External Email - Use Caution
Hello FreeSurfer Developers,
I am attempting to run recon-all on a group of nifti T1’s (parameters
listed below). All the T1’s look good (no noticeable artifacts) and the
cortical parcellations work well, and log files say completed without
error. Howe
External Email - Use Caution
Dear Doug,
We are working on PET images and our tracer has a lot of non-specific binding
close to meninges. To do so we want to be able to mask out meninges and other
areas outside the brain. Following up on your suggestion as in
https://secure-web.
It is likely due to the slice thickness. recon-all was build with the
assumption that the data would be high res (~1mm). It becomes hard to
resolve cortex at lower resolutions, so, while recon-all-clinical will
finish and give you results, there is no way to get around the
resolution limits.
samseg does not have a CC seg. You can get the CC with something like
mri_cc -aseg samseg/seg.mgz -o samseg/seg+cc.mgz -lta samseg/cc_up.lta
you can ignore the lta output
On 1/28/2025 7:00 PM, Taghizadeh Mortezaei, Nima wrote:
Dear FreeSurfer Support Team,
I am using FreeSurfer version 7.4.1
