Hi Bruce, I waited 24 hours, and then the job, at that point it was killed by the computing center I use. They have a max analysis time of 24 hours. Perhaps the last steps are not being reached due to the large topological defects, however I never encountered this problem before with FS5.3, what do you recommend?
Thanks, Jasmin On Thu, Jun 1, 2017 at 3:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jasmin > > how long did you wait? Is the process still running? The last step in the > log is not a very long one. Maybe someone/something killed your job > prematurely? I see no reason in the log that it wouldn't have finished > > > Bruce > > > On Thu, 1 Jun 2017, Jasmin Alves wrote: > > Hi Bruce, >> So it does not matter that the recon-all.done script never appeared in the >> script folder? Or that the isrunning.lh+rh script is still in the folder? >> >> I plan to run the hippocampal subfield analysis on these folders, so I am >> wondering if the subfield analysis can still function without the >> recon-all.done script being in the folder. >> >> Thanks, >> Jasmin >> >> On Thu, Jun 1, 2017 at 11:15 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Jasmin >> >> actually things look pretty reasonble given the degree of motion >> corruption. Is it still running? I would expect it to finish ok. >> I doubt you can get realiable thickness estimates off this kind >> of data, but you should be able to do e.g. fMRI analysis. >> >> There were a bunch of big defects so the topology fixing took a >> lot longer than usual, but it did complete >> >> cheers >> Bruce >> >> >> On Thu, 1 Jun 2017, Jasmin Alves wrote: >> >> Hi Bruce, >> I uploaded two subjects directories to the FTP >> site. >> >> Thanks, >> Jasmin >> >> On Wed, May 31, 2017 at 3:24 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> you can put it on our ftp site: >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer. >> nmr.mgh.harvard >> >> .edu_fswiki_FtpFileExchange&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0N >> U5BOUHhpN0H8p7C >> >> Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR >> 4K7nrT1lSDT4_oo >> >> >> LOM&s=SWUWcgct6aIswjAqZt3RiFgjtOfIpqIKiryZ4Xu1aSM&e= >> but at that point you might as well tar and >> gzip the entire >> subject dir and upload it >> On Wed, 31 May 2017, Jasmin Alves wrote: >> >> Hi Bruce, >> Thanks for the reply, below is a couple >> of sentences >> from the recon-all.log >> >> reading initial pial vertex positions >> from >> white.preaparc... >> >> mean border=65.6, 300 (300) missing >> vertices, mean >> dist 2.2 [2.0 (%0.1)->3.2 >> (%99.9))] >> >> %21 local maxima, %44 large gradients >> and %29 min >> vals, 639 gradients >> ignored >> >> perforing initial smooth deformation to >> move away >> from white surface >> >> tol=1.0e-04, sigma=2.0, host=hpc17, >> nav=16, nbrs=2, >> l_surf_repulse=1.000, >> l_tspring=1.000, l_nspring=0.500, >> l_intensity=0.200, >> l_curv=1.000 >> >> mom=0.00, dt=0.05. >> >> >> I also attached a screenshot of the >> log. >> >> >> Is there a place I should upload the >> files? >> >> >> Thanks, >> >> Jasmin >> >> >> On Wed, May 31, 2017 at 12:28 PM, Bruce >> Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Jasmin >> >> typically that means there is a >> big >> topological defect, which >> definitely can be caused by >> motion. What is >> the last couple of >> lines of the recon-all.log file of >> one of the >> subjects? Can you >> upload an image we can look at? >> >> cheers >> Bruce >> >> >> On Wed, 31 May 2017, Jasmin Alves >> wrote: >> >> Hello, >> I have used FS6.0 to do >> recon-all on >> about 57 >> brains, but for some reason, >> recon-all is not working on >> some brains, >> recon-all >> is not able to get past >> "Automatic topology fixer", >> after the >> command has >> been running for 24 hours. >> >> Is it possible there is too >> much motion >> in the >> image? Or does FS6.0 >> possibly take longer to >> complete for >> some brains? >> >> Thanks, >> Jasmin >> >> -- >> Jasmin Alves >> Doctoral Candidate >> Medical Biology Graduate >> Program >> University of Southern >> California >> jal...@usc.edu >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm >> r.mgh.harvard.e >> >> >> du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv >> i0NU5BOUHhpN0H8 >> >> >> p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=WKDQAULkieLjxSoEKmbYe3 >> vl8MelA4BdRVo3y >> >> >> >> 7hhYtM&s=kd6PbBhNyCt1A17Nz3F8PBlHrz3uOwKoafDjYtq4xKQ&e= >> >> >> The information in this e-mail is >> intended only for >> the person to whom >> it is >> addressed. 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If >> the e-mail >> was sent to you in >> error >> but does not contain patient >> information, please >> contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> >> -- >> Jasmin Alves >> Doctoral Candidate >> Medical Biology Graduate Program >> University of Southern California >> jal...@usc.edu >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm >> r.mgh.harvard.e >> >> du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv >> i0NU5BOUHhpN0H8 >> >> p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLa >> JXR4K7nrT1lSDT4 >> >> _ooLOM&s=qabnnnfyc7W50hRGrdQ_49og8Z3BoC4WMLHMqOnyev4&e= >> >> >> 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 >> Partners Compliance >> HelpLine at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part >> ners.org_compli >> >> anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc >> _gI&r=LH_W279i0 >> >> KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_ooLOM& >> s=PcQnCYSjsxdh7 >> >> viM-cml1T0i_b6yo4TMAAzgs7Nt6uA&e= . If the e-mail was sent to >> you in >> error >> but does not contain patient information, please contact the >> sender >> and properly >> dispose of the e-mail. >> >> >> >> >> -- >> Jasmin Alves >> Doctoral Candidate >> Medical Biology Graduate Program >> University of Southern California >> jal...@usc.edu >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm >> r.mgh.harvard.e >> du_mailman_listinfo_freesurfer&d=DwIBAg&c=clK7kQUTWtAVEOVIgv >> i0NU5BOUHhpN0H8 >> p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W- >> Ibh0SCMa2DLmtX9mHsa >> 5KKP-s&s=hRwIqSvnivcn2Fq_clewi1C8D05Qw2smP28HsGHKtMk&e= >> >> >> 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 Partners Compliance >> HelpLine at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.part >> ners.org_compli >> anceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc >> _gI&r=LH_W279i0 >> KTyqa6rNRHLug&m=-ccc_7_kuh64gwu4W-Ibh0SCMa2DLmtX9mHsa5KKP-s& >> s=KRfTs08CU2sbL >> AvfTwDIKa8PfD-d0mzHuBoqZbLgtsU&e= . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> >> >> >> -- >> Jasmin Alves >> Doctoral Candidate >> Medical Biology Graduate Program >> University of Southern California >> jal...@usc.edu >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail. > nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c= > clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7_ > ZUjRDEh6wPdCaB71enVHBAjTp0Ls22m4shTklqMFM&s=om73zSBAd4AgvHfAtEX5Uw7Ynllfrx > Fe3tWrKskbnJQ&e= > > > 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 Partners Compliance > HelpLine at > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > partners.org_complianceline&d=DwIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN > 0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7_ZUjRDEh6wPdCaB71enVHBAjTp0Ls22 > m4shTklqMFM&s=43K8iWeiOMMDjdT7FFtr6P-c0TL8xs9ZfG885jPhj6k&e= . If the > e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jal...@usc.edu
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