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PETsurfer wasn't released until the v6.0.0 stable build. You can see it in the release notes here: https://secure-web.cisco.com/1n9uot8CDL1X4zb4xQXVdkvdqbv2ngmmjy0xI-YpaJo1tCf...
I'd suggest downloading the newest release which will have the most updated code.
You should be able to run PETsurfer from FS builds v6.0, v7.1, v7.2+ (gtmseg, mri_gtmpvc, etc.) on v5.3.0 reconstructions. (Note: it's often recommended for reproducibility sake to use the same version of FS if you can spare the compute time).
On Wed, Nov 3, 2021 at 8:07 AM Brusaferri, Ludovica < LBRUSAFERRI@mgh.harvard.edu> wrote:
Hi!
Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal commands such as tkregister it works , but if I try PETsurfer commands I have errors such as "mri_gtmpvc: Command not found”. Any idea?
Thank you, Ludovica
On Nov 3, 2021, at 10:05, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
There is nothing special you have to do. What version of FS do you have? You still have to source the FS environment. If you can run recon-all, you should be able to run PETsurfer
On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
Hi!
I have been using freesurfer regularly and I am now trying to implement a few commands from PETsurfer https://secure-web.cisco.com/1BqgJn5GtD8lBmMhFIdkypD8JUZh4G9z6XnAbXLEtWVfk5a.... It seems like I cannot use any of the commands listed in the wiki (such as gtmseg or mri_coreg), although they should be part of the freesurfer package (as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline to install the PETsurfer extension? If so, could you please guide me through? Thanks so much in advance!
Kindly, Ludovica
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