No no. That’s perfect

I forgot for a half second we had raccoons in there 😅. either way have fun with making non-standard surfaces!

Let me know if you run into any problems on the way! Happy to help get things set up or debugged at any stage!

Oooh sounds fun! Do reach out if you run into any trouble running anything! Happy to provide precon_all support and possibly just very interested in also seeing a raccoon brain!

Special shout out to those not on bluesky including Eugene Duff, Borja Ibañez, and where it all started with 🐷's at the Centro Nacional Investigaciones Cardiovascualres in Madrid. And finally if you made it this far I'll confess... no it doesn't work in 🐭... yet 10/10

Finally, this project couldn’t have been done without the support and help of my amazing collaborators including @tingsterx.bsky.social @neuroecologylab.bsky.social @magdalenaboch.bsky.social @josepemanzano.bsky.social @k4tj4.bsky.social @r3rt0.bsky.social. 9/10

For all the details check out our preprint www.biorxiv.org/content/10.1... , or better yet, run it yourself, the code is here: github.com/neurabenn/pr.... 8/10

Then use precon_all to automate the cortical surface reconstruction for you! Better yet, create a surface template for spatial normalization using your unique species data 7/10

All of this means that precon_all can give you a cortical surface in a semi-automated manner for a species you’ve never seen before. But what if you’ve seen one species a lot… too much perhaps? 6/10

What if it fails though (And let's be honest, it might sometimes)? Then you edit as if it were a human brain in Freesurfer and rerun the filling and tessellation steps. 5/10

What do you need to run precon_all? First you need a T1, or an image with T1 like contrast. Then you need to provide a user defined brain mask, two hemisphere masks, a “noncortical” mask which removes anything you don’t want included, and a “subcortical” mask which fills in the subcortex. 4/10

Its design models Freesurfer, including built in modularity for separated brain extraction, segmentation, and filling and tessellation. If you've run Freesurfer for your human data then the output and interface should hopefully be a seamless experience 3/10

Precon_all simplifies the creation of cortical surfaces for comparative neuroanatomy. But how? We created a unified processing pipeline from image to cortical surface combining FSL, Connectome Workbench, Advanced Normalization Tools (ANTS), and of course… Freesurfer! 2/10