if the results agree
or differ.
All the best,
Anderson
2013/3/9 Laura M. Tully tully.la...@googlemail.com
Hi Anderson,
Thanks, that reference is particularly helpful.
Re: the usage of the white versus pial area question - I
Hi All, I wanted to clarify a point. Publications of cortical thickness
differences are usually produced with maps called mean thickness
difference maps.
I dug through the mail archive but did not find an answer
(Q1)
These statistical parametric maps are I assume produced by computing a
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