You can use in a loop with your subjects. It extracts the fields I want and some others including the etiv to a table named AsegVol. You may change the number of the fields to get what you need. The code I am sending you addresses hippocampus, putamen and caudate (both sides).

________________________________________________________________________ for i in $(ls -d suj*)

do

asegstats2table --segno 11 12 17 50 51 53 -s $i --tablefile AsegVol done

________________________________________________________________________ Notice that suj is the prefix of all my subjects in freesurfer/subjects folder I hope it helps you. Em Qua, 2013-10-02 às 08:50 +0200, Daniel Ferreira escreveu:

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


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