Hi Dani,
etiv is in the header, not in the table where the individual strucures are) and looks like this:
# Measure IntraCranialVol, ICV, Intracranial Volume, 1736177.143497, mm^3
asegstats2table grabs it also.
Best, Martin
On 10/03/2013 04:54 AM, Daniel Ferreira wrote:
Hi,
Thanks Marcos for your reply. My problem is that asegstats2table does not output values for eTIV. I do not manage to figure out why.
But maybe your script could work. Anyone knows what is the corresponding FieldName Index for eTIV?? I checked a aseg.stats file and did not find it.
Thanks a lot
Dani
Message: 7 Date: Wed, 02 Oct 2013 10:32:51 -0300 From: Marcos Martins da Silva <marcosm@hucff.ufrj.br mailto:marcosm@hucff.ufrj.br> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: Daniel Ferreira <danifer@ull.es mailto:danifer@ull.es> Cc:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <1380720771.1845.9.camel@alien mailto:1380720771.1845.9.camel@alien> Content-Type: text/plain; charset="utf-8"
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 AsegVoldone
Notice that suj is the prefix of all my subjects in freesurfer/subjects folder I hope it helps you. Em Qua, 2013-10-02
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