Fwd: missing eTIV in asegstats2table - Freesurfer

27 Oct 2013


      Hi Douglas,
You are right, sorry for not including the thread. Below I paste our
previous conversation. I also attach again the files you asked me for.
Thanks,
best
Daniel
Message: 13
Date: Wed, 23 Oct 2013 10:49:44 -0400
From: Douglas Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] missing eTIV in asegstats2table
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 5267E208.4090305@nmr.mgh.harvard.edu
Content-Type: text/plain; charset="iso-8859-1"
Hi Daniel, what is this in reference to? If this is a follow up on a
previous thread, please include the rest of the thread and the file in
the same email. I go through way too many emails to keep track of who's
doing what. thanks!
doug
On 10/23/13 4:13 AM, Daniel Ferreira wrote:
Dear Douglas,
Please, find attached aseg.stats files for subj1 and subj2.
Thanks
Daniel
Message: 4
Date: Tue, 08 Oct 2013 11:39:11 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] missing eTIV in asegstats2table
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 5254271F.4040508@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Can you send the aseg.stats file for subj1 and subj2?
On 10/08/2013 07:53 AM, Daniel Ferreira wrote:
Dear Douglas,
I generated my table with version 5.3.
Attached is an example for two subjects (in .txt and .xls formats).
Best regards
Dani
Message: 18
Date: Mon, 07 Oct 2013 11:05:51 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] missing eTIV in asegstats2table
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 5252CDCF.9050804@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
what version was the table generated with? 5.3 does not use ICV in the
table anymore. It uses eTIV. Can you send an example of one of your tables?
On 10/07/2013 03:12 AM, Daniel Ferreira wrote:
Dear Douglas and Martin,
Thanks for your replies.
So far I have always been able to get eTIV when running
asegstats2table (last column on the spreadsheet). But my current
FreeSurfer version (5.3.0) is not grabbing it.
I can found eTIV in the header and extract it for all the subjects
with mri_segstats (as below in blue), but output is quite messy. I
would rather prefer to get it as in asegstats2table format.
Any idea?
Thanks a lot,
Dani
for i in FAD*; do echo $i; mri_segstats --subject $i --etiv-only >>
table_eTIV; done
Message: 4
Date: Wed, 2 Oct 2013 08:50:23 +0200
From: Daniel Ferreira danifer@ull.es
Subject: Re: [Freesurfer] missing eTIV in asegstats2table
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
    CACNza6eGqfsZ2Sfj9EVJxDD4pQv8PW7=nbCYwwMEPtER0C0o7w@mail.gmail.com
Content-Type: text/plain; charset="iso-8859-1"
Dear Douglas,
Thanks for your quick answer. Yes, all my subjects have the measure "
EstimatedTotalIntraCranialVol" in their "aseg.stats" file. The problem is
that when I run "asegstats2table", this variable is not exported to the
created text file.
I wonder if there is some way to extract eTIV for all my subjects at the
same time. I manage to do it with "mri_segstats", but what I get is
individual values for all my subjects in the terminal, so it is quite
boring to pass all the values to a table.
Thanks a lot,
Dani
Message: 1
Date: Tue, 01 Oct 2013 11:58:57 -0400
From: Douglas N Greve greve@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] missing eTIV in asegstats2table
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 524AF141.3060100@nmr.mgh.harvard.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
It should still be there. I changed the name to
EstimatedTotalIntraCranialVol, eg the line now looks like
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total
Intracranial Volume, 1509814.835086, mm^3
On 10/01/2013 10:50 AM, Daniel Ferreira wrote:
Hi,
I just run my first asegstats2table in version 5.3 of FS. Is not eTIV
included in the generated file anymore?
I know that I can get eTIV with mri_segstats --subject subjid
--etiv-only but, is it any way to get the values for all my subjects
in a text file as asegstas2table does?
Thanks a lot
Dani
-- 
Daniel Ferreira, PhD.
Department of Neurobiology, Care Sciences and Society, Division of Clinical
Geriatrics (Karolinska Institute, Sweden)
daniferp@gmail.com | daniel.ferreira.padilla@ki.se