External Email - Use Caution
Hello,
We've run into an issue with freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b (on Rocks release 7.0, kernel 3.10.0-957.12.2.el7.x86_64). It appears some runs are failing at the mris_sphere stage, but not producing any very informative errors, just repeated "singular matrix in quadratic form" at the end of mris_sphere as below. I was wondering if anyone had any suggestions for further troubleshooting please?
recon-all is being invoked in two stages, with a manual brain mask replacing /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz in between them. This is being managed by a python script, but I think the sequence being executed is the following:
$ recon-all -i /SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_desc-gradwarp.nii.gz -T2 /SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T2w_run-1_desc-gradwarp.nii.gz -autorecon1 -noskullstrip -noT2pial -cw256 -cubic -3T -openmp 4 -s sub-11233210_ses-followup -status /SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log -log /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log
$ mri_convert /SAN/medic/insight46/analysis/drc_brain/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_space-orig_desc-drc-brain-mask.nii.gz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz --cw256 --conform -rt nearest
$ mri_mask -T 1 /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/T1.mgz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz
$ recon-all -autorecon2, -autorecon3 -cw256 -cubic -T2pial -openmp 4 -s sub-11233210_ses-followup -status /SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log -log /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log
The first recon-all (autorecon1) completes okay, the autorecon2,3 stage fails on occasion (this works for most scans). Its last output looks like this (full copy attached):
@#@FSLOADPOST 2020:06:17:02:37:18 mris_curvature N 12 1.14 1.51 1.48 #-------------------------------------------- #@# Sphere lh Wed Jun 17 02:37:18 BST 2020 /state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/scripts
mris_sphere -rusage /state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
setting seed for random number genererator to 1234 7.1.0 7.1.0
== Number of threads available to mris_sphere for OpenMP = 4 == reading original vertex positions... scaling brain by 0.309... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=fry-6, 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
singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form @#@FSTIME 2020:06:17:02:37:18 mris_sphere N 6 e 256.90 S 2.38 U 723.85 P 282% M 2286104 F 0 R 931286 W 0 c 79152 w 33537 I 0 O 0 L 1.14 1.51 1.48 @#@FSLOADPOST 2020:06:17:02:41:35 mris_sphere N 6 2.62 2.15 1.75 Linux fry-611-142.local 3.10.0-1062.9.1.el7.x86_64 #1 SMP Fri Dec 6 15:49:49 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-11233210_ses-followup exited with ERRORS at Wed Jun 17 02:41:35 BST 2020
For more details, see the log file /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks for your time, Ian
Not sure what is going on there. Can you take a look at lh.inflated and lh.white.preaparc to make sure that they don't look crazy?
On 6/23/2020 11:17 AM, Malone, Ian wrote:
External Email - Use Caution
Hello,
We've run into an issue with freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b (on Rocks release 7.0, kernel 3.10.0-957.12.2.el7.x86_64). It appears some runs are failing at the mris_sphere stage, but not producing any very informative errors, just repeated "singular matrix in quadratic form" at the end of mris_sphere as below. I was wondering if anyone had any suggestions for further troubleshooting please?
recon-all is being invoked in two stages, with a manual brain mask replacing /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz in between them. This is being managed by a python script, but I think the sequence being executed is the following:
$ recon-all -i /SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_desc-gradwarp.nii.gz -T2 /SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T2w_run-1_desc-gradwarp.nii.gz -autorecon1 -noskullstrip -noT2pial -cw256 -cubic -3T -openmp 4 -s sub-11233210_ses-followup -status /SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log -log /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log
$ mri_convert /SAN/medic/insight46/analysis/drc_brain/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_space-orig_desc-drc-brain-mask.nii.gz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz --cw256 --conform -rt nearest
$ mri_mask -T 1 /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/T1.mgz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz /scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz
$ recon-all -autorecon2, -autorecon3 -cw256 -cubic -T2pial -openmp 4 -s sub-11233210_ses-followup -status /SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log -log /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log
The first recon-all (autorecon1) completes okay, the autorecon2,3 stage fails on occasion (this works for most scans). Its last output looks like this (full copy attached):
@#@FSLOADPOST 2020:06:17:02:37:18 mris_curvature N 12 1.14 1.51 1.48 #-------------------------------------------- #@# Sphere lh Wed Jun 17 02:37:18 BST 2020 /state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/scripts
mris_sphere -rusage /state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
setting seed for random number genererator to 1234 7.1.0 7.1.0
== Number of threads available to mris_sphere for OpenMP = 4 == reading original vertex positions... scaling brain by 0.309... projecting onto sphere... surface projected - minimizing metric distortion... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=fry-6, 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
singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form @#@FSTIME 2020:06:17:02:37:18 mris_sphere N 6 e 256.90 S 2.38 U 723.85 P 282% M 2286104 F 0 R 931286 W 0 c 79152 w 33537 I 0 O 0 L 1.14 1.51 1.48 @#@FSLOADPOST 2020:06:17:02:41:35 mris_sphere N 6 2.62 2.15 1.75 Linux fry-611-142.local 3.10.0-1062.9.1.el7.x86_64 #1 SMP Fri Dec 6 15:49:49 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-11233210_ses-followup exited with ERRORS at Wed Jun 17 02:41:35 BST 2020
For more details, see the log file /SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks for your time, Ian
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Douglas N. Greve -
Malone, Ian