oh, yes, I think that is probably your problem. The left/right topology fixing alone took more than 10 hours I think, so probably you got to 24 and they killed it. If they gave you 48 or even 30 it might have finished On Thu, 1 Jun 2017, Jasmin Alves wrote:
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 fischl@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 <fischl@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 <fischl@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=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7C
Sfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=XqQAHjgWJJzdMsidvqrtLaJXR4K7nrT1lSDT4_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 <fischl@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 jalves@usc.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e
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-- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves@usc.edu