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
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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
hmmm, if you rerun does it complete? On Tue, 17 Sep 2019, Lauricella, Michael wrote:
External Email - Use CautionHi 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 CautionHi 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Lauricella, Michael