External Email - Use Caution Hi Bruce,
No error message, just runs forever and eventually breaks my SSH connection to the cloud I'm running it on. But when I do "-make all" afterwards it starts a few steps before mris_spheres, so I have to redo and often crashes again. Thank you for your help! Best, Michael -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Tuesday, September 17, 2019 10:16 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_sphere question Hi Michael I think that is the last message that mris_sphere prints so I believe it has finished. Does it exit with an error message or just keep running forever? Bruce On Tue, 17 Sep 2019, Lauricella, Michael wrote: > > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
