Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed}
External Email - Use Caution Hello, We've experienced random crashes when using the -parallel flag with the official FS docker container at https://secure-web.cisco.com/1Db9ik7eIvMj7kgkeTafe0s_PlT0VyO4BIvoM6Chj4jvyesjHAuR-kZyjg4ueyTkvPI2tO3aWk76nJniaideisxRFreGgC6FYkFflnw3OJSb2vizDEGe9I7_5KxymQSiL_4xv8wD673W6RdSI1m9IsESb2d-XzAu607hYqEI8dlEnHdiHr5ZAJMdz0-aiK0PYe_TawyFsTVoTaka9SYiXIQ/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Ffreesurfer%2F. It looks like this issue: https://secure-web.cisco.com/1RTUH2ziWrAzuafGfyVCoxnmVd6xWSC1pjYKx0ENFxB4V7TrwK2DIeOzM_0SxoK0wCKIy4l_c2CnAyb_S4Jjk04MEmATnQrr7iSlt-SRGu38Kf53mx7_br6eN1MS_T55qftLf_tXHqrUIHOO6Yi1JDx5z3Bm4P6KAIQ5NwYf48lOKx7RV-Jh0d4yWKrTZLUVX9JSnwKDOkBN6WpqbBgd9Ew/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67588.html. Is there a fixed recon-all that I can use with that image (or maybe a new image coming soon)? Thanks, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1vnPdwWhDIRo0dgACPHUy8Cs0L0bRI0jZF0TyQMe6r95oCZi5ZZJrHwieBuwTyFHuXGfSk-EFFswgKI0y4TShj-ugXmlLhN4ZMce8CQGrkghGM_5NKI_GBnrhl7xI1ESkPP351SklVdFREt2FF3H-LGVYQ81FNvEo5KGxT45BBlfYIaW2kbjipETH3zboahRGW81CHHztSz-xDdpqsCRX2g/http%3A%2F%2Fwww.flywheel.io%2F> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Flywheel is Hiring
External Email - Use Caution Hello Freesurfer and Neuroinformatics Experts, At Flywheel <https://secure-web.cisco.com/11jOUe69pAmrkatJBPAWf3tKPRB9iRsFQ1T1VU_vkte1Jm4fQUF1s9okgZSFRDcI4VFR6ejEC4VbMcsgt84Vknlp_v3GZZDC9Giq3puPW2-ZKBIUVCnExiySzLILVZd3FnnTshEwQK3hJHGSekmPb6H_r4wM-kad7bshswSR42G9KN5W_hfoCRYTb9216Fg2wlVUOsty-1uDjx7iCiN-lAh9MF9bskYvmL0mqR6WGUzhAX4yIv7P0_2G-ybxSNVfv9nrZ04s6cQT0ZT6B6z2AMQ/https%3A%2F%2Fflywheel.io%2F>, we are developing a data sharing and distributed computing platform serving biomedical imaging and life sciences research. We are hiring <https://secure-web.cisco.com/1fl-xuQEhMmhR5ixf6wZmLmzBbB3uWIuQ-GPTt40NoYIdzPs8jFUQkm75dnacy9dtyV88oBv3vFfJEvrG2q4Pw7EDACJ7zlYob69DkD306vc5ZLbjNBwHs6ZxzNMTb1R1mb_k0FIdSCPz-vPvcWB1tpfoSUklbNPoqXOz5cjW0_5qLSQDKQ40yzKd00_VmLzz_AdjIDja-QzWMJnrydPwPZ88v_ycXPHnWznjDCtJoQcFw29ytGxmBh3gjFsErnmeMhl9zZK68kEVRx2c1kva1A/https%3A%2F%2Fjobs.lever.co%2Fflywheel-2%2F78bcf30b-504b-4ce4-9162-1cb22bfd28e8> to grow our Scientific Solutions Engineering team of PhDs and Engineers. Specifically, we are looking for coders with mad skills in reproducible scientific cloud computing (python, Docker), workflow / pipeline implementation (NiPype, CWL, Toil, Cromwell, Snakemake, Nextflow, Galaxy, SevenBridges, Arvados, COINSTAC, etc.), Machine Learning workflows (Kubeflow, Airflow, SKLearn, MLflow, etc.), and a research background in medical imaging or bioinformatics. Knowledge of the Brain Imaging Data Structure (BIDS) standard is a huge plus. Compensation is competitive, company is inclusive, and we are open to hire remotely (half of us are). If you are interested, please have a look at our job ad here <https://secure-web.cisco.com/1fl-xuQEhMmhR5ixf6wZmLmzBbB3uWIuQ-GPTt40NoYIdzPs8jFUQkm75dnacy9dtyV88oBv3vFfJEvrG2q4Pw7EDACJ7zlYob69DkD306vc5ZLbjNBwHs6ZxzNMTb1R1mb_k0FIdSCPz-vPvcWB1tpfoSUklbNPoqXOz5cjW0_5qLSQDKQ40yzKd00_VmLzz_AdjIDja-QzWMJnrydPwPZ88v_ycXPHnWznjDCtJoQcFw29ytGxmBh3gjFsErnmeMhl9zZK68kEVRx2c1kva1A/https%3A%2F%2Fjobs.lever.co%2Fflywheel-2%2F78bcf30b-504b-4ce4-9162-1cb22bfd28e8>. If you know someone who might be interested, please pass along the link. We really do cool things. Cheers, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1p9cujki7p3fAOSgSS0m9jUN6Ox0zw7VzFNuhwyeKuHQM59gJaCiJa0DILSZChIG5ymqnozwZqqUeWNwckntpP-Hmyrs3bUdE0pg632hJbTekOi0AF49ppg3f0ww3E8KX5vxw0bGlgvH_3HG0QpZE16b2N4aszFR1BXsjXEHDtrrsemGzDLtJgzjk90jdijDfjpuNrwonEXVSIDhrcmmOwuoUz-2Cio8_J130Om7W5lsBhAwQx7ARIM5gxON1Yxj1QvCb3sJ-eEf6N46CfTcrHA/http%3A%2F%2Fwww.flywheel.io%2F> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cannot find rh.white.H
External Email - Use Caution Hello, We're seeing this error a lot: "Cannot find rh.white.H" which is generated here <https://secure-web.cisco.com/1kFmpUflCYrLlkn0X825hErhILvuejPNzV2WrombAVtg_sM4GT1g_2GUF6a8ZpRLVYi6pkG1WL5R_6FXRwzi6naGRJeM7eDTmdEF-qJnBHyt5W5477N06HJUDcSZV4VKP4uEWN7jv5UaPYN359YbKBW5yzUfr9B0_s3qNTfysJplHplUIbwiqmCVwtIfKMz7yXNuZZXM4FoZcbX1-iJQn_WZ-OrPOy86L9-F_bHcRD-NMim4sO1ulpWfa_sOXqCEpXur17Xf6obk1monjfSBi3A/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Frecon-all%23L3610>. It does not occur if -parallel is turned off. I see that reconbatchjobs does "exec" on the commands sequentially in the order of the list, but it runs each in the background: exec $JOB >> $LOG 2>&1 & so I thought it might just be slightly possible that these two commands: set cmd1 = (rm -f $hemi.white.$suffix) set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) could end up in a race condition where the file is linked and then immediately removed if somehow the ln command is executed before the rm command. However, I tried reproducing this behavior with a test script but the rm always happens before the ln. Any help would be appreciated! Thanks, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1KxdUXSlflua-8jA7AL5CzR1vwNWqcPAt_z76LcUsPIdfrRmC2dUPKB5OQjPwfI_jJhAZe2cqlldgaNHGreNViKQUc8HWIh1UnI4eQW4PHcuCADZ_aF04n5OnjAwF_LEoRNv0nXMW3oxAUuH3CTQlGSfM9hl2zeEho-vAJ01wD1qhOrci0dfnp4FgfjX8QDdjl7x9By5VVtEj02Q5ED4l7TeC286ILTihn0s4abzLg_CLEKV4JUAvu6bDSQD7FMzVt_OR0Sr6Px4kg4nS-Be7NA/http%3A%2F%2Fwww.flywheel.io%2F> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cannot find rh.white.H
External Email - Use Caution Hi Bruce, From recon-all.log: mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 21.097*4pi (265.116) --> -20 handles ICI = 150.9, FI = 1460.6, variation=23079.795 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 252 vertices thresholded to be in k1 ~ [-0.15 0.35], k2 ~ [-0.07 0.04] total integrated curvature = 0.687*4pi (8.638) --> 0 handles ICI = 1.5, FI = 8.6, variation=149.492 128 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 132 vertices thresholded to be in [-0.09 0.18] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022 done. PIDs (2310 2313 2316 2319 2322 2325 2328 2331 2334 2337 2340 2343) completed and logs appended. /usr/local/freesurfer/subjects/sub-TOME3024/surf Cannot find rh.white.H So mris_curvature writes rh.white.preaparc.H and then the ln command creates the symbolic link, "rh.white.H". See this line of recon-all <https://secure-web.cisco.com/1dc5h6q_BNNnkKvP366xprYw_CVHClTguAez02XCpx-7Av8eKKhu_Hx3W6nh4Dwg9LrLwI8A0H1YvJh6s_b8Vr85hRIL3uPlCua-YdKaIkguyxEkT8qWmnZlj3xwr-TrcyrfjmJGccX4o-Fm0gLJh7zCxNoYV2Iffys-NM8I-s0nm3Ct0D1ZrHk0aM77GzI7eoJ1eN06yOKVcpLH_-dCus-zLQTHrysqPdyo1YE9r4b0HUBqALO1LDlE3BBQV_WPtsFlwdwUKOKxBgxji9okoKg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Frecon-all%23L3556>. It is hard to see how this works at all when using the -parallel flag since reconbatchjobs runs all these commands in parallel. The commands are all launched in sequence using "exec" (see here <https://secure-web.cisco.com/11sboSdXnmw-2AXpA7TQo4FAGJ0L-yc5Y3JHpAK8m7yfRV6fLk62ulE3lqarFR4VYeuf6ZVckptU3N4v49m8r0W3ayz6TPilh01hyBD-iuFzk_SS4GDqm7dcshbv5NDVuj0AVvaDAMWxsFYDjzrbAJ2kI76mHe1_ub7zDxm4nHgRS7UcAT7_EKB2KClKvmY0Fo2c_puV4QGyu81CbgALey8XrqLcTXOR8n6PCeWNJLREgTy6xpzGbEExURA9F8RmBiCTpPFIWlvPCmBGaBRnFFw/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Freconbatchjobs%23L67>), but since they are run in the background, the quicker jobs will finish first. I wrote a short test script to check that. I suppose it could work if mris_curvature creates the file when it starts up. Then the symbolic link could be created. Perhaps there is a race between creating rh.white.preaparc.H and when the ln -s rh.white.preaparc.K rh.white.K command. Or am I missing something here? Andy. On Tue, Jan 19, 2021 at 5:37 PM Fischl, Bruce wrote: > Hi Andy > > > > I think the rh.white.H is generated by mris_curvature. Does that help? > > > > Cheers, > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Andy Worth > *Sent:* Tuesday, January 19, 2021 5:29 PM > *To:* Freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Cannot find rh.white.H > > > > *External Email - Use Caution* > > Hello, > > > > We're seeing this error a lot: "Cannot find rh.white.H" which is generated > here > <https://secure-web.cisco.com/1kFmpUflCYrLlkn0X825hErhILvuejPNzV2WrombAVtg_sM4GT1g_2GUF6a8ZpRLVYi6pkG1WL5R_6FXRwzi6naGRJeM7eDTmdEF-qJnBHyt5W5477N06HJUDcSZV4VKP4uEWN7jv5UaPYN359YbKBW5yzUfr9B0_s3qNTfysJplHplUIbwiqmCVwtIfKMz7yXNuZZXM4FoZcbX1-iJQn_WZ-OrPOy86L9-F_bHcRD-NMim4sO1ulpWfa_sOXqCEpXur17Xf6obk1monjfSBi3A/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Frecon-all%23L3610> > . > > > > It does not occur if -parallel is turned off. > > > > I see that reconbatchjobs does "exec" on the commands sequentially in the > order of the list, but it runs each in the background: > > > > exec $JOB >> $LOG 2>&1 & > > > > so I thought it might just be slightly possible that these two commands: > > > > set cmd1 = (rm -f $hemi.white.$suffix) > > set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) > > > > could end up in a race condition where the file is linked and then > immediately removed if somehow the ln command is executed before the rm > command. > > &
[Freesurfer] Shiny new 7.2!
External Email - Use Caution Is it true that all that is needed for a new official FS docker container to come into existence is to merge pull request #866 <https://secure-web.cisco.com/10DeE1N6s0_SCCbPo6uqcazn6bfeF4GN2L9n26obY0mrz4ZlTVnDUKxVT1YzBMlwp0KbO4TSuOngCuBwCElKYrcOdrOy8Y20quEmFXEVF7wjt9QI3Xin2tr0GsILl4HzWGR05GCVz1dNQLlRdICroHw7JV2tmn1C8C0VcN8rTUdWl9bC17AGShSg40vkPtpYGMNUFOghFpzZez5GrsBvU6TVZlHZ_Jm2Lx6tAdEKXt5qjtLtJKnXVZe844-WIvJxNQPLYnEpYrxDsT3XB-vxeNQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fpull%2F866%2Ffiles>? That would be so very nice. We like the official release! 4.1K pulls of previous versions on dockerhub can't be wrong. Kind regards, Andy Worth Senior Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1q0M-qEiBJlwu49m9WEWx5rGqctEdeZiwaiHNtscHhu8sb16hqzebWbF1Sfj-EjfWCX7lDoW67QRFRfCgYgLehGKi56izNPbyIXYZZ4l-GSTrzV1azm8oHE5ugsK-J9UMGeWn9NcFwQBaBjyGp7fbnwp70uxJaAR2tI8BTcmvqHcZneqm1cqfU32D0FmY2MFPw44EFK49acGqQc1FzdNaEvH8TqwmLfcfLVYs7D_eeM1wFHUErx_ZWWNsWQxtZWnTgAAm11r8zDBNAmZJeSxNMQ/http%3A%2F%2Fwww.flywheel.io%2F> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
