Hi Emma, Thanks for your reply. I just tried running the recon-all process from the beginning using the -all flag and it seems to have fixed whatever the error was and the processing completed successfully. Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 25 Aug 2017, at 11:11 pm, Boyd, Emma <ebo...@mgh.harvard.edu> wrote: > > Hi Bronwyn, > > Doug is out of the office today. What is the command you ran after deleting > everything in the surf folder? Can you send us the recon-all.log? > > Best, > Emma > > > --------- > Emma Boyd > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bronwyn Overs > <b.ov...@neura.edu.au> > Sent: Thursday, August 24, 2017 9:14 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Recon-all error > > Hi Douglas, > > Do you have any thoughts about the new missing directory error I am getting > detailed below? > Kind regards, > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > neura.edu.au <http://neura.edu.au/> > <https://twitter.com/neuraustralia> > <https://www.facebook.com/NeuroscienceResearchAustralia> > <http://www.neura.edu.au/help-research/subscribe> >> On 17 Aug 2017, at 1:16 pm, Bronwyn Overs <b.ov...@neura.edu.au >> <mailto:b.ov...@neura.edu.au>> wrote: >> >> Hi Douglas, >> >> Thanks for your reply. I followed your suggestion and deleted everything in >> the surf folder for each subject. I am not getting the following error: >> >> Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg >> No such file or directory >> mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg >> No such file or directory >> Linux katana.neura.edu.au <http://katana.neura.edu.au/> >> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 >> x86_64 GNU/Linux >> >> recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C> >> >> Should I try running the recon-all -all for each subject? >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >>> On 17 Aug 2017, at 8:27 am, Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> That means that the surfaces are out of sync. the -make-all only works >>> in certain circumstances. You can delete everything in the surf folder >>> (it should all be recreated anyway with -autorecon2-cp) >>> >>> >>> On 08/15/2017 10:04 PM, Bronwyn Overs wrote: >>>> Dear mailing list, >>>> >>>> I am trying to batch a series of 30 MRI images using the following >>>> command: >>>> recon-all -autorecon2-cp -subjid ID001 -qcache >>>> >>>> But for each image the process exits with the following errors: >>>> --------------------------------------------------- >>>> #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -------------- >>>> ----------------------- >>>> mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg >>>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval >>>> ./tmp.mris_preproc.18138/ID_001.1.mgh --sval >>>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>>> >>>> --jac --sfmt curv --noreshape --no-cortex >>>> Source registration surface changed to sphere.reg >>>> Target registration surface changed to sphere.reg >>>> srcsubject = ID_001 >>>> srcval = >>>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>>> srctype = curv >>>> trgsubject = fsaverage >>>> trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh >>>> trgtype = >>>> srcsurfreg = sphere.reg >>>> trgsurfreg = sphere.reg >>>> srchemi = lh >>>> trghemi = lh >>>> frame = 0 >>>> fwhm-in = 0 >>>> fwhm-out = 0 >>>> label-src = (null) >>>> label-trg = (null) >>>> OKToRevFaceOrder = 1 >>>> Reading source surface reg >>>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg >>>> Loading source data >>>> Reading curvature file >>>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>>> ERROR: number of vertices in >>>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>>> >>>> does not match surface (109952,110385) >>>> ERROR: reading curvature file >>>> Linux katana.neura.edu.au <http://katana.neura.edu.au/> >>>> <http://katana.neura.edu.au <http://katana.neura.edu.au/>> >>>> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 >>>> x86_64 x86_64 GNU/Linux >>>> >>>> recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017 >>>> >>>> To report a problem, see >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> >>>> I came across an earlier post in relation to a similar error >>>> (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html >>>> >>>> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html>) >>>> where >>>> it was recommended that you run “recon-all -s subjid -make all” to >>>> rebuild all files where the dependency chain is wrong. I ran this for >>>> each of the subjects and then tried to rerun my original recon-all >>>> command again but got the same error. Do you have any alternate >>>> suggestions for fixing this problem? >>>> >>>> Kind regards, >>>> >>>> Bronwyn Overs >>>> Research Assistant >>>> >>>> Neuroscience Research Australia >>>> >>>> Neuroscience Research Australia >>>> Margarete Ainsworth Building >>>> Barker Street Randwick Sydney NSW 2031 Australia >>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>> >>>> neura.edu.au <http://neura.edu.au/> <http://neura.edu.au >>>> <http://neura.edu.au/>> >>>> >>>> Follow @neuraustralia on twitter >>>> <https://twitter.com/neuraustralia >>>> <https://twitter.com/neuraustralia>>Follow NeuRA on facebook >>>> <https://www.facebook.com/NeuroscienceResearchAustralia >>>> <https://www.facebook.com/NeuroscienceResearchAustralia>>Subscribe to >>>> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe >>>> <http://www.neura.edu.au/help-research/subscribe>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto: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> >>> 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/> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto: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: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 > 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.
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