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 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 <[email protected]> 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 >> [email protected] <mailto:[email protected]> >> 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 > [email protected] <mailto:[email protected]> > 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 > [email protected] <mailto:[email protected]> > 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. 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