Hi Jason,
the default recon-all won't work for a monkey brain since it uses lots of information about what a human brain looks like. There is some documentation around as to how to run it on monkey brains - check the wiki. It requires more manual interventions.
cheers Bruce
On Thu, 27 May 2010, Jason Connolly wrote:
Dear Freesurfer experts,
We are attempting to segment a template monkey brain.
The following is the command line input:
recon-all -i /usr/local/freesurfer/subjects/template_2/mri/orig/MonkTempl_w81096_T1.nii.gz -s template -all -notal-check -force -noaseg
It runs for a few hours and then we get the following error:
"cannot find seed region for corpus collosum"
Do we have to manually mark this somehow in tkmedit?
Any advice would be appreciated!
Thank you,
Jason.
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