I think it has to go through the whole recon as it uses wmparc.mgz and that is one of the last things created
On 1/5/2023 4:16 AM, Verónica E wrote:
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Dear all,
I am planning to run the thalamic segmentation (as implemented on FreeSurfer 7.1). The data has been already preprocessed with FreeSurfer 5.3, but I want to rerun the recon step on the newer FreeSurfer version. My question is, which recon output images does the thalamic segmentation use as input? It would make a considerable difference for us if we could only rerun up to e.g. the normalization instead of the whole recon (e.g. to get the aseg.mgz file) in FreeSurfer 7.
Sincerely, Verónica
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