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