Dear all,
Is there any commands in Freesurfer, which segment only the subcortical structures for me? The -autorecon2 calculates also the surfaces which seems unnecessary. However, I don't know whether the final surfaces have an effectt on subcortical volumes. There was a question about it on the Freesurfer's mailing list, but no answer ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031576.html). Which is the most time-efficient way to get subcortical segmentation with Freesurfer?
Thanks, Gabor
Hi Gabor
run recon-all through to the mri_ca_label step. We do have some code for correcting the aseg with surface (which are typically more accurate), but I don't think we run it by default (Nick or Doug can correct me if I'm wrong)
cheers Bruce On Sat, 18 Jan 2014, Gabor Perlaki wrote:
Dear all,
Is there any commands in Freesurfer, which segment only the subcortical structures for me? The -autorecon2 calculates also the surfaces which seems unnecessary. However, I don't know whether the final surfaces have an effectt on subcortical volumes. There was a question about it on the Freesurfer's mailing list, but no answer(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031576.ht ml). Which is the most time-efficient way to get subcortical segmentation with Freesurfer?
Thanks, Gabor
Unfortunately, you have to label the whole brain. The labelling of subcortical structures can be affected by cortical when they are right next to each other.
doug
On 01/18/2014 08:06 AM, Gabor Perlaki wrote:
Dear all,
Is there any commands in Freesurfer, which segment only the subcortical structures for me? The -autorecon2 calculates also the surfaces which seems unnecessary. However, I don't know whether the final surfaces have an effectt on subcortical volumes. There was a question about it on the Freesurfer's mailing list, but no answer (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031576.html). Which is the most time-efficient way to get subcortical segmentation with Freesurfer?
Thanks, Gabor
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Gabor Perlaki