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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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: <5267e208.4090...@nmr.mgh.harvard.edu > <mailto:5267e208.4090...@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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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.4040...@nmr.mgh.harvard.edu > <mailto:5254271f.4040...@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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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.9050...@nmr.mgh.harvard.edu > <mailto:5252cdcf.9050...@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 <dani...@ull.es <mailto:dani...@ull.es>> > Subject: Re: [Freesurfer] missing eTIV in asegstats2table > To:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CACNza6eGqfsZ2Sfj9EVJxDD4pQv8PW7=nbcywwmepter0c0...@mail.gmail.com > <mailto:CACNza6eGqfsZ2Sfj9EVJxDD4pQv8PW7=nbcywwmepter0c0...@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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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: <524af141.3060...@nmr.mgh.harvard.edu > <mailto:524af141.3060...@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) > danif...@gmail.com <mailto:danif...@gmail.com> | > daniel.ferreira.padi...@ki.se <mailto:daniel.ferreira.padi...@ki.se> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
