Hi Emma

what do you mean "will not convert into a .nii file"? What happens? And can you include the mri_info output again. We get a *lot* of emails and it is quite helpful if each one is self-contained

cheers Bruce

On Wed, 20 Feb 2019, Bunting, Emma wrote:

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Hi,

In response to: Surface to Volume conversion post,

Yes, the brains were registered in fsaverage space. The issue I am facing is my sig.mgh output from GLM will not convert into a .nii file using mri_convert.

I am trying to load them both as overlays not view them directly. The sig.mgh file loads fine, it is the .nii file that sees the problem.

Similarly, if I do GLM directly with a .nii output, I see the same issues.

You asked me to run mri_info on both the .mgh and .nii.gz files, which I gave in my previous email.

Please let me know how to proceed from here!

Best wishes,

Emma Bunting

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: 04 February 2019 17:00 To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 180, Issue 5   Send Freesurfer mailing list submissions to         freesurfer@nmr.mgh.harvard.edu

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1. gray matter volume of the entorhinal cortex       (Laboratorio de Neurociencia Funcional)    2. Re: problem using recon-all (Shachar Gal)    3. Re: problem using recon-all (Glasser, Matthew)    4. Re: Surface to Volume conversion (Bunting, Emma)    5. Re: gray matter volume of the entorhinal cortex (Bruce Fischl)    6. Re: Surface to Volume conversion (Bruce Fischl)    7. Re: gray matter volume of the entorhinal cortex       (Laboratorio de Neurociencia Funcional)    8. free surfer install issues (Jordan Fowler)    9. Re: free surfer install issues (Greve, Douglas N.,Ph.D.)   10. (no subject) (Jordan Fowler)

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Message: 1 Date: Mon, 4 Feb 2019 10:08:06 +0100 From: Laboratorio de Neurociencia Funcional neuroaginglnf@gmail.com Subject: [Freesurfer] gray matter volume of the entorhinal cortex To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID:         CABUYonO85t9vP8NBw9HtWuET2n4i-9s-Q_LevCxZ_rK3U4YAew@mail.gmail.com Content-Type: text/plain; charset="utf-8"

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Dear Freesurfers,

gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a slice-by-slice basis to correct pial surface misplacements and erroneous white matter segmentation, which volume measure of the EC would be more precise?

I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats were thresholded at a specific probability value (% of case overlapping). Which probability value was used? Is there a reference paper explaining how probabilistic maps of EC were built based on ex vivo MRI contrast?

Thank you in advance.

Best, Jose L. Cantero