External Email - Use Caution Hi Bruce,
Sometimes it completes. About 20% of the time I get this problem for anyone. I don't think it's specific to a certain subject. 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 10:53 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mris_sphere question hmmm, if you rerun does it complete? On Tue, 17 Sep 2019, Lauricella, Michael wrote: > 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://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer&d=DwIDaQ&c=iORugZls2LlYyCAZRB3XLg& > r=LfvXlA0kIui4WmLLCYdWlZdLsYFY_HKuPRMZoERJi_o&m=wDKDRoscofjbwXBayxe0Xl > 3ZJe_ADuGgm0djvLYBcNc&s=04816km8Ktp-KqrA37Scn_k4WuUW-xi0Ha0OnqlUrVw&e= > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
