Hi,
I am trying to extract the pial surface for one of my subjects using freesurfer. Unfortunately, the last couple times that I ran recon-all, it generated a surface that was overly smoothed. I suspect this is due to a poor contrast in my MRI images. I tried to edit them via matlab and run them again. First, I got a talairach transform error and when I re-ran it with the -notal-check flag, I got a global region empty error. I was wondering if there is a way to enhance the mri images in freesurfer to obtain better contrast for a more accurate pial surface. Please let me know what is the best way to tackle this problem.
I do not think it's the version of freesurfer, because the pial surface was created fine for some of the other subjects.
Thank you, YP
Send us the dataset and we will take a look Bruce
On Jun 29, 2011, at 12:34 PM, Yagna Pathak yp79@cornell.edu wrote:
Hi,
I am trying to extract the pial surface for one of my subjects using freesurfer. Unfortunately, the last couple times that I ran recon-all, it generated a surface that was overly smoothed. I suspect this is due to a poor contrast in my MRI images. I tried to edit them via matlab and run them again. First, I got a talairach transform error and when I re-ran it with the -notal-check flag, I got a global region empty error. I was wondering if there is a way to enhance the mri images in freesurfer to obtain better contrast for a more accurate pial surface. Please let me know what is the best way to tackle this problem.
I do not think it's the version of freesurfer, because the pial surface was created fine for some of the other subjects.
Thank you, YP _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Yagna Pathak