I'm not familiar with the logic. The program is calling Remesher::removeCollapsedTrias() from remesher.cpp in loops. The program will get out of loop when Remesher::removeCollapsedTrias() returns -1.

I can take a closer look if I have access to the data.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Iglesias Gonzalez, Juan E. Sent: Monday, February 12, 2024 3:46 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Bocchetta, Martina m.bocchetta@ucl.ac.uk Subject: [Freesurfer] Problem with mris_remiesh in recon-all

Dear experts, My collaborator Martina Bocchetta is encountering a weird problem with recon-all, specifically with mris_remesh after the topology correction (see below). Any insight? Thanks in advance, /Eugenio

mris_remesh --remesh --iters 3 --input /path/to/subject/surf/rh.orig.premesh --output /path/to/subjects/surf/rh.orig

iters = 3 standard remeshing without target adjusted l: 0.707317 remeshing to edge length 0.707317 with 3 iterations Remesher::removeCollapsedTrias( 132651 , 132650 ) v_to_t[vidx] : [265322, 265325, ] Trias are identical : ... removing ... Remesher::removeTria( 265325 ) e_to_t[ 661301 ] before: [265322, 265325, ] e_to_t[ 661301 ] after: [265322, ] e_to_t[ 134659 ] before: [265325, 265322, ] e_to_t[ 134659 ] after: [265322, ] e_to_t[ 661307 ] before: [265325, 265322, ] e_to_t[ 661307 ] after: [265322, ] Remesher::removeTria( 265322 ) e_to_t[ 661301 ] before: [265322, ] e_to_t[ 661301 ] after: e_to_t[ 661307 ] before: [265322, ] e_to_t[ 661307 ] after: e_to_t[ 134659 ] before: [265322, ] e_to_t[ 134659 ] after: NEXTIDX : 132658 Remesher::removeCollapsedTrias( 132658 , 132650 ) v_to_t[vidx] : Trias are identical : ... removing ... Remesher::removeTria( 265325 ) Remesher::removeTria( 265322 ) NEXTIDX : 132651

... and you fall in an infinite loop with messages like these printed over and over.

-- Juan Eugenio Iglesias http://www.jeiglesias.com