Hi Tashrif
it is most likely not a bug in mris_fix_topology, but rather a defect that is too large to accurately correct. The topology correction complexity is quadratic in the side of the largest defects, so small ones are fast and big ones are super slow. In most cases the really big ones are caused by other things going wrong that the topology fixer wouldn't have corrected in any case (e.g. skull being attached to brain, hemispheres incorrectly connected, etc....). You should check the ?h.inflated.nofix and ?h.orig.nofix surfaces to see what is going on
cheers Bruce
On Sun, 10 May 2020, Billah, Tashrif wrote:
Hi there,
The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2` does not finish for some of our data:
#@# Fix Topology lh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w lh
#@# Fix Topology rh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w rh
Waiting for PID 57296 of (57296 57299) to complete... Waiting for PID 57299 of (57296 57299) to complete...
We kept them running for about 48 hours in multiple attempts, yet no luck. Moreover, mris_fix_topology is a binary file so I am unable to debug through.
Any suggestion on where to look at?
Best, Tashrif