External Email - Use Caution Hi Joanna,
if I remember correctly, you won't see any screen output until the process is finished using parallel. So, I suppose it doesn't freeze. Have you kept the process running for some time? Also you state that you want to use only 2 jobs at a time. However, in the command line you specify 3 jobs. Best, Falk ............................................... [http://secure-web.cisco.com/1Xg2HcdvF9dRzTa2ZFIhf3Kl-wpULX1tKJmpGmfMvcbKrMbdfqPxQLXGI3SEiMfs71F3UZU3EuqqMhA0oIo1WB9bky3inuOGAkia2rEVe1p9i8J5iaE9ltDdQ-pprMR55f-eqheOd1qYmeIH4Y6sWyuCBV5i24RVsog0Hm3hG-vf2J7pDXBLccGZM4cuTrozS-tcHZ_c4BCAuZgyBbV3syYOHXmB7l_9zfYrJ7x_fTouneytuqEbDPfONopAUwdnP14DDVwmfLtRO0zqoMpAwidr6MNYJbSqEtmVirfuScODi4lOLs4uomfZ-rqFGGZVSje4b6IoNcJRGi7xJVp2dGQ/http%3A%2F%2Fwww.med.ovgu.de%2Funimagdeburg_mm%2Fummd_focus.gif] Universitätsklinik für Neurologie Otto-von-Guericke-Universität Magdeburg Medizinische Fakultät Leipziger Str. 44 39120 Magdeburg Telefon: +49-391-6117-512 falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> http://secure-web.cisco.com/1grYGf0PQcjazx2N4roUOAW2_0PA5oVwsmBNBZj2LsRbmuKhR_gF1PcYo82U8iwTR0GDrLED138iZ4apaZW1qeDjy_QtGRMFjoEfmANz8DJezCZQEKjWI9aGyfV0NhfKCmbVcbxDfED9hdqGPoz2KeZTlQ2YAt-lDH_X5eiygyP9QWFseyPC_jN3n6sxsCUEwo8l6FsodP3kyQ7j_0vLsh5WcjmRDo8fvExX-edNK02sJiq5KCcESvhODnhUXXXgWo0W3Cn8kwS8RF82aIMLVPV7W39jx6eeBjf7xiMGuqCMwn1rdlzLo1nyx5ND48pU9l_dq-Slh413P6QGx0hA39Q/http%3A%2F%2Fwww.kneu.ovgu.de%2Fkneu.html ________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Joanna L Eckhardt <jeckha...@health.ucsd.edu> Gesendet: Montag, 9. Mai 2022 23:27:02 An: freesurfer@nmr.mgh.harvard.edu Betreff: [Freesurfer] Recon-all Freezes on Parallel External Email - Use Caution Dear FreeSurfer Team, I have been trying to use the parallel command (following FreeSurfer tutorial) to run multiple subjects (Windows os running Ubuntu VM). I only have 2 cores, so I have it set to 2 jobs instead of 8 as in the tutorial. When I use the code from the tutorial, there is an error with the .nii, and I assume it is because my files are .nii.gz. developer@developer-VirtualBox:~/FreeSurfer/Cannabis_Reduced$ ls *.nii | parallel --jobs 3 recon-all -s {.} -i {} -all -qcache ls: cannot access '*.nii': No such file or directory So I changed the code to .gz with everything else the same, and FreeSurfer does nothing (it stalls/freezes). Is this just because my computer cannot handle the job? Is there anything else I can do to run parallel? If not, I can always just run 1 subject at a time, but I want to check and see if there is another way to get this to work. Thank you for your time! Joanna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
