Can you send us the file through our filedrop?

On 8/1/16 10:02 PM, Isabelle Deschamps wrote:

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So you're saying that the dimension changed after you ran freeview and saved the volume? Can you replicate it? ie, if you make a copy of the brainmask.mgz, then edit the copy, does it do the same thing every time you make a copy and edit it?

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Yes it does. I tried multiple time your suggestion (copying brain mask) and the same error happens. I tried erasing different brain areas of the brain mask to understand the source of the problem, and for these 4 participants it does not seem to matter what I erase or not. The dimensions change.

Thank you for your help,

Isabelle

Isabelle

On Jul 30, 2016, at 11:23 AM, "freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:

...

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Today's Topics:

1. Fwd: question about volume of mask (Dorsa Haji Ghaffari)
2. brain mask and T1 are not the same size (Isabelle Deschamps)
3. Re: error during longitudinal -long stream (Jinsong Tang)
4. Research Assistants needed for longitudinal brain development study at Boston Children's Hospital (Gaab, Nadine)
5. Re: error during longitudinal -long stream (Martin Reuter)
6. MNI coordinates of all the vertices of fsaverage (Sabin Khadka)
7. Running Retinotopy in FSFAST, Design Matrix has Empty Regressors (Taylor, Johnmark)
8. mri_normalize, 110 is too dark (tvg[fs])
9. Re: brain mask and T1 are not the same size (Douglas Greve)
10. Re: mri_normalize, 110 is too dark (Bruce Fischl)
11. Where are time series from adjusted (post selxavg3) ROIs (ERIK JAHNER)
12. Re: significance overlay in freeview (Caroline Beelen)
13. Running recon-all with T1 and FLAIR (Silas)
14. Re: error during longitudinal -long stream (Jinsong Tang)

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Message: 1 Date: Fri, 29 Jul 2016 12:08:43 -0400 From: Dorsa Haji Ghaffari <ghdor@umich.edu mailto:ghdor@umich.edu> Subject: [Freesurfer] Fwd: question about volume of mask To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID:

<CAAe2pvAtEfwUj6=7G+qe8JkNXm23SJ8PYF4zncfkBsHxOtNpPA@mail.gmail.com mailto:CAAe2pvAtEfwUj6=7G+qe8JkNXm23SJ8PYF4zncfkBsHxOtNpPA@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

Hi Bruce,

I was able to reslice the thalamus mask correctly, but when I measure the volume of the resliced thalamus, is not the same as the original thalamus. I was wondering why that is happening and which volume is more accurate. I appreciate any suggestions. I have attached both masks. Also can you tell me how to measure the volume of the resliced thalamus in Freesurfer?

Thank you

Dorsa