Hi Daniel

Well, I have done much flattening recently (like for many years) but the two things to try are:

1. Making sure there isn’t still a single edge left that you need to cut that prevents the unfolding.
2. Try  including longer range distances, and possibly more of them.

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Glen, Daniel (NIH/NIMH) [E]
Sent: Sunday, April 27, 2025 4:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_flatten limitations

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Hi Bruce,

Thanks for that reminder about the flat maps as patches. I typically use the flat maps after conversion to gifti, so they are then their own full surfaces. With the center away from (0,0,0), the patch does indeed show up, but it's out of the usual view, so I have to zoom out to see it. I've recentered the surface to be around 0,0,0 to make this a little easier.  It might be helping with the flattening too because I'm getting close to a good result. Sometimes the randomness of the flattening process fails, but a retry can work, occasionally requiring a few tries. The terminal output includes the random seed used, so I can use that if I were to rerun the mris_flatten.

I still have an important issue in that there is an artifact of either one or two round swirls of misplaced nodes. These can be inside the contiguous flat map or even outside the flattened map as a separate circle, away from the rest of the flat surface. For the interior swirls, it's easier to visualize that with some annotation mapped from the original surface to the flat map. I did that visualization with suma because I know that better, but I can see the same swirls in the surface mesh using freeview. These are the steps I've taken so far. Do you have any recommendations?

Thanks,

Daniel

mkdir surf

# put initial data in the directory

cp somedir/isosurf.gii surf/

cd surf

mris_convert isosurf.gii lh.smoothwm.3d

mv  lh.smoothwm.3d lh.smoothwm

# make cuts on surface in GUI

freeview

# load surface. make series of cuts using GUI (mark points, Scissors - open path)

# save as patch lh.mycut.flat.3d

# flatten cut data

# increasing the distances to 10 10 and dilation to 8 moves the swirl outside

mris_flatten -distances 5 5 -dilate 4 lh.mycut.3d lh.mycut.flat.3d

# convert flat map to gifti surface

mris_convert -p lh.mycut.flat.3d lh.smoothwm.flat.gii

# make spec file for suma

quickspec -spec my_surfaces.spec -tsnad gii surfacename lh.smoothwm.gii Y SAME \

    -tsnad gii flat lh.smoothwm.flat.gii N lh.smoothwm.gii