[Freesurfer] recon-all-clinical synthseg error

External Email - Use Caution Hi! I'm trying to run recon-all-clinical but I'm running into an error with the SynthSeg at the very beginning. Do you have any hints what the problem might be here? Here's the full error message: the following problem occured with image [mypath]/mri/

Re: [Freesurfer] recon-all-clinical synthseg error

Freesurfer version you are > running. From your path /usr/local/freesurfer it looks like you are > running a Freesurfer release, e.g.., 7.4.1. > > - R. > > On Feb 25, 2024, at 21:45, Agata Wolna wrote: > > External Email - Use Caution > > Hi! > > I

Re: [Freesurfer] recon-all-clinical synthseg error

ning the script in a singularity containers). Best wishes, Agata pon., 26 lut 2024 o 11:02 Agata Wolna napisał(a): > Hi! > > Thanks for getting back to me. I'm running it on CentOS Linux 7 in a > singularity container. What I did is to pull the freesurfer container from > the Do

[Freesurfer] editing segmentations from recon-all-clinical

External Email - Use Caution Hi! I have a question regarding the recon-all-clinical pipeline: is it possible to edit the outputs of the synthseg segmentation run as a part of the pipeline (synthseg.mgz) similarly to editing recons from the standard freesurfer pipeline, and getting