Hi Bruce,

I'm a beginner in FS, so I just followed tutorial instructions for generating the files carefully... I generated it by typing in for instance (after recon-all process was done): aparcstats2table --hemi lh --meas thickness --subjects A01_T1 A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table followed by the command: gnumeric lh.aparc.thickness.table

It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770 CPU @ 3.4GHz x 8)

Attached the log file (A09).

Thank you very much!

Greetings, Caroline

-----Oorspronkelijk bericht----- Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Bruce Fischl Verzonden: zondag 6 maart 2016 16:14 Aan: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] mean thickness

Hi Caroline

how did you generate the Gnumeric file? And what operating system/hardware are you using? Also, please send us the recon-all.log for one of the subjects that you see this happening

cheers Bruce

On Fri, 4 Mar 2016, Caroline Beelen wrote:

Dear Freesurfer team,

Forgive me if this is a foolish question…

I wanted to overlook cortical thickness, area and volume measures in Gnumeric file after recon-all (checking edits made). However, for several subjects I noticed that the values of mean thickness (final column) were calculated wrong, whereas this is not the case for their independent cortical thickness values. For instance, this happened to subject A09. I’m including the excel file to show the example. In the gnumeric file the number for this subject was depicted as 2/4964 instead of 2.4 etc.. What could have went wrong?

Thank you for your answer in advance.

Kind regards, Caroline

Hi Douglas,

I'm not sure whether the gnumeric file is an ascii file. Attached you'll find the file. It seems the case when you open it in the terminal screen that the nr's look fine... (with command cat). However as soon as you type the command gnumeric etc. it creates a wrong table from the start (see file). Can I somehow change this?

Greetings, Caroline

-----Oorspronkelijk bericht----- Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Douglas N Greve Verzonden: dinsdag 8 maart 2016 0:24 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] mean thickness

the table file lh.aparc.thickness.table should be an ascii file. when you look at it with cat/more/less, what do you see? Can you send that table file?

On 03/07/2016 04:33 AM, Caroline Beelen wrote:

Hi Bruce,

I'm a beginner in FS, so I just followed tutorial instructions for generating the files carefully... I generated it by typing in for instance (after recon-all process was done): aparcstats2table --hemi lh --meas thickness --subjects A01_T1 A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table followed by the command: gnumeric lh.aparc.thickness.table

It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770 CPU @ 3.4GHz x 8)

Attached the log file (A09).

Thank you very much!

Greetings, Caroline

-----Oorspronkelijk bericht----- Van: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Namens Bruce Fischl Verzonden: zondag 6 maart 2016 16:14 Aan: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] mean thickness

Hi Caroline

how did you generate the Gnumeric file? And what operating system/hardware are you using? Also, please send us the recon-all.log for one of the subjects that you see this happening

cheers Bruce

On Fri, 4 Mar 2016, Caroline Beelen wrote:

...

Dear Freesurfer team,

Forgive me if this is a foolish question...

I wanted to overlook cortical thickness, area and volume measures in Gnumeric file after recon-all (checking edits made). However, for several subjects I noticed that the values of mean thickness (final column) were calculated wrong, whereas this is not the case for their independent cortical thickness values. For instance, this happened to subject A09. I'm including the excel file to show the example. In the gnumeric file the number for this subject was depicted as 2/4964 instead of 2.4 etc.. What could have went wrong?

Thank you for your answer in advance.

Kind regards, Caroline

---

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