Rysia, btw, there is a flag you can run in recon-all to check if the vertex numbers on all the files are the same:
recon-all -s subjid -vno_match_check it calls the script vno_match_check, which is a handy qa tool. Nick On Thu, 2008-12-11 at 15:18 +0000, Burmicz, Ryzarda wrote: > Hello, > > > > When running recon-all –qcache –s <subject> with a view to running > qdec analyses I get the following error message, which I think I > understand, however I am having trouble with the –make all option of > recon-all that is recommended in a previous thread: > > > > “Reading curvature file /PICKACARDB01/surf/lh.jacobian_white > > ERROR: number of vertices in /PICKACARDB01/surf/lh.jacobian_white does > not match surface (150934, 150818) > > ERROR: reading curvature file > > > > recon-all exited with ERRORS at Tue Dec 9 ...” > > > > This subject was originally run on 4.0.1 (Linux-centos4_x86_64 > version) > > And then corrected and rerun on 4.0.3 (Linux-centos4_x86_64 version) > > > > (I understand that this is not always a good thing to do rerunning on > a different version so don’t know if this has anything to do with > it..). I think I am correct in saying that they problem might be due > to rerunning portions of recon-all (in this case we reran from – > autorecon2-wm to correct a wm error) such that the new surface > vertices do not match such that the lh.jacobian_white file in this > case is now invalid. > > > > My query is as follows: > > > > I have experimented with running “recon-all –s <subject> -make all” to > fix the above problem but it seems to be going through the entirety of > the recon-all processing stream... I thought it only ran the parts > that were missing, or in the case that dependency files are older than > a particular file. Have I misunderstood this flag, or is it running > through the whole of recon-all simply because we are running it on > 4.0.3, so it is updating all of the recon-all files up to autorecon2- > wm that were created from version 4.0.1? > > > > It is interesting that the error happens in this case only on the > jacobian_white surface, in other subjects it has occurred for all > smoothing surface files on a single hemisphere (.e.g. volume, sulc, > curv, thickness, jacobian_white ..) and in many just the .volume files > are missing... it is confusing. > > > > Naturally I would love to avoid reprocessing these subjects from > scratch! But I can see how this might not be possible. > > > > Thanks very much for your time, > > > > Rysia > > > > > > > _______________________________________________ > 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
