Oh, I see it would prevent us from getting the aseg.stats file. That's not good; we want the whole enchilada :-)
Never mind; will follow your previous suggestion and run recon-all all the way through; Thanks Doug; Mehul On Tue, Jun 4, 2013 at 11:41 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > It would stop the error but still prevent you from getting the stats file. > If you don't need the stats file, you can add -nosegstats to the cmd line > as the last option. > doug > > > > On 06/04/2013 02:32 PM, Mehul Sampat wrote: > >> Hi Doug, >> >> Thanks; Will do so. >> >> Also I forgot to mention one thing in the previous email: >> >> for case -autorecon3, also there is: >> set DoSegStats = 1; (in recon-all script in 5.3 this is line 5526) >> >> would it help, if "set DoSegStats = 1" was used only in >> -autorecon3 and not in the >> -autorecon2 or -autorecon2-cp ? or would this break other stuff. >> >> Mehul >> >> >> >> >> >> On Tue, Jun 4, 2013 at 11:24 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> this is a bug in mri_segstats. For now, you will need to run >> recon-all to the end to generate the ribbon.mgz file >> doug >> >> On 06/04/2013 02:12 PM, Mehul Sampat wrote: >> >> Hi Doug, >> Yes, we see the same error as in msg28047.html; here is the >> line from my recon-all.log: >> >> mghRead(/mnt/horizon/stage/**HLC/9999/004_151_3106223 >> <tel:3106223>/WBS/Baseline/**Freesurfer/mri/ribbon.mgz, -1): >> >> could not open file >> >> In msg28047.html, Milkos suggested that the issue could be the >> following line in recon-all >> " set DoSegStats = 1" >> >> (in recon-all script in 5.2 this is line 5225; under the case >> "-autorecon2" ) >> (in recon-all script in 5.3 this is line 5401; under the case >> "-autorecon2" ) >> >> I think he is right; first i was confused why this issue was >> not seen with -autrecon2-cp >> >> because there is " set DoSegStats = 1" for >> -autrecon2-cp too; >> (in recon-all script in 5.3 this is line 5480; under the case >> "-autorecon2-cp") >> >> But normally we run -autorecon3 or -all before running >> -autorecon2-cp; so in this case >> the ribbon exists and the error does not show up with >> -autorecon2-cp (if -all or -autorecon3 is run before). >> >> Mehul >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Tue, Jun 4, 2013 at 10:49 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>>> >> wrote: >> >> The error in msg28047.html is that there was no >> ribbon.mgz. Is >> that the >> error you are receiving? >> <http://www.mail-archive.com/** >> freesur...@nmr.mgh.harvard.**edu/msg28047.html<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html> >> > >> On 06/04/2013 01:45 PM, Mehul Sampat wrote: >> > Hi Zeke, >> > Thanks for looking into this; had a quick followup item >> to report. >> > So for the same subject "recon-all -all" runs through >> smoothly; >> > (it was only recon-all -autorecon1 -autorecon2 that >> generated >> the error) >> > >> > I had not seen the error before since in the past, my >> workflow >> was as >> > follows: >> > >> > 1. run recon-all with -all >> > 2. add control points if required >> > 3. run recon-all with -autorecon2-cp and autorecon3 >> > >> > This ran through without any errors; >> > >> > Now to save some processing time, the modified workflow is: >> > 1. run recon-all with -autorecon1 -autorecon2 >> > 2. add control points if required >> > 3. run recon-all with -autorecon2-cp and autorecon3 >> > (It was step 1 in this modified workflow that generated >> the issue) >> > >> > Mehul >> > ps: the recon-all.log file from the error reported >> earlier is >> attached >> > for reference (i sent it to you but forgot to send it to >> the mailing >> > list earlier) >> > >> > >> > >> > >> > On Thu, May 30, 2013 at 8:31 AM, Z K >> <zkauf...@nmr.mgh.harvard.edu >> <mailto:zkauf...@nmr.mgh.**harvard.edu<zkauf...@nmr.mgh.harvard.edu> >> > >> <mailto:zkauf...@nmr.mgh.**harvard.edu<zkauf...@nmr.mgh.harvard.edu> >> <mailto:zkauf...@nmr.mgh.**harvard.edu<zkauf...@nmr.mgh.harvard.edu> >> >> >> > >> <mailto:zkauf...@nmr.mgh.**harvard.edu<zkauf...@nmr.mgh.harvard.edu> >> <mailto:zkauf...@nmr.mgh.**harvard.edu<zkauf...@nmr.mgh.harvard.edu> >> > >> >> >> <mailto:zkauf...@nmr.mgh.**harvard.edu<zkauf...@nmr.mgh.harvard.edu> >> >> <mailto:zkauf...@nmr.mgh.**harvard.edu<zkauf...@nmr.mgh.harvard.edu>>>>> >> wrote: >> > >> > Could you provide the recon-all.log file? >> > >> > -Zeke >> > >> > On 05/30/2013 10:24 AM, Gennan Chen wrote: >> > > Does 5.3 assume recon-all -all will always run >> first? Since >> > ribbon.mgz >> > > will not get created till autorecon3. In V4, that >> is part of >> > autorecon2 >> > > though. >> > > >> > > Gen >> > > >> > > >> > > On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat >> > <mpsam...@gmail.com <mailto:mpsam...@gmail.com> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com>> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com>>> >> > > <mailto:mpsam...@gmail.com >> <mailto:mpsam...@gmail.com> <mailto:mpsam...@gmail.com >> <mailto:mpsam...@gmail.com>> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com>>>>**> >> wrote: >> > > >> > > ps: i believe my error is the same as the one >> in this >> thread: >> > > >> > > >> > > >> > >> http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.** >> edu/msg28047.html<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html> >> > > >> > > >> > > Mehul >> > > >> > > >> > > On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat >> > <mpsam...@gmail.com <mailto:mpsam...@gmail.com> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com>> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com>>> >> > > <mailto:mpsam...@gmail.com >> <mailto:mpsam...@gmail.com> <mailto:mpsam...@gmail.com >> <mailto:mpsam...@gmail.com>> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com> >> <mailto:mpsam...@gmail.com <mailto:mpsam...@gmail.com>>>>**> >> wrote: >> > > >> > > Hi Folks, >> > > I am running recon-all with -autorecon1 >> > > -autorecon2, -nomotioncor -notal-check >> -nonuintensitycor >> > > (this is with fs version 5.3) >> > > it almost runs through but toward the end, >> when >> > mri_segstats is >> > > called I get the error message: >> > > .../mri/ribbon.mgz, -1): could not open file >> > > any ideas why this could be occurring ? >> > > Thanks >> > > Mehul >> > > >> > > >> > > >> > > ______________________________**_________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >>> >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >>>> >> > > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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 Partners >> > Compliance >> > > HelpLine at >> > > >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> 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. >> > > >> > > >> > > >> > > >> > > ______________________________**_________________ >> > > Freesurfer mailing list >> > > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >>> >> > > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >>> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > >> > >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> >> <tel:617-726-7422>> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
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