Re: [Freesurfer] Fwd: missing eTIV in asegstats2table

When I run asegstats2table -i aseg.stats_subj2 -t junk

I get EstimatedTotalIntraCranialVol as the last column.

doug

On 10/27/2013 06:06 PM, Daniel Ferreira wrote:

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 mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <5267E208.4090305@nmr.mgh.harvard.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <5254271F.4040508@nmr.mgh.harvard.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <5252CDCF.9050804@nmr.mgh.harvard.edu mailto: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 mailto:danifer@ull.es> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <CACNza6eGqfsZ2Sfj9EVJxDD4pQv8PW7=nbCYwwMEPtER0C0o7w@mail.gmail.com mailto: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 mailto:greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: <524AF141.3060100@nmr.mgh.harvard.edu mailto: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 mailto:daniferp@gmail.com | daniel.ferreira.padilla@ki.se mailto:daniel.ferreira.padilla@ki.se

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