we don't have a way to do this yet. If you want recon-all type stats,
you can run synthseg storing the output in subject/mri, then look at the
recon-all.log file to get the mri_segstats command that creates the
aseg.stats file, modify the command line to use the synthseg output and
change the .stats file name
On 10/4/2022 9:42 AM, Young, Jenna M wrote:
External Email - Use Caution
Hello all,
I'm trying to perform a comparison of the global and regional
phenotype statistics produced by `recon-all` with the outputs of
SynthSeg 2.0. Based on the wiki, it looks like I should be able to
pass the segmentation from SynthSeg to recon-all (somehow) and run it
through steps further down the pipeline.
My current best guess at a command to do this is:
recon-all -autorecon2-pial -autorecon3 -s SUBJECTID -i INPUT_IMAGE.nii.gz
At this point, I have 2 questions:
1. Is -autorecon2-pial the correct step to insert the SynthSeg
segmentations into the recon-all pipeline?
2. What is the correct way to pass an existing segmentation file to
recon-all, and how do you also pass it the original brain image?
Thanks in advance for your suggestions.
Jenna
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