Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

2019-02-19 Thread Greve, Douglas N.,Ph.D. 
did  you analyze them with different versions of FS?


On 2/15/19 3:28 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Thanks for taking a look at the file I sent! I think I have figured 
> out the issue for the most part. While it shows that there is data in 
> the recon-all log for the various cortical regions and eTIV, the data 
> I extracted using aparcstats2table gives me zeros. Part of the problem 
> seems to be that in the table aparcstats2table produces using the 
> Destrieux atlas, some variables are listed twice, but in a different 
> format. For example, frontomarginal thickness is listed as both 
> rh_G_and_S_frontomargin_thickness and as 
> rh_G_&_S_frontomargin_thickness. Some subjects have data for one 
> variable and some for the other variable. This happened for 13 
> variables. I've attached an excel file with data from 2 subjects that 
> shows the variables that are listed twice and how some subjects have 
> data for some variables and others have data for other variables. 
> Please let me if you have any ideas of why this may have happened.
>
> Thanks!
> Morgan
>
> -- 
>
> Morgan Botdorf, M.S.
>
> Graduate Student
>
> Neurocognitive Development Lab
>
> University of Maryland, College Park
>
> mbotd...@terpmail.umd.edu 
>
> Office: 301.405.5922 
>
>
>
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Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

2019-02-15 Thread Morgan Botdorf 
External Email - Use Caution

Thanks for taking a look at the file I sent! I think I have figured out the
issue for the most part. While it shows that there is data in the recon-all
log for the various cortical regions and eTIV, the data I extracted using
aparcstats2table gives me zeros. Part of the problem seems to be that in
the table aparcstats2table produces using the Destrieux atlas, some
variables are listed twice, but in a different format. For example,
frontomarginal thickness is listed as both
rh_G_and_S_frontomargin_thickness and as rh_G_&_S_frontomargin_thickness.
Some subjects have data for one variable and some for the other variable.
This happened for 13 variables. I've attached an excel file with data from
2 subjects that shows the variables that are listed twice and how some
subjects have data for some variables and others have data for other
variables. Please let me if you have any ideas of why this may have
happened.

Thanks!
Morgan

-- 

Morgan Botdorf, M.S.

Graduate Student

Neurocognitive Development Lab

University of Maryland, College Park
mbotd...@terpmail.umd.edu

Office: 301.405.5922


aparcstats2table_output_error.xlsx
Description: MS-Excel 2007 spreadsheet
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Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

2019-02-11 Thread Greve, Douglas N.,Ph.D. 
When you say that, eg, BrainSegVolNotVent is zero, is this in the 
aseg.stats file? In looking at your log, it appears that 
BrainSegVolNotVent is non-zero, eg,

BrainSegVolNotVent  1304558.000


On 2/11/19 5:51 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Yes, attached is the recon-all.log file for one subject.
>
> -Morgan
>
> -- 
>
> Morgan Botdorf, M.S.
>
> Graduate Student
>
> Neurocognitive Development Lab
>
> University of Maryland, College Park
>
> mbotd...@terpmail.umd.edu <mailto:mbotd...@terpmail.umd.edu>
>
>
> >Date: Thu, 7 Feb 2019 22:29:43 +
> >From: "Greve, Douglas N.,Ph.D."  <mailto:dgr...@mgh.harvard.edu>>
> >Subject: Re: [Freesurfer] zero values when run recon-all with T2pial
> >       flag (V6.0)
> >To: "freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>" 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> >Message-ID: <6ea86bbf-6001-e95d-dcee-84cc8ba5d...@mgh.harvard.edu 
> <mailto:6ea86bbf-6001-e95d-dcee-84cc8ba5d...@mgh.harvard.edu>>
> >Content-Type: text/plain; charset="utf-8"
>
> >
>
> >I have not. Can you send the recon-all.log file?
>
>
> >On 2/1/19 6:01 PM, Morgan Botdorf wrote:
> >
> > External Email - Use Caution
> >
> > Dear all,
> >
> > I recently ran recon-all on data using the T2pial flag to improve the
> > pial surface (using version 6.0). The T2 images seemed to improve the
> > pial surfaces; however, when I extract stats using the Destrieux
> > atlas, I get zero values for several regions and for
> > BrainSegVolNotVent and eTIV. If I run recon-all without the T2 image,
> > I get data for these regions,?BrainSegVolNotVent, and eTIV. Has anyone
> > run into similar issues using the T2pial flag or have an idea of what
> > may be causing this problem?
> >
> > Thank you in advance?for your help!
> >
> > Morgan
>
>
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Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

2019-02-07 Thread Greve, Douglas N.,Ph.D. 
I have not. Can you send the recon-all.log file?

On 2/1/19 6:01 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> I recently ran recon-all on data using the T2pial flag to improve the 
> pial surface (using version 6.0). The T2 images seemed to improve the 
> pial surfaces; however, when I extract stats using the Destrieux 
> atlas, I get zero values for several regions and for 
> BrainSegVolNotVent and eTIV. If I run recon-all without the T2 image, 
> I get data for these regions, BrainSegVolNotVent, and eTIV. Has anyone 
> run into similar issues using the T2pial flag or have an idea of what 
> may be causing this problem?
>
> Thank you in advance for your help!
>
> Morgan
>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] zero values when run recon-all with T2pial flag (V6.0)

2019-02-01 Thread Morgan Botdorf 
External Email - Use Caution

Dear all,

I recently ran recon-all on data using the T2pial flag to improve the pial
surface (using version 6.0). The T2 images seemed to improve the pial
surfaces; however, when I extract stats using the Destrieux atlas, I get
zero values for several regions and for BrainSegVolNotVent and eTIV. If I
run recon-all without the T2 image, I get data for these
regions, BrainSegVolNotVent, and eTIV. Has anyone run into similar issues
using the T2pial flag or have an idea of what may be causing this problem?

Thank you in advance for your help!

Morgan
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