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/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>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/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>> 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>>> wrote: > > > > > > ps: i believe my error is the same as the one in this thread: > > > > > > > > > > > > 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>>> > 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:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > 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 . 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:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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 > > -- > 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 > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 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 . 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.
