External Email - Use Caution
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 ________________________________ 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
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Today's Topics:
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)
----------------------------------------------------------------------
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"
External Email - Use Caution
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
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:
External Email - Use Caution
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
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
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
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)
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"
External Email - Use Caution
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
freesurfer@nmr.mgh.harvard.edu