External Email - Use Caution
Dear Freesurfer Experts,
I'm fairly new to freesurfer, but have a set-up in which I have been able to run many successful recon-all runs. One problem that I have sometimes, maybe about 20% of the time, is that the run will freeze and crash at this step:
mris_sphere -rusage /mnt/freesurfer_subjs/SUBJECT_ID/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
here's the end of the logfile:
"== Number of threads available to mris_sphere for OpenMP = 2 == scaling brain by 0.287... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=mgt-i, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234
-------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %21.21 pass 1: epoch 2 of 3 starting distance error %20.95 unfolding complete - removing small folds... starting distance error %20.57 removing remaining folds... final distance error %20.59 MRISunfold() return, current seed 1234"
Does anyone have any ideas why this might be happening? Maybe this is a computationally intensive step? If I run a few recon-alls concurrently it almost always crashes at this step.
The command I run is: recon-all -all -openmp 2 -qcache -nuintensitycor-3T -s SUBJECT_ID -sd /mnt/freesurfer_subjs/
Thank you so much for your help!
Best, Michael