glad to hear it Bruce On Fri, 31 Jan 2020, Laurel Quinlan wrote:
External Email - Use Caution Hi Bruce, Thank you for your help! I removed the IsRunning.lh+rh script as well and reran the recon. Everything seems to have worked! -Laurel ____________________________________________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Tuesday, January 28, 2020 3:37 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Cc: Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities Hi Laurel if a subject dir already exists recon-all will exit unless you specify -force. Alternatively you can try using the -make all flag, which should rerun only the steps that are needed (assuming the reboot didn't happen e.g. in the middle of writing a file) cheers Bruce On Tue, 28 Jan 2020, Laurel Quinlan wrote: > > External Email - Use Caution > > Hi Doug, > > Thanks for looking over that file. It is the correct recon-all file for one > of the problem brains. I discovered that there was a system reboot of some > sort when the recon-all was processing for these problem brains, so that is > likely what caused the process to stop. How can I restart the recon-all > process for these brains? I have tried just rerunning the recon-all command > but the process exits within a few moments each time. I am wondering if > there is something I need to delete that was partially processed during the > first attempt. > > Thanks, > > Laurel > >___________________________________________________________________________ _ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <dgr...@mgh.harvard.edu> > Sent: Friday, January 24, 2020 9:34 AM > To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all errors - mri_segstats and > mri_relabel_hypointensities > It did not look like there was an explicit error in that log file, it just > stops at mris_volmask. Is that the right recon-all? Also, please just send > the text file so that we don't have to unzip it. > > On 1/22/2020 4:39 PM, Laurel Quinlan wrote: > > External Email - Use Caution > > Hi FS Support, > > I have two brains for which recon-all exited with errors after I > edited the wm.mgz volume. It seems that the problem occurs during the > mri_segstats and mri_relabel_hypointensities steps (if I'm reading the > output of the command "tail scripts/recon-all.log" correctly). I > attached one of the recon-all.log files as a zipped txt file. Please > let me know if you have troubleshooting suggestions. > > Thank you for your help! > > Laurel Quinlan > Research Specialist > Center for Healthy Minds > University of Wisconsin-Madison > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >
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