temporal lobe errors in rh.white and lh.white surfaces but not in rh.orig and lh.orig surfaces
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Hi,
I am using recon-all to generate pial and white matter surfaces for MPRAGE data but am having trouble in the temporal lobes for all of my subjects. The pial surfaces look very good, but the white matter surfaces are poor. Notably, the wm.mgz volume and the lh.orig and rh.orig surfaces seem to correctly include all of the white matter in the temporal lobe. However, the rh.white and lh.white surfaces miss a substantial portion of the white matter. On the ReconAllDevTable I see that the ?.orig surfaces are generated before the ?.white surfaces. Can you suggest how I might be able to fix the ?.white surfaces?
In case it is relevant, I had to create an xopts.txt file with the following options in order to obtain correct skull-stripping and pial surfaces for this data: mri_normalize -mprage -b 2 -n 5 I am using freesurfer development version with a date of 05-03-2018.
I have attached an image of the ?.orig and the ?.white surfaces superimposed on the wm.mgz and brainmask.mgz volumes.
Thank you,
Neva
Hi Neva
if you upload a subject we will take a look.
cheers Bruce On Wed, 19 Dec 2018, Neva M Corrigan wrote:
External Email - Use Caution
Hi,
I am using recon-all to generate pial and white matter surfaces for MPRAGE data but am having trouble in the temporal lobes for all of my subjects. The pial surfaces look very good, but the white matter surfaces are poor. Notably, the wm.mgz volume and the lh.orig and rh.orig surfaces seem to correctly include all of the white matter in the temporal lobe. However, the rh.white and lh.white surfaces miss a substantial portion of the white matter. On the ReconAllDevTable I see that the ?.orig surfaces are generated before the ?.white surfaces. Can you suggest how I might be able to fix the ?.white surfaces?
In case it is relevant, I had to create an xopts.txt file with the following options in order to obtain correct skull-stripping and pial surfaces for this data: mri_normalize -mprage -b 2 -n 5
I am using freesurfer development version with a date of 05-03-2018.
I have attached an image of the ?.orig and the ?.white surfaces superimposed on the wm.mgz and brainmask.mgz volumes.
Thank you,
Neva
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Hi, I have uploaded a data set to the ftp server. Thank you, Neva
From: Neva M Corrigan nevao@uw.edu Date: Tuesday, December 18, 2018 at 5:49 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: temporal lobe errors in rh.white and lh.white surfaces but not in rh.orig and lh.orig surfaces
Hi,
I am using recon-all to generate pial and white matter surfaces for MPRAGE data but am having trouble in the temporal lobes for all of my subjects. The pial surfaces look very good, but the white matter surfaces are poor. Notably, the wm.mgz volume and the lh.orig and rh.orig surfaces seem to correctly include all of the white matter in the temporal lobe. However, the rh.white and lh.white surfaces miss a substantial portion of the white matter. On the ReconAllDevTable I see that the ?.orig surfaces are generated before the ?.white surfaces. Can you suggest how I might be able to fix the ?.white surfaces?
In case it is relevant, I had to create an xopts.txt file with the following options in order to obtain correct skull-stripping and pial surfaces for this data: mri_normalize -mprage -b 2 -n 5 I am using freesurfer development version with a date of 05-03-2018.
I have attached an image of the ?.orig and the ?.white surfaces superimposed on the wm.mgz and brainmask.mgz volumes.
Thank you,
Neva
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Neva M Corrigan