Hi Julia, I've taken a look at the data you sent us last week and it looks like the issue is stemming from the topology fixer. If you look through the input scan you've given us, you can see that the contrast between wm/gm is especially low in certain regions. This low contrast to noise ratio is making it hard for recon-all to produce a good wm segmentation which in turn gives the topology fixer trouble "cleaning up" the surfaces. This is causing your memory allocation error.
You may be able to improve the segmentation by including an expert.opts file with mri_segment adjustments (-wlo flag). Check out our resources on expert.opts files and the mri_segment option bellow: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segment I hope this helps. Best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Julia Ströhlein <stroehl...@sportmed.uni-paderborn.de> Sent: Tuesday, February 26, 2019 1:54 AM To: 'Freesurfer support list' Subject: Re: [Freesurfer] MRISalloc error during automatic reconstruction External Email - Use Caution Hi Bruce, did you receive the link I sent you last week? Best Julia -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 19. Februar 2019 16:37 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] MRISalloc error during automatic reconstruction Hi Julia did you upload the entire subject dir (gzipped and tarred)? And what happened with ftp? We can help you get that working. I would think the whole subject dir would be too big for the filedrop, but feel free to send me the link cheers Bruce On Tue, 19 Feb 2019, Julia Ströhlein wrote: > External Email - Use Caution > > Hi Bruce, > > I created a link with the Martinos File Drop System, because ftp > upload did not work. > It's probably the best idea to send the links to your personal mail address? > > Best > Julia > > -----Ursprüngliche Nachricht----- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce > Fischl > Gesendet: Montag, 18. Februar 2019 15:52 > An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Betreff: Re: [Freesurfer] MRISalloc error during automatic > reconstruction > > Hi Julia > > why don't you tar and gzip the subject directory and put it on our ftp > site so we can take a look > > cheers > Bruce > On Mon, 18 Feb 2019, Julia Ströhlein wrote: > >> External Email - Use Caution >> >> Hi Bruce, >> thanks for the advice. I ran the subject again with 4.5G, but it >> ended with the same error. It only happens with this subject, the >> stream worked fine for all the other subjects. >> However, I tried running the subject with my Macbook, and it also >> ended with an error (see the recon-all.log attached). I think it has >> something to do with the MRI of the subject. Do you have any ideas? >> Thanks for any help. >> Best, >> Julia >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce >> Fischl >> Gesendet: Mittwoch, 13. Februar 2019 15:58 >> An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Betreff: Re: [Freesurfer] MRISalloc error during automatic >> reconstruction >> >> Hi Julia >> >> I think you only have about 1.5G free memory at the beinning of >> running recon-all, which is not enough for this subject. It looks >> like some other process is using another 2G, which might be enough if >> you can free it up. In general though you probably want a machine >> with more ram >> >> cheers >> Bruce >> >> >> On Wed, 13 Feb >> 2019, Julia Ströhlein wrote: >> >>> External Email - Use Caution >>> >>> Hi, >>> of course. >>> >>> Julia >>> >>> -----Ursprüngliche Nachricht----- >>> Von: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce >>> Fischl >>> Gesendet: Dienstag, 12. Februar 2019 16:12 >>> An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>> Betreff: Re: [Freesurfer] MRISalloc error during automatic >>> reconstruction >>> >>> Hi Julia >>> >>> can you send us the recon-all.log file? >>> >>> cheers >>> Bruce >>> On Tue, 12 Feb 2019, >>> Julia Ströhlein wrote: >>> >>>> >>>> External Email - Use Caution >>>> >>>> Dear experts, >>>> >>>> while running one of my subjects, I got this error: >>>> >>>> >>>> >>>> MRISalloc(732595, 480): could not allocate vertices >>>> >>>> Cannot allocate memory >>>> >>>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 >>>> >>>> 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux >>>> >>>> >>>> >>>> recon-all -s P_04 exited with ERRORS at Mon Feb 4 16:40:03 EST >>>> 2019 >>>> >>>> >>>> >>>> Do you know what went wrong and how I can fix this? >>>> >>>> Best regards, >>>> >>>> Julia >>>> >>>> >>>> >>>> >>>> >>>> Unbenannt >>>> >>>> >>>> >>>> >>>> >>> >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
